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opencc-zeroApr 2022View details →

How hydrology and landscape shape Odonata assemblages in marshlands crossed by ditches

One of the major current ecological challenges is to understand how to reconcile human activities with biodiversity conservation concerns. This issue is particularly relevant in freshwater ecosystems where biodiversity is globally under severe threat. Artificial waterbodies, such as ditch networks, are part of the few remaining wetlands in agricultural landscapes and hence play a crucial role in maintaining aquatic biodiversity in these landscapes. We investigated the responses of adult Odonata assemblages at different spatial scales in a marshland crossed by ditches to two factors expected to be pivotal influences on assemblages. At the local scale, this was mainly the water regime in ditches and, at a broader scale, the composition of the landscape. Both taxonomic alpha and beta diversity, and functional trait composition were considered as response variables. Significant differences were found between the responses of the two Odonata suborders. We showed that Zygoptera species richness decreased and species turnover increased with the duration of drying episodes in ditches. Geographical distances between local assemblages as well as landscape characteristics, notably woodland cover, meadow cover, and ditch network length, also significantly shaped the distribution of Zygoptera. For Anisoptera, species richness was not explained by environmental variables and beta diversity was associated only with local conditions; it increased with increasing dissimilarity in water quality and riparian vegetation. We also found evidence of functional trait syndromes (combinations of correlated traits) in Odonata assemblages, but without clear relationships to environmental gradients. This study reveals the structuring role of water regime for Odonata in ditch networks and demonstrates the need to jointly consider environmental variables at different spatial scales to properly understand the distribution of Odonata. Our findings have important conservation implications as the water regime is heavily managed in such ecosystems. Even though the relationship between functional composition and environmental gradients was found to be of limited extent in this study, we discuss how it might provide new insights for Odonata assemblage structure and be useful, locally, for stakeholders and managers. Lastly, we call for further multiscale investigations considering both the taxonomic and functional responses of Odonata assemblages (functional analyses with multiple traits and several species being scarce in this taxonomic group) in other anthropogenic freshwater ecosystems to gather more lessons for their conservation.

opencc-zeroApr 2022View details →

Habitat shapes diversity of gut microbiomes in a wild population of blue tits Cyanistes caeruleus

Microbiome constitutes and important axis of individual variation that, together with genes and the environment, influences an individual's physiology and fitness. Microbiomes are dependent not only on an individual's body condition but also on external factors, such as diet or stress levels, and as such can be involved into feedbacks between the external ecological factors and internal physiology. In our study we used a wild population of blue tits (Cyanistes caeruleus) to investigate the impact of external habitat composition on the microbiome of adult birds. We hypothesized, that – through differences in plant composition, potentially affecting diet complexity – habitat type may impact the diversity and structure of the gut microbiome. Blue tits breeding in dense deciduous forests tended to have more diverse microbiomes, and significantly different in terms of microbiome composition from birds breeding in open, sparsely forested hay meadows. Distinct study plots also tended to differ in a number of parameters describing microbiome diversity. We observed no microbiome differentiation according to individual characteristics such as sex or age. The study emphasizes, that external environment is one of the important modulators of microbiome diversity and calls for more such studies in wild animal populations.

Breeding status shapes territoriality and vocalization patterns in spotted owls

Vocal territory defense can vary within a species due to many factors such as sex and breeding status, influencing territory size and thus population density across a landscape. Therefore, understanding what influences variation in territorial vocalizations can help to illuminate trade-offs between territoriality and other life history demands, which benefits our general understanding of animal ecology as well as helps to inform emerging passive acoustic monitoring approaches. Here, we investigated how sex and breeding status affected territoriality and vocal behavior in the California spotted owl (Strix occidentalis occidentalis) in the Sierra Nevada, California, USA, using high-resolution acoustic/GPS tags. We discovered that territorial vocal behavior was related to breeding status and to a lesser extent sex. Breeding owls with fledged young had a less diverse vocal repertoire, produced fewer and quieter territorial calls, and typically called only when close to their nest. Males were also more likely to engage in territorial calling than females. Breeding spotted owls also maintained significantly smaller territories—but utilized larger home ranges—than non-breeding individuals. Our results suggest that breeding spotted owls may reduce their investment in territorial behaviors to mitigate the demands and risks associated with rearing young. Further, our results have important implications for the passive acoustic monitoring of spotted owls and, more broadly, highlight the utility of using multiple call types to detect species of interest.

Diversification of body shape in catfishes of the Ganga River

Catfishes of the order Siluriformes are an exceptionally diverse group occupying significant fraction of the world's freshwater ichthyofauna. Catfish species renders a model system for phylogenetic and evolutionary studies. However, there is dearth of knowledge on the phylogenetic history with reference to morphological diversity of catfishes in the Ganga River. Geometric morphometrics is an efficient approach to quantify shape variations and has lately found application in range of taxonomic, phylogenetic and evolutionary studies. This study utilizes photographs of 39 Gangetic catfishes to evaluate inter-specific phenotypic relationship through geometric morphometrics. PERMANOVA revealed significant relationship (F = 4.50, p < 0.0001) between shape of all the species. Procrustes ANOVA revealed significant relationship between shape and size (F = 17.67, p < 0.0001) and between shape (F = 34.95, p < 0.0001) of all species. The first two principal components of PCA accounted for 69.41% (PC1 44.41% and PC2 25.00%) of the total variance while the first two canonical variates of CVA accounted for 55.89% (CV1 34.06% and CV2 21.83%) of the total variance. The CVA-extracted Mahalanobis and Procrustes distances were found to be highly significant (p < 0.0001) between distinct groups and non-significant (p > 0.0001) between closely related groups. Morphospace phenogram depicted that the species under Mystus, Sperata, Glyptothorax, Ompok, Eutropiichthys, Bagarius and Gagata clustered together in their respective genus, indicating that species of respective genus share common phenotypic traits and have evolutionary relatedness. Species like Chaca chaca, Clarias magur, Sisor rabdophorus, Heteropneustes fossilis, Silonia silondia and Clupisoma garua showed clear distinctness, which may be attributed to different set of morphological traits. The study affirms the implication of geometric morphometrics in discriminating Gangetic catfishes and showcasing phenotypic relatedness between respective groups. This study has high implications in understanding the ecological and evolutionary problems in relation to morphological diversity in catfishes.

opencc-zeroDec 2022View details →

Data from: Underlying geology and climate interactively shape climate change refugia in mountain streams

Identifying climate-change refugia is a key adaptation strategy for reducing global warming impacts. Knowledge of the effects of underlying geology on thermal regime along climate gradients and the ecological responses to the geology-controlled thermal regime is essential to plan appropriate climate adaptation strategies. In the present study, the dominance of volcanic rocks in the watershed is used as a landscape-scale surrogate for cold groundwater inputs to clarify the importance of underlying geology in stream ecosystems along climate gradients. First, using hundreds of monitoring stations distributed across multiple catchments, we explored the relationship between watershed geology and the mean summer water temperature of mountain streams along climate gradients in the Japanese archipelago. Mean summer water temperature was explained by the interaction between the watershed geology and climate in addition to independent effects. The cooling effect supported by volcanic rocks reached up to 3.3°C among study regions, which was more pronounced in streams with less summer precipitation or lower air temperatures. Next, we examined the function of volcanic streams as cold refugia under contemporary and future climatic conditions. Community composition analyses revealed that volcanic streams hosted distinct stream communities composed of more cold-water species compared with non-volcanic streams. Scenario analyses based on multiple GCMs and RCPs revealed a geology-related pattern of thermal habitat loss for cold-water species. Non-volcanic streams rapidly declined in thermally suitable habitats for lotic sculpins even under the lowest emission scenario (RCP 2.6). In contrast, most volcanic streams will be sustained below the thermal threshold, especially for low and mid-level emission scenarios (RCP 2.6, 4.5). However, the distinct stream community in volcanic streams and geology-dependent habitat loss for lotic sculpins was not uniform and was more pronounced in streams with less summer precipitation or lower air temperatures. These findings highlight that underlying geology, climate variability, and their interaction should be considered simultaneously for effective management of climate-change refugia in mountain streams.

Data from: Hierarchical variation in phenotypic flexibility across timescales and associated survival selection shape the dynamics of partial seasonal migration

Population responses to environmental variation ultimately depend on within-individual and among-individual variation in labile phenotypic traits that affect fitness, and resulting episodes of selection. Yet, complex patterns of individual phenotypic variation arising within and between time periods, and associated variation in selection, have not been fully conceptualised or quantified. We highlight how structured patterns of phenotypic variation in dichotomous threshold traits can theoretically arise and experience varying forms of selection, shaping overall phenotypic dynamics. We then fit novel multistate models to ten years of band-resighting data from European shags to quantify phenotypic variation and selection in a key threshold trait underlying spatio-seasonal population dynamics: seasonal migration versus residence. First, we demonstrate substantial among-individual variation alongside substantial between-year individual repeatability in within-year phenotypic variation ('flexibility'), with weak sexual dimorphism. Second, we demonstrate that between-year individual variation in within-year phenotypes ('supraflexibility') is structured and directional, consistent with the threshold trait model. Third, we demonstrate strong survival selection on within-year phenotypes, and hence on flexibility, that varies across years and sexes, including episodes of disruptive selection representing costs of flexibility. By quantitatively combining these results, we show how supraflexibility and survival selection on migratory flexibility jointly shape population-wide phenotypic dynamics of seasonal movement.

The choanal anatomy of the Sebecus icaeorhinus Simpson, 1937 and the variation of the palatine shape in notosuchians (Crocodyliformes, Mesoeucrocodylia)

Sebecidae is a clade of large carnivorous crocodyliforms that thrived in the Cenozoic and is the only lineage of the diverse and terrestrial group Notosuchia that survived the end-Cretaceous mass extinction event. Sebecus icaeorhinus is the best-known taxon from this clade, both in terms of its cranial and postcranial anatomy (known primarily from the holotype and the specimen MPEF-PV 1776 respectively). An additional material represented by a partial skull (MMP 235) is the only specimen that has preserved a complete choanal region. Here we describe new information from this specimen based on an X-ray computed tomography and identify through comparisons with other taxa a large degree of variability in the palatal anatomy within Sebecidae, in particular in the shape and extension of the palatine (the bone that defines the anterior position and shape of the secondary choana). We quantify here the variation in the shape of the palatine bone of sebecids through a 2D morphogeometric analysis within the context of notosuchian crocodyliforms. Although traditional accounts of palatal evolution in crocodyliforms linked variation of this structure to the adaptation to the aquatic environment, our analysis allows the recognition of eight palatine morphotypes among terrestrial crocodyliforms with very distinct paleoecological traits, including carnivorous, omnivorous, and possibly herbivorous taxa. Furthermore, we show that sebecids had a higher morphological disparity in the choanal region than other terrestrial groups of Notosuchia, underscoring the importance of this region for comparative, morphofunctional, and phylogenetic studies.

Data set - Island area and historical geomorphological dynamics shape multifaceted diversity of barrier island floras

<div> The influence of island dynamics and characteristics on taxonomic diversity, particularly species richness, are well studied. Yet, our knowledge on the influence of island dynamics and characteristics on other facets of diversity, namely functional and phylogenetic diversity, is limited, constraining our understanding of assembly processes on islands (e.g., biogeographic history, dispersal and environmental filtering, and species interactions). Using barrier islands, a highly dynamic and so far, understudied island type, we investigate how multiple facets of vascular plant diversity (functional, phylogenetic and taxonomic diversity) are shaped by island geomorphology, modern and historic area, and habitat heterogeneity. In line with our expectation, historical dynamics in island geomorphology affected phylogenetic and taxonomic diversity via habitat heterogeneity. However, island area was the best predictor across all facets of diversity. Specifically, larger islands had higher functional and phylogenetic diversity than expected by chance while most of the smaller islands had lower diversity. The influence of area on functional diversity acted via habitat heterogeneity, with habitat heterogeneity influencing negatively functional diversity. Our results suggest that larger islands accumulate functionally and phylogenetically unique species. Further, results for functional diversity pointed towards potential area-heterogeneity trade-offs, with these trade-offs likely resulting from increased interspecific competition favoring a specific set of trait values (of stronger competitors), particularly on smaller islands. Together, these results demonstrate that going beyond taxonomic diversity contributes to identifying underlying processes shaping diversity-area relationships. </div>

opencc-by-4.0Apr 2022View details →

Chanalyzer: a computational geometry approach for the analysis of protein channel shape and dynamics

Dataset of molecular dynamics trajectories described in the "Chanalyzer: a computational geometry approach for the analysis of protein channel shape and dynamics" work. Trajectories of differently functionalized MscL channel forms.  The *_xyzr.tar.gz files contain the processed frames in the xyzr format, which is a compatible input for NanoShaper The conf.prm file is the parameter file that has been used for the NanoShaper tool

Community science reveals links between migration arrival timing advance, migration distance, and wing shape

Substantial global data show that many taxa are shifting their phenologies in response to climate change. For birds, migration arrival dates in breeding regions have been shifting earlier, and there is evidence that both evolutionary adaptation and behavioural flexibility influence these shifts. As more efficient flyers may be able to demonstrate more flexibility to respond to changing conditions during migratory flight, we hypothesize that differences among passerine species in flight efficiency, as reflected by morphology, may be associated with the magnitude of shifts in arrival date in response to climate warming. We applied a logistic model to eighteen years of eBird data to estimate mean arrival date for 44 common passerines migrating to northeast North America. We then used linear mixed-effects models to estimate changes in mean arrival date and compared these changes to morphological proxies for flight efficiency and migratory distance using phylogenetic generalized least squares models. On average, passerine species shifted their arrival dates 0.120 days earlier each year, with 27 of the 44 species shifting to significantly earlier arrival times, and two shifting to significantly later ones. Of the 15 species with non-significant shifts, 13 trended toward earlier arrivals. Longer migration distances and higher wing aspect ratios were associated with greater shifts towards earlier arrivals. Migration distance and aspect ratio were also significantly correlated to each other. This suggests that changes in arrival date are affected by factors pertaining to migratory flight over long distances namely, flight efficiency and migration distance. These traits may be able predict the magnitude of arrival date shift, and by extension identify species that are most at risk to climate change due to inflexible arrival timing.

opencc-by-4.0Jun 2022View details →

Models & Unity Task for Shape of U: The non-monotonic relationship between object-location memory and expectedness

These are the fitted models as well as the Unity task for Shape of U: The non-monotonic relationship between object-location memory and expectedness to appear Psychological Science. For more information please see <a href="https://github.com/JAQuent/schemaVR">here</a>. Non-registered versions of these files can also be downloaded via <a href="https://github.com/JAQuent/schemaVR/blob/master/downloads_and_moves_files_from_osf.R">this script</a>.

FishShapes v1: functionally relevant measurements of teleost shape and size on three dimensions

Teleost fishes account for 96% of all fish species and exhibit a spectacular variety of body forms. Teleost lineages range from deep-bodied to elongate (e.g. eels, needlefish), laterally compressed (e.g. ribbonfish) to globular (e.g. pufferfish) and include uniquely shaped lineages such as seahorses, flatfishes and ocean sunfishes. Adaptive body shape convergence within fishes has long been hypothesized but the nature of the relationships between fish form and ecological and environmental variables remain largely unknown at the macroevolutionary scale. To facilitate the investigation of the interacting factors influencing teleost body shape evolution we measured 8 functionally relevant linear traits on adult-sized specimens along with specimen mass. Linear measurements of standard length, maximum body depth, maximum fish width, lower jaw length, mouth width, head depth, minimum caudal peduncle depth and minimum caudal peduncle width were taken in millimeters with calipers, or tape measures for oversized specimens. We measured these traits on a total of 16523 specimens (1-3 specimens per species) at the Smithsonian National Museum of Natural History and took approximately 7000 person hours of data collection to complete. The data went through a three-step error-checking process to clean and validate the data and then species averages were calculated. We present the complete specimen dataset, which encompasses approximately one fifth of extant teleost species diversity, spanning ~90% of teleost families and ~96% of orders. The species and family names are compatible with the FishBase taxonomy (Pauly & Froese, 2019) and the order information with the phylogenetically informed taxonomy of Betancur-R et al. (2014). This dataset is licensed under a Creative Commons Attribution - Non-Commercial 4.0 International License (CC BY-NC), please cite this paper when using the data or a subset of it.

A novel trophic cascade between cougars and feral donkeys shapes desert wetlands

Introduced large herbivores have partly filled ecological gaps formed in the late Pleistocene, when many of the Earth's megafauna were driven extinct. However, extant predators are generally considered incapable of exerting top-down influences on introduced megafauna, leading to unusually strong disturbance and herbivory relative to native herbivores. We report on the first documented predation of juvenile feral donkeys (Equus africanus asinus) by cougars (Puma concolor) in the Mojave and Sonoran Deserts of North America. We then investigated how cougar predation corresponds with differences in feral donkey behavior and associated effects on desert wetlands. Focusing on a feral donkey population in Death Valley National Park, we compared donkey activity patterns and impacts between wetlands with and without cougar predation. Donkeys were primarily diurnal at wetlands with cougar predation, thereby avoiding cougars. However, donkeys were active throughout the day and night at sites without predation. Donkeys were ~87% less active (measured as hours of activity a day) at wetlands with predation (p<0.0001). Sites with predation had reduced donkey disturbance and herbivory, including ~46% fewer access trails, 43% less trampled bare ground, and 192% more canopy cover (PERMANOVA, R2 = 0.22, p=0.0003). Our study is the first to reveal a trophic cascade involving cougars, feral equids, and vegetation. Cougar predation appears to rewire an ancient food web, with diverse implications for modern ecosystems. Our results suggest that protecting apex predators could have important implications for the ecological effects of introduced megafauna.

Data from: Neurotransmitter content heterogeneity within an interneuron class shapes inhibitory transmission at a central synapse

Neurotransmitter content is deemed the most basic defining criterion for neuronal classes, contrasting with the intercellular heterogeneity of many other molecular and functional features. Here we show, in the adult mouse brain, that neurotransmitter content variegation within a neuronal class is a component of its functional heterogeneity. Most Golgi cells (GoCs), the well-defined class of cerebellar interneurons inhibiting granule cells (GrCs), contain cytosolic glycine, accumulated by the neuronal transporter GlyT2, and GABA in various proportions. To assess the functional consequence of this neurotransmitter variation, we paired GrCs recordings with optogenetic stimulations of single GoCs, which preserve the intracellular transmitter mixture. We show that the strength and decay kinetics of GrCs IPSCs, which are entirely mediated by GABAA receptors are negatively correlated to the presynaptic expression of GlyT2 by GoCs. We isolate a slow spillover component of GrCs inhibition that is also affected by the expression of GlyT2, leading to a 56 % decrease in relative charge. Acute manipulations of cytosolic GABA and glycine supply recapitulate the modulation of IPSC charge, supporting the hypothesis that presynaptic loading of glycine negatively impact the GABAergic transmission in mixed interneurons through a competition for vesicular filling. Our results suggest that heterogeneity of neurotransmitter supply within the GoC class may provide a presynaptic mechanism to tune the gain of the stereotypic granular layer microcircuit, thereby expanding the realm of possible dynamic behavior.

Prey naiveté alters the balance of consumptive and non-consumptive predator effects and shapes trophic cascades in freshwater plankton

Predators drive trophic cascades by reducing prey biomass and altering prey traits, selecting for prey that exhibit constitutive and induced anti-predator defenses that decrease susceptibility to consumption. These defense traits are often costly, generating a tradeoff between consumptive (CEs) and non-consumptive predator effects (NCEs). The ecological and evolutionary experience that prey share with a given predator may determine their position along this tradeoff curve, affecting the nature and strength of top-down control of ecosystems. Conceptual models predict that predator-experienced prey suffer greater NCEs than predator-naive prey, which suffer stronger CEs and total predator effects (CEs + NCEs), but this has not been tested in diverse prey communities. We tested these predictions by comparing the effects of predation (CEs + NCEs) and predation risk (NCEs only) of planktivorous fish on food web structure in pond mesocosms with diverse natural communities of either predator-naive or predator-experienced zooplankton. Contrary to expectations, top-down control of zooplankton and phytoplankton biomass was strengthened by prey community experience: in systems with experienced relative to naive zooplankton communities both predation risk (NCEs only) and predation (CEs + NCEs) had stronger effects on zooplankton prey biomass and trophic cascades were twice as strong. These results show that the ecological and evolutionary experience of diverse prey communities alters the balance of consumptive and non-consumptive predator effects and influences trophic cascade strength.

Data from: Neuropeptide signalling shapes feeding and reproductive behaviours in male C. elegans

Sexual dimorphism occurs where different sexes of the same species display differences in characteristics not limited to reproduction. For the nematode Caenorhabditis elegans, in which the complete neuroanatomy has been solved for both hermaphrodites and males, sexually dimorphic features have been observed both in terms of the number of neurons and in synaptic connectivity. In addition, male behaviours, such as food-leaving to prioritise searching for mates, have been attributed to neuropeptides released from sex-shared or sex-specific neurons. This dataset compiles the results obtained in our investigation of how LURY-1 neuropeptides regulate feeding and mating behaviours in C. elegans. These contain confocal micrographs and z-stacks of fluorescence reporter imaging used to demonstrate the expression pattern of lury-1 and npr-22, including micrographs used for cell identification of lury-1 expressing neurons in the male worm. Other behavioural data from mating efficiency assays, pharyngeal pumping assays and food leaving assays are also shown. These include male turning behaviour examined through video recordings of male mating; the videos are also included as part of this dataset. In this study ("Neuropeptide signalling shapes feeding and reproductive behaviours in male C. elegans"), our findings indicate sex-specific roles of this peptide in feeding and reproduction in C. elegans. This provides further insight into neuromodulatory control of sexually dimorphic behaviours.

opencc-by-4.0May 2022View details →

Latitudinal resource gradient shapes multi-variate defense strategies in a long-lived shrub

Herein lies the data and R code for the analyses for the manuscript titled, "Latitudinal resource gradient shapes multi-variate defense strategies in a long-lived shrub", published in Ecology.

Patch quality and habitat fragmentation shape the foraging patterns of a specialist folivore

Research on use of foraging patches has focused on why herbivores visit or quit patches, yet little is known about visits to patches over time. Food quality, as reflected by higher nutritional quality and lower plant defences, and physical patch characteristics, which offer protection from predators and weather, affect patch use and hence should influence their revisitation. Due to the potentially high costs of moving between patches, fragmented habitats are predicted to complicate foraging decisions of many animals. We aimed to determine how food quality, shelter availability and habitat fragmentation influence tree reuse by a specialist folivore, the koala, in a fragmented agricultural landscape. We GPS- tracked 23 koalas in northern New South Wales, Australia and collated number of revisits, average residence time, and average time-to-return to each tree. We measured tree characteristics including food quality (foliar nitrogen and toxic formylated phloroglucinol compounds, FPCs concentrations), tree size and tree connectedness. We also modelled the costs of locomotion between trees. Koalas re-visited isolated trees with high leaf nitrogen disproportionately often. They spent longer time in trees with high leaf nitrogen, and in large trees used for shelter. They took longer to return to trees with low leaf nitrogen. Tree connectivity reduced travel costs between patches, being either individual or groups of trees. FPC levels had no detectable effect on patch revisitation. We conclude that food quality and shelter drive koala tree re-visits. Scattered, isolated trees with nutrient-rich leaves are valuable resource patches for koalas despite movement costs to reach them.

opencc-by-4.0Jun 2022View details →

Sex-biased admixture and assortative mating shape genetic variation and influence demographic inference in admixed Cabo Verdeans

Inferred ROH and IBD calls from Korunes et al (2022). bioRxiv DOI: https://doi.org/10.1101/2020.12.14.422766 Samples originally collected and analyzed in Beleza et al. 2013, PLoS Genetics. Inferred local ancestry information can be found at <a href="https://doi.org/10.5281/zenodo.4021277">https://doi.org/10.5281/zenodo.4021277</a> See README.txt in upload for more detailed information.