Find research datasets worth reusing

Figure 5 in Three ways to distinguish species: using behavioural, ecological, and molecular data to tell apart two closely related ants, Camponotus renggeri and Camponotus rufipes (Hymenoptera: Formicidae)

Figure 5. Box plots of Kimura two-parameter (K2P) distance of 672 bp cytochrome c oxidase subunit I sequences within and between Camponotus renggeri and Camponotus rufipes. Boxes indicate interquartile range (upper line, quartile 3; lower line, quartile 1). Horizontal lines with boxes indicate median and whiskers the minimum and the maximum values. Outliers are shown as individual circles.

Figure 4 in Three ways to distinguish species: using behavioural, ecological, and molecular data to tell apart two closely related ants, Camponotus renggeri and Camponotus rufipes (Hymenoptera: Formicidae)

Figure 4. Genetic structure analyses of Camponotus renggeri (yellow) and Camponotus rufipes (red) workers from Mogi- Guaçu (Brazil), using microsatellites. A, model-based assignment of individuals to the most likely number of clusters (K = 2) using STRUCTURE software. B, model-based assignment of individuals to different classes of hybrids or 'pure' species. Each individual is represented by a vertical line and the colours indicate the probability of the individual being assigned to a group in (A), or a hybrid or 'pure species' class in (B). C, scatterplot of the model-free principal coordinates analysis considering the two first principal coordinates (PCo1 and 2).

Figure 2 in Three ways to distinguish species: using behavioural, ecological, and molecular data to tell apart two closely related ants, Camponotus renggeri and Camponotus rufipes (Hymenoptera: Formicidae)

Figure 2. Main vegetation physiognomies of the cerrado reserve at Mogi-Guaçu, Brazil. Cerrado sensu stricto consists of a dense scrub of shrubs and trees and a fair amount of herbaceous vegetation, whereas the cerradão is a closed woodland with a reduced ground layer. Nests of Camponotus renggeri (N = 46) were found in cerrado sensu stricto (22%) and cerradão (78%), whereas Camponotus rufipes (N = 40) occurred only in cerrado sensu stricto. Drawing by L. Mota.

Figure 1 in Three ways to distinguish species: using behavioural, ecological, and molecular data to tell apart two closely related ants, Camponotus renggeri and Camponotus rufipes (Hymenoptera: Formicidae)

Figure 1. Workers of (A) Camponotus renggeri and (B) Camponotus rufipes. The two species are usually differentiated in the field by nuances in the integument colour (C. renggeri is shiny; C. rufipes is matte), and colour of the legs (yellowish in C. renggeri; reddish in C. rufipes). Photographs courtesy of L. Mota.

Figure 6 in Three ways to distinguish species: using behavioural, ecological, and molecular data to tell apart two closely related ants, Camponotus renggeri and Camponotus rufipes (Hymenoptera: Formicidae)

Figure 6. Analyses of the cytochrome c oxidase subunit I haplotypes of Camponotus renggeri (yellow) and Camponotus rufipes (red). A, neighbour-joining tree constructed with Kimura two-parameter distances between C. renggeri and C. rufipes with bootstrap support values based on 10 000 replications indicated on each branch. B, median-joining network amongst the obtained haplotypes. Values on the branches represent the numbers of mutational steps distinguishing the haplotypes, represented as circles whose areas are proportional to the number of individuals with that haplotype.

Figure 3 in Three ways to distinguish species: using behavioural, ecological, and molecular data to tell apart two closely related ants, Camponotus renggeri and Camponotus rufipes (Hymenoptera: Formicidae)

Figure 3. Frequency distribution of nest categories in Camponotus renggeri and Camponotus rufipes in the cerrado reserve at Mogi-Guaçu, Brazil. The species differed in the structure and building materials used for nesting.

opencc-by-4.0Oct 2018View details →

Figure 1 in First quantitative data on the ectoparasitic mites of Sceloporus torquatus (Squamata) from the Ecological Reserve of Pedregal de San Angel in Central Mexico

Figure 1 Parasitic mites associated withSceloporus torquatus in the REPSA, Mexico City. A – Argasidae, Ornithodoros talaje. B-C, Pterygosomatidae, scale bars 200 μm: B – Geckobiella pelaezi; C – Geckobiella texana. D, Trombiculidae,Eutrombicula alfreddugesi, scale bars 80 μm: D – Ventral view, E – Dorsal view.

opencc-by-4.0Oct 2018View details →

Figure 2 in First quantitative data on the ectoparasitic mites of Sceloporus torquatus (Squamata) from the Ecological Reserve of Pedregal de San Angel in Central Mexico

Figure 2 Prevalence, abundance, and mean intensity of four species of mites that infest the lizard Sceloporus torquatus in the Reserva Ecológica del Pedregal de San Ángel, Mexico City. Error bars denote confidence intervals (84%). Different letters indicate statistically significant differences.

opencc-zeroSep 2021View details →

Data from: Fractal triads efficiently sample ecological diversity and processes across spatial scales

The relative influence of ecological assembly processes, such as environmental filtering, competition, and dispersal, vary across spatial scales. Changes in phylogenetic and taxonomic diversity across environments provide insight into these processes, however, it is challenging to assess the effect of spatial scale on these metrics. Here, we outline a nested sampling design that fractally spaces sampling locations to concentrate statistical power across spatial scales in a study area. We test this design in northeast Utah, at a study site with distinct vegetation types (including sagebrush steppe and mixed conifer forest), that vary across environmental gradients. We demonstrate the power of this design to detect changes in community phylogenetic diversity across environmental gradients and assess the spatial scale at which the sampling design captures the most variation in empirical data. We find clear evidence of broad-scale changes in multiple features of phylogenetic and taxonomic diversity across aspect. At finer scales, we find additional variation in phylodiversity, highlighting the power of our fractal sampling design to efficiently detect patterns across multiple spatial scales. Thus, our fractal sampling design and analysis effectively identify important environmental gradients and spatial scales that drive community phylogenetic structure. We discuss the insights this gives us into the ecological assembly processes that differentiate plant communities found in northeast Utah.

opencc-zeroOct 2021View details →

Data from: Ecological and social pressures interfere with homeostatic sleep regulation in the wild

Sleep is fundamental to the health and fitness of all animals. The physiological importance of sleep is underscored by the central role of homeostasis in determining sleep investment – following periods of sleep deprivation, individuals experience longer and more intense sleep bouts. Yet, most sleep research has been conducted in highly controlled settings, removed from evolutionarily-relevant contexts that may hinder the maintenance of sleep homeostasis. Using tri-axial accelerometry and GPS to track the sleep patterns of a group of wild baboons (Papio anubis), we found that ecological and social pressures indeed interfere with homeostatic sleep regulation. Baboons sacrificed time spent sleeping when in less familiar locations and when sleeping in proximity to more group-mates, regardless of how long they had slept the prior night or how much they had physically exerted themselves the preceding day. Further, they did not appear to compensate for lost sleep via more intense sleep bouts. We found that the collective dynamics characteristic of social animal groups persist into the sleep period, as baboons exhibited synchronized patterns of waking throughout the night, particularly with nearby group-mates. Thus, for animals whose fitness depends critically on avoiding predation and developing social relationships, maintaining sleep homeostasis may be only secondary to remaining vigilant when sleeping in risky habitats and interacting with group-mates during the night. Our results highlight the importance of studying sleep in ecologically relevant contexts, where the adaptive function of sleep patterns directly reflects the complex trade-offs that have guided its evolution.

opencc-zeroDec 2022View details →

Data from: Commercial Bombus impatiens colonies function as ecological traps for wild queens

1. In response to anthropogenic environmental change, the cues that animals use throughout their lifecycle to optimize fitness may become unreliable, resulting in an ecological trap. 2. Here we investigated whether commercial bumble bee (Bombus impatiens) colonies managed for early spring crop pollination act as ecological traps for wild nest-searching Bombus queens by subverting their natural nest usurpation behavior. 3. An average of 10 dead wild queens were recovered from each standard colony during the two-week period of the experiment, but colonies with queen excluders were successful in preventing wild queen deaths. The use of queen excluders did not impact colony performance in terms of resident queen survival, colony reproduction, colony weight gain or worker body size. 4. Sites where wild nest-searching queens were small had higher rates of failed usurpation, suggesting smaller-sized queens are disproportionately at risk from failed usurpation. Furthermore, sites where commercial colonies without queen excluders were introduced for spring crop pollination had fewer bumble bee visits to a later-blooming crop compared to sites without commercial colonies. 5. Synthesis and applications. Our findings reveal a novel mechanism by which commercial colonies can negatively impact wild bumble bee populations and their pollination services. At the same time, we demonstrate a simple and inexpensive risk mitigation tool – a queen excluder – was 100% effective at eliminating this risk without compromising colony performance. Commercial colonies used outdoors during the bumble bee nest-searching period should be fit with queen excluders to prevent negative impacts on wild pollinator communities and their services.

opencc-zeroDec 2021View details →

Data for: Zebra finch song ecology: monitoring of breeding, observational transects, focal and year-round acoustic recordings, and a large-scale simultaneous playback experiment

Male songbirds sing to establish territories and to attract mates. However, increasing reports of singing in non-reproductive contexts and by females show that song use is more diverse than previously considered. Therefore, alternative functions of song, such as social cohesion and synchronisation of breeding, by and large were overlooked even in such well-studied species as the zebra finch (Taeniopygia guttata). In these social songbirds only the males sing and pairs breed synchronously in loose colonies following aseasonal rain events in their arid habitat. As males are not territorial, and pairs form long-term monogamous bonds early in life, conventional theory predicts that zebra finches should not sing much at all; yet they do and their song is the focus of hundreds of lab-based studies. We hypothesise that zebra finch song functions to maintain social cohesion and to synchronise breeding. Here we test this idea using data from five years of field studies, including observational transects, focal and year-round audio recordings, and a large-scale playback experiment. We show that zebra finches frequently sing while in groups, that breeding status influences song output at the nest and at aggregations, that they sing year-round, and that they predominantly sing when with their partner, suggesting that song remains important after pair formation. Our playback reveals that song actively features in social aggregations as it attracts conspecifics. Together, these results demonstrate that birdsong has important functions beyond territoriality and mate choice, illustrating its importance in coordination and cohesion of social units within larger societies.

opencc-zeroJan 2023View details →

Data and code from: Shifting social-ecological fire regimes explain increasing structure loss from Western wildfires

Higuera, P.E., M.C. Cook, J.K. Balch, E.N. Stavros, A.L. Mahood, and L.A. St. Denis. 2023. Shifting social-ecological fire regimes explain increasing structure loss from Western wildfires. PNAS Nexus 2: In Press. Structure loss is an acute, costly impact of the wildfire crisis in the western United States ("West"), motivating the need to understand recent trends and causes. We document a 246% rise in West-wide structure loss from wildfires between 1999–2009 and 2010–2020, driven strongly by events in 2017, 2018, and 2020. Increased structure loss was not due to increased area burned alone. Wildfires became significantly more destructive, with a 160% higher structure loss rate (loss/kha burned) over the past decade. Structure loss was driven primarily by wildfires from unplanned human-related ignitions (e.g. backyard burning, power lines, etc.), which accounted for 76% of all structure loss and resulted in 10 times more structures destroyed per unit area burned compared to lightning-ignited fires. Annual structure loss was well explained by area burned from human-related ignitions, while decadal structure loss was explained by state-level structure abundance in flammable vegetation. Both predictors increased over recent decades and likely interacted with increased fuel aridity to drive structure-loss trends. While states are diverse in patterns and trends, nearly all experienced more burning from human-related ignitions and/or higher structure loss rates, particularly California, Washington, and Oregon. Our findings highlight how fire regimes – characteristics of fire over space and time – are fundamentally social-ecological phenomena. By resolving the diversity of Western fire regimes, our work informs regionally appropriate mitigation and adaptation strategies. With millions of structures with high fire risk, reducing human-related ignitions and rethinking how we build are critical for preventing future wildfire disasters.

opencc-zeroFeb 2023View details →

Predicting daily activity time through ecological niche modeling and microclimatic data

1. Climate temporality is a phenomenon that affects species' activity and distribution patterns across spatial and temporal scales. Despite the global availability of microclimatic data, their use to predict activity patterns and distributions remains scarce, particularly at fine temporal scales (e.g., < month). Predicting activity patterns based on climatic data may allow us to foresee some of the consequences of climate change, particularly for ectothermic vertebrates. 2. The Gila monster exhibits marked daily and seasonal activity patterns linked to physiology and reproduction. Here we evaluate if ecological niche models fitted using microclimate data can predict temporal activity patterns using the Gila monster (Heloderma suspectum) as a study system. Further, we identified if the activity patterns are related to physiological constraints. 3. We used dated occurrences from museum specimens and human observations to generate and test ecological niche models using minimum-volume ellipsoids. We generated hourly microclimatic data for each occurrence site for ten years using the NicheMapR package. For ecological niche modeling, we compared the traditional seasonal approach versus a daily activity pattern strategy for model construction. We tested both using the omission rate of independent observations (citizen science data). Finally, we tested if unimodal and bimodal activity patterns for each season could be recreated through ecological niche modeling and if these patterns followed known physiological constraints. 4. The unimodal and bimodal activity patterns previously reported directly from tracking individuals across the year were recovered by using niche modeling and microclimate across the species' geographical range. We found that upper thermal tolerances can explain the daily activity patterns of this species. 5. We conclude that ecological niche models trained with microclimatic data can be used to predict activity patterns at fine temporal scales, particularly on ectotherm species of arid zones coping with rapid climate modifications. Further, the use of fine temporal scale variables can lead to a better niche delimitation, enhancing the results of any research objective that uses correlative models.

opencc-zeroMar 2023View details →

Data from: The spatial patterns of community composition, their environmental drivers and their spatial scale dependence vary markedly between fungal ecological guilds

Aim How community composition varies in space and what governs the variation has been extensively investigated in macroorganisms. However, we have only limited knowledge for microorganisms, especially fungi, despite their ecological and economic significance. Based on previous research, we define and test a series of hypotheses regarding the composition of fungal communities, its most influential drivers and their spatial scale dependence. Location Czech Republic. Time period Present. Taxa studied Fungi. Methods We analyzed the distance decay relationships, community composition and its drivers (physical distance, litter and soil chemistry, tree composition, climate) in fungi, using multivariate analyses. We compared the results across three fungal ecological guilds (ectomycorrhizal fungi, saprotrophs and yeasts), two forest microhabitats (litter and bulk soil) and six spatial scales (from 5 m to 80 km) that comprehensively cover the Czech Republic. Results We found that, similar to macroorganisms, the ectomycorrhizal fungi and saprotrophs showed marked distance-decay relationships, and their community composition was driven mainly by vegetation and dispersal at local scales, but at regional scales, by environmental effects. In contrast, the third fungal guild, the unicellular yeasts, showed little distance decay, suggesting extraordinary spatial homogeneity, as often seen in microorganisms, such as bacteria. Main conclusions Our results underscore the remarkable variation in the community ecology of fungi, which seems to range well-known patterns both from the macro- and the microworld. Knowledge of these patterns advances our understanding of the ecology of fungi, rather understudied organisms of significant ecological and economic importance, which our findings identify as a potentially suitable model for bridging the gaps between the biogeography of micro- and macroorganisms.

opencc-by-4.0Jan 2023View details →

A synthesis of hydroclimatic, ecological, and socioeconomic data for transdisciplinary research in the Mekong

Various climate, hydro-meteorological, ecological, and socio-economic datasets are synthesized and made available for the Mekong River Basin. The sources of each dataset are also mentioned in the associated readme file. Dam attribute data, inundation data, and Cambodia census data can be made available upon request to the authors.

opencc-zeroApr 2023View details →

Data from: Quantifying and estimating ecological network diversity based on incomplete sampling data

An ecological network refers to the ecological interactions among sets of species. Quantification of ecological network diversity and related sampling/estimation challenges have explicit analogues in species diversity research. A unified framework based on Hill numbers and their generalizations was developed to quantify taxonomic, phylogenetic, and functional diversity. Drawing on this unified framework, we propose three dimensions of network diversity that incorporate the frequency (or strength) of interactions, species' phylogenies and traits. As with surveys in species inventories, nearly all network studies are based on sampling data and thus also suffer from under-sampling effects. Adapting the sampling/estimation theory and the iNEXT (interpolation/extrapolation) standardization developed for species diversity research, we propose the iNEXT.link method to analyze network sampling data. The proposed method integrates the following four inference procedures: (i) Assessment of sample completeness of networks, (ii) asymptotic analysis via estimating the true network diversity, (iii) non-asymptotic analysis based on standardizing sample completeness via rarefaction and extrapolation with network diversity, and (iv) estimation of the degree of unevenness or specialization in networks based on standardized diversity. Interaction data between European trees and saproxylic beetles are used for illustrating the proposed procedures. The software iNEXT.link is developed to facilitate all computations and graphics.

opencc-zeroApr 2023View details →

Data from: N-dimensional hypervolumes in trait-based ecology: does occupancy rate matter?

Many methods for estimating functional diversity of biological communities rely on measuring geometrical properties of n-dimensional hypervolumes in a trait space. To date, these properties are calculated from individual hypervolumes or from their pairwise combinations. Our capacity to detect functional diversity patterns due to the overlap of multiple hypervolumes is thus limited. Here, we propose a new approach for estimating functional diversity from a set of hypervolumes. We rely on the concept of occupancy rate, defined as the mean or absolute number of hypervolumes enclosing a given point in the trait space. Furthermore, we describe a permutation test to identify regions of the trait space in which the occupancy rate of two sets of hypervolumes differs. We illustrate the utility of our approach over existing methods with two examples on aquatic macroinvertebrates. The first example shows how occupancy rate relates to the stability of trait space utilisation due to increased flow intermittency and allows the identification of taxa in regions of the trait space with low occupancy rates. The second example shows how the permutation test based on occupancy rates can detect differences in trait space utilisation due to river morphology variation even with a high degree of overlap among input hypervolumes. Our newly developed approach is particularly suitable in functional diversity analysis when investigating patterns of overlap among multiple hypervolumes. We thus emphasise the need to consider analyses based on occupancy rate into functional diversity estimation.

opencc-zeroApr 2023View details →

Data for: Simulated climate change causes asymmetric responses in insect life history timing potentially disrupting a classic ecological speciation system

Climate change may alter phenology within populations with cascading consequences for community interactions and ongoing evolutionary processes. Here, we measured the response to climate change in two sympatric, recently diverged (~170 years) populations of Rhagoletis pomonella flies specialized on different host fruits (hawthorn and apple) and their parasitoid wasp communities. We tested whether warmer temperatures affect dormancy regulation and its consequences for synchrony across trophic levels and temporal isolation between divergent populations. Under warmer temperatures, both fly populations developed earlier. However, warming significantly increased the proportion of maladaptive pre-winter development in apple, but not hawthorn, flies. Parasitoid phenology was less affected, potentially generating ecological asynchrony. Observed shifts in fly phenology under warming may decrease temporal isolation, potentially limiting ongoing divergence. Our findings of complex sensitivity of life-history timing to changing temperatures predict that coming decades may see multifaceted ecological and evolutionary changes in temporal specialist communities.