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Subspecies and Distribution. R. a. acuminatus Peters, 1871 - Krakatau I andJava. R. a. audax K. Andersen, 1905 — Bali and Lombok Is. . a. calypso K. Andersen, 1905 — Enggano I. R. a. circe K. Andersen, 1906 — Nias I. R. a. sumatranus K Andersen, 1905 - W Sumatra and N Borneo. Subspecific identity of mainland populations in SE Asia, as well as the Philippines (Negros, Busuanga, Palawan, and Balabac Is) is uncertain, although mainland populations resemble individuals fromJava or Lombok. in Rhinolophidae
Subspecies and Distribution. R. a. acuminatus Peters, 1871 - Krakatau I andJava. R. a. audax K. Andersen, 1905 — Bali and Lombok Is. . a. calypso K. Andersen, 1905 — Enggano I. R. a. circe K. Andersen, 1906 — Nias I. R. a. sumatranus K Andersen, 1905 - W Sumatra and N Borneo. Subspecific identity of mainland populations in SE Asia, as well as the Philippines (Negros, Busuanga, Palawan, and Balabac Is) is uncertain, although mainland populations resemble individuals fromJava or Lombok.
Individual versus computer-supported collaborative self-explanations: how do their writing analytics differ? Coh-Metrix results and students' excerpts.
<p>Coh-Metrix results and students' excerpts of the publication: Albó, L., Beardsley, M., Amarasinghe, I. & Hernández-Leo, D. (2020). Individual versus computer-supported collaborative self-explanations: how do their writing analytics differ? In International conference on Advanced Learning Technologies and Technology-enhanced Learning (ICALT). </p>
Data from: Profound reversible seasonal changes of individual skull size in a mammal
Postnatal size changes in most vertebrates are unidirectional and finite once the individual reaches full size. In rare cases, changes of body length may occur in response to harsh environmental conditions. Such reactionary changes are distinct from seasonal, often anticipatory morphological changes, such as the reversible size change of some adult bird brains. A unique pattern of profound anatomical change known as Dehnel's phenomenon has been described for the body, skull and brain size of red-toothed shrews and some mustelids. The seasonal 20% decrease and 15% re-growth of the most common proxy, braincase height, were documented at population level from extracted skulls post-mortem. Quantifying intra-individual change had so far been methodologically prohibitive. Here, we followed the intra-individual change in skull size and body mass throughout the full cycle in wild recaptured shrews (Sorex araneus). Using X-ray images we showed that individuals decreased the size of their braincases in anticipation of winter by an average of 15.3%. Braincases then partially regrew in spring by 9.3%. Body mass decreased by 17.6% and then dramatically increased by 83.4% in spring. Thus, we demonstrate that the dramatic changes incurred by Dehnel's phenomenon occur in the individual's bone and other tissues.
Data from: Friends and Family: a software program for identification of unrelated individuals from molecular marker data. And from: Genetic diversity, relatedness and inbreeding of ranched and fragmented Cape buffalo populations in southern Africa
The identification of related and unrelated individuals from molecular marker data is often difficult, particularly when no pedigree information is available and the data set is large. High levels of relatedness or inbreeding can influence genotype frequencies and thus genetic marker evaluation, as well as the accurate inference of hidden genetic structure. Identification of related and unrelated individuals is also important in breeding programmes, to inform decisions about breeding pairs and translocations. We present Friends and Family, a Windows executable program with a graphical user interface that identifies unrelated individuals from a pairwise relatedness matrix or table generated in programs such as COANCESTRY and GenAlEx. Friends and Family outputs a list of samples that are all unrelated to each other, based on a user-defined relatedness cut-off value. This unrelated data set can be used in downstream analyses, such as marker evaluation or inference of genetic structure. The results can be compared to that of the full data set to determine the effect related individuals have on the analyses. We demonstrate one of the applications of the program: how the removal of related individuals altered the Hardy-Weinberg equilibrium test outcome for microsatellite markers in an empirical data set. Friends and Family can be obtained from https://github.com/DeondeJager/Friends-and-Family.
Data from: Characterizing population and individual migration patterns among native and restored bighorn sheep (Ovis canadensis)
Migration evolved as a behavior to enhance fitness through exploiting spatially and temporally variable resources and avoiding predation or other threats. Globally, landscape alterations have resulted in declines to migratory populations across taxa. Given the long time periods over which migrations evolved in native systems, it is unlikely restored populations embody the same migratory complexity that existed before population reductions or regional extirpation. 2. We used GPS location data collected from 209 female bighorn sheep (Ovis canadensis) to characterize population and individual migration patterns along elevational and geographic continuums for 18 populations of bighorn sheep with different management histories (i.e., restored, augmented, and native) across the western United States. 3. Individuals with resident behaviors were present in all management histories. Elevational migrations were the most common population-level migratory behavior. There were notable differences in the degree of individual variation within a population across the three management histories. Relative to native populations, restored and augmented populations had less variation among individuals with respect to elevational and geographic migration distances. Differences in migratory behavior were most pronounced for geographic distances, where the majority of native populations had a range of variation that was 2 to 4 times greater than restored or augmented populations. 4. Synthesis and applications. Migrations within native populations include a variety of patterns that translocation efforts have not been able to fully recreate within restored and augmented populations. Theoretical and empirical research has highlighted the benefits of migratory diversity in promoting resilience and population stability. Limited migratory diversity may serve as an additional factor limiting demographic performance and range expansion. We suggest preserving native systems with intact migratory portfolios and a more nuanced approach to restoration and augmentation in which source populations are identified based on a suite of criteria that includes matching migratory patterns of source populations with local landscape attributes.
Data from: Individual niche trajectories drive fitness variation
1. Variation in fitness across individuals is central to population growth, species coexistence, and evolution by natural selection. Fitness variation associated with resource use is hugely consequential, but how this variation is generated and maintained within natural populations remains unclear. In particular, individual fitness may depend on many cumulative foraging decisions over time, but this hypothesis remains untested. 2. We used multi-tissue stable isotope analysis to determine isotopic niche trajectories within species, populations and sexes of thin-toed frogs, and explored how this temporal dimension of diet affects individual reproductive investment, body condition, and parasite load. 3. We found that individual frogs shifted their diets less than expected under a null model, likely due to functional tradeoffs that limit the incorporation of new prey types over time. However, within the observed range of diet shifts, individuals that modified their diet to a greater degree exhibited higher fitness, although this effect was sex-dependent. 4. We suggest that these different relationships between isotopic niche trajectory length and fitness within thin-toed frogs are driven by variability in the resource environment, negative density-dependence and allometric constraints. These strong fitness effects suggest that the temporal dimension of diet change is a potential target of natural selection and, therefore, could drive correlated evolution in phenotypic traits underlying diet flexibility. Our findings add a new level of complexity to the understanding of ecological and evolutionary consequences of niche variation by demonstrating that temporal variation in foraging consistency within populations leads to different fitness payoffs.
Dysbiosis individualizes fitness effect of antibiotic resistance in the mammalian gut
<p>The fitness cost of antibiotic resistance in the absence of antibiotics is crucial to the success of suspending antibiotics as a strategy to lower resistance. Here we show that after antibiotic treatment the cost of resistance within the complex ecosystem of the mammalian gut is personalized. Using mice as an <i>in vivo</i> model, we find that the fitness effect of the same resistant mutation can be deleterious in a host, but neutral or even beneficial in other hosts. Such antagonistic pleiotropy is shaped by the microbiota, as in germ-free mice resistance is consistently costly across all hosts and in hosts with similar microbiotas the host specific effect of resistance is reduced. An eco-evolutionary model of competition for resources identifies a general mechanism underlying between host variation and predicts that the dynamics of compensatory evolution of resistant bacteria should be host specific, a prediction that was supported by experimental evolution<i> in vivo</i>. The microbiome of each human is close to unique and our results suggest that the short-term costs of resistance and its long-term within-host evolution will also be highly personalized, a finding that may contribute to the observed variable outcome of withdrawing antibiotics to reduce resistance levels.</p>
Data from: Seasonal shifts in feeding patterns: individual and population realized specialization in a high Arctic fish
Species with a broad and flexible diet may be at an advantage in a rapidly changing environment such as in today's Arctic ecosystems. Polar cod (Boreogadus saida), an abundant and ecologically important circumpolar Arctic fish, is often described as a zooplankton generalist feeder, which suggests that it may cope successfully with changes in prey composition. This description is justified based on the relatively broad diet of polar cod across sites and seasons. In this case study, we used polar cod dietary data from fall and winter and from two distinct environments, dominated either by Arctic or Atlantic water masses in Svalbard. Our results point to the importance of time and space when drawing conclusions on dietary plasticity and degree of specialization. Polar cod diet differed significantly between fall and the winter and between Arctic and Atlantic domains. Polar cod from Arctic domains displayed a strong realized population specialization on T.libellua in fall, and the larger dietary niche width observed in the winter was the product of realized individual specialization, with increased feeding on fish prey. Overall, we did not observe a generalized feeding behavior. If dietary niche width is to inform conservation management, we argue it must be recognized that populations from a single species may adopt seasonally contrasting degrees of dietary specialization and that these populations may differ in their vulnerability to climate-induced changes in prey community composition.
Individual differences determine the strength of ecological interactions
<p>Biotic interactions are central to both ecological and evolutionary dynamics. In the vast majority of empirical studies, the strength of intraspecific interactions is estimated by using simple mea- sures of population size. Biologists have long known that these are crude metrics, with experiments and theory suggesting that interactions between individuals should depend on traits, such as body size. Despite this, it has been difficult to estimate the impact of traits on competitive ability from ecological field data, and this explains why the strength of biotic interactions has empirically been treated in a simplistic manner. Using long-term observational data from four different populations, we show that large Trinidadian guppies impose a significantly larger competitive pressure on conspecifics than individuals that are smaller; in other words, competition is asymmetric. When we incorporate this asymmetry into integral projection models, the predicted size structure is much closer to what we see in the field compared with models where competition is independent of body size. This difference in size structure translates into a twofold difference in reproductive output. This demonstrates how the nature of ecological interactions drives the size structure, which, in turn, will have important implications for both the ecological and evolutionary dynamics.</p>
Survival probability in a small shorebird decreases with the time an individual carries a tracking device
<p>Effects of tracking devices on survival are generally considered to be small. However, most studies to date have been conducted over a time-period of only one year, neglecting the possible accumulation of negative effects and consequently stronger negative impacts on survival when the individuals have carried the tracking devices for longer periods. We studied the effects of geolocators in a closely monitored and colour-ringed southern dunlin (<i>Calidris alpina schinzii</i>) population breeding in Finland. Our capture-recapture data spans 2002-2018 and includes individual histories of 338 colour-ringed breeding adult dunlins (the term 'recapture' includes resightings of colour-ringed and individually recognizable birds). These data include 53 adults that were fitted with leg-flag mounted geolocators in 2013-2014. We followed their fates together with other colour-ringed birds not equipped with geolocators until 2018. Geolocators were removed within 1-2 years of attachment or were not removed at all, which allowed us to examine whether carrying a geolocator reduces survival and whether the reduction in survival becomes stronger when geolocators are carried for more than one year. We fit multi-state open population capture-recapture models to the encounter history data. When assessing geolocator effects, we accounted for recapture probabilities, time since marking, and sex and year effects on survival. We found that carrying a geolocator reduced survival, which contrasts with many studies that examined return rates after one year. Importantly, survival declined with the time the individual had carried a geolocator, suggesting that the negative effects accumulate over time. Hence, the longer monitoring of birds carrying a geolocator may explain the difference from previous studies. Despite their larger mass, females tended to be more strongly affected by geolocators than males. Our results warrant caution in conducting tracking studies and suggest that short-term studies examining return rates may not reveal all possible effects of tracking devices on survival.</p>
Data from: Early-life conditions determine the between-individual heterogeneity in plasticity of calving date in reindeer
1. Phenotypic plasticity has become a key-concept to enhance our ability to understand the adaptive potential of species to track the pace of climate change by allowing a relatively rapid adjustment of life history traits. 2. Recently, population-level trends of an earlier timing of reproduction to climate change have been highlighted in many taxa but only few studies have explicitly taken into consideration between-individual heterogeneity in phenotypic plasticity. 3. Using a long-term data of a semi-domesticated reindeer (<i>Rangifer tarandus</i>) population, we demonstrated that females differed greatly in their mean calving date but only slightly in the magnitude of their plastic response to the amount of precipitation in April. We also showed that despite the absence of a population trend, females individually responded to the amount of precipitation in April by delaying their calving dates. 4. Females' calving date under average climatic conditions was best predicted by their birthdate, their physical condition in March-April-May before their first calving season and by their first calving date. The degree of their phenotypic plasticity was not dependent on any of the females' attributes early in life tested in this study. However, females who delayed their calving dates in response to a higher amount of precipitation in April slightly produced less calves over their reproductive life. 5. These findings confirmed that early life conditions of female reindeer can shape their phenotypic value during reproductive life, supporting the importance of maternal effects in shaping individuals' lifetime reproductive success. Whether females differed in the magnitude of their plastic response to climatic changes has received contrasted responses for various ungulate species. This calls for more research to enhance our understanding of the underlying mechanisms leading to the complexity of plastic responses among populations to cope with current climate change.
Data from: Host-plant use of a polyphagous mirid, Apolygus lucorum: molecular evidence from migratory individuals
While the host-plant use of insect herbivores is important for understanding their interactions and coevolution, field evidence of these preferences is limited for generalist species. Molecular diet analysis provides an effective option for gaining such information, but data from field-sampled individuals are often greatly affected by the local composition of their host plants. The polyphagous mirid bug Apolygus lucorum (Meyer-Dür) seasonally migrates across the Bohai Sea, and molecular analysis of migrant bugs collected on crop-free islands can be used to estimate the host-plant use of A. lucorum across the large area (northern China) from where these individuals come. In this study, the host-plant use of A. lucorum adults was determined by identifying plant DNA using a three-locus DNA barcode (rbcL, trnH-psbA and ITS) in the gut of migrant individuals collected on Beihuang Island. We successfully identified the host plant families of A. lucorum adults, and the results indicated that captured bugs fed on at least 17 plant families. In addition, gut analyses revealed that 35.9% of A. lucorum individuals fed on multiple host plants but that most individuals (64.1%) fed on only one plant species. Cotton, Gossypium hirsutum L., DNA was found in 35.8% of the A. lucorum bugs examined, which was much higher than the percentage of bugs in which other host plants were found. Our work provides a new understanding of multiple host-plant use by A. lucorum under natural conditions, and these findings are available for developing effective management strategies against this polyphagous pest species.
Ontolex-lemon and TIAD versions of Apertium Indonesian-Malay (individual language) dictionary
<p>OntoLex-lemon and TSV conversion of Apertium Bidix. For more details, see <a href="https://www.aclweb.org/anthology/2020.lrec-1.401/">https://www.aclweb.org/anthology/2020.lrec-1.401/</a></p> <p>Authors of the original data:</p> 2012-2018, Francis M. Tyers 2018, Marc Riera Irigoyen 2012-2016, Kevin Brubeck Unhammer 2012, Raymond HS 2012, Septina Dian Larasati
Data from: Standardization and validation of a panel of cross-species microsatellites to individually identify the Asiatic wild dog (Cuon alpinus)
The Asiatic wild dog or dhole (Cuon alpinus) is a highly elusive, monophyletic, forest dwelling, social canid distributed across south and Southeast Asia. Severe pressures from habitat loss, prey depletion, disease, human persecution and interspecific competition resulted in global population decline in dholes. Despite a declining population trend, detailed information on population size, ecology, demography and genetics is lacking. Generating reliable information at landscape level for dholes is challenging due to their secretive behaviour and monomorphic physical features. Recent advances in non-invasive DNA-based tools can be used to monitor populations and individuals across large landscapes. In this paper, we describe standardization and validation of faecal DNA-based methods for individual identification of dholes. We tested this method on 249 field-collected dhole faeces from five protected areas of the central Indian landscape in the state of Maharashtra, India. Results We tested a total of 18 cross-species markers and developed a panel of 12 markers for unambiguous individual identification of dholes. This marker panel identified 101 unique individuals from faecal samples collected across our pilot field study area. These loci showed varied level of amplification success (57-88%), polymorphism (3-9 alleles), heterozygosity (0.23-0.63) and produced a cumulative misidentification rate or PID(unbiased) and PID(sibs) value of 4.7x10-10 and 1.5x10-4, respectively, indicating a high statistical power in individual discrimination from poor quality samples. Conclusion Our results demonstrated that the selected panel of 12 microsatellite loci can conclusively identify dholes from poor quality, non-invasive biological samples and help in exploring various population parameters. This genetic approach would be useful in dhole population estimation across its range and will help in assessing population trends and other genetic parameters for this elusive, social carnivore.
Dataset for: Majority of olfactory-receptor neurons have individually neutral effects on behavior
<p><strong>Summary</strong></p> <p>Animals use olfactory receptors to navigate danger, mates, and food. However, for complex olfactory systems, it is unknown what proportion of olfactory-receptor neurons (ORNs) can individually drive avoidance or attraction. Similarly it is unclear what rules govern behavioral responses to ORN-activity combinations. We used optogenetic analysis in Drosophila to map the behavior elicited by nearly all ORN classes; just one-fifth of ORNs drove either avoidance or attraction. Although wind and hunger are closely linked to olfaction, neither context had much effect on single-ORN-class behavior. Various models have been used to explain the way multiple ORNs combine their behavioral influences, including several simple pooling rules. To assess these, we activated two-way combinations and compared patterns of single- and double-ORN responses: these comparisons were inconsistent with simple pooling. We conclude that the majority of ORN types have neutral behavioral effects individually, but participate in broad, odor-elicited ensembles with potent behavioral effects arising from complex interactions.</p>
Dataset: A Comparison of Individual and Group Behavior in a Competition with Cheating Opportunities
<p>This is the dataset and corresponding do-file to reproduce the results from the paper:</p> <p>Dannenberg, Astrid, and Elina Khachatryan. 2020. “A comparison of individual and group behavior in a competition with cheating opportunities.” Journal of Economic Behavior & Organization, 177: 533–47.</p>
Data from: Individual asymmetry as a predictor of fitness in the bat Carollia perspicillata
The measurement of fitness in wild populations is a challenging task, and a number of proxies have been proposed with different degrees of success. Developmental instability/stability (DI) is an organismal property associated with variance in bilateral asymmetry (fluctuating asymmetry – FA), and a correlated effect on fitness. This study provides evidence to corroborate the hypothesis that asymmetry partly reflects DI and is correlated with a reduction in fitness measured by survival and reproduction in bats. We studied two Colonies of the bat Carollia perspicillata in Southeastern Brazil over five years, marking and recapturing individuals. Gaussian mixture models for signed forearm asymmetry distribution indicated that ~20% of asymmetry variation was due to DI heterogeneity among individuals. Forearm Asymmetry (ForA), Body Condition (Scaled Mass Index – SMI) and Forearm Length (ForL) were used as predictors of survival probability in Cormack-Jolly-Seber models. Asymmetry was negatively associated with survival, whereas SMI and ForL were positively associated. The male C. perspicillata defend sites within the roost that are favoured by female harems, but there are mating opportunities for bachelor males, leading to both territorial disputes and sperm competition. As predicted by sexual selection, ForA was negatively associated with relative Testicle Length, a measure of reproductive potential. In females, ForA was negatively associated with the probability of two pregnancies (as opposed to one) in a given breeding season. The effect magnitudes and directions of associations suggest that asymmetry, even though not perfectly reflecting DI variation, is a useful predictor for fitness components in C. perspicillata.
Dataset for "Appreciating our 60 years of life": Developing a transactional model of narrative identity and relationships experienced within an individualized, technological intervention for dementia care
<p>Interview transcripts and participant information for <strong>“Appreciating our 60 years of life”: Developing a transactional model of narrative identity and relationships experienced within an individualized, technological intervention for dementia care. </strong></p> <p>Collected as part of the SENSE-GARDEN Multisite Trial (https://sense-garden.eu/). This work was supported by AAL under Grant AAL/Call2016/054-b/2017, co-funded by the European Commission and National Funding Agencies of Norway, Belgium, Romania, and Portugal.</p>
Predictive biomarkers of individual trajectories in elderly persons with subtle cognitive decline: APOE genotype data
<p>The mentalizing network (MN) treats social interactions based on our understanding of other people's intentions and includes the medial prefrontal cortex (mPFC), temporoparietal junction (TPJ), posterior cingulate cortex (PCC), precuneus (PC) and amygdala. Not all elders are equally affected by the aging-related decrease of mentalizing abilities. Personality has recently emerged as a strong determinant of functional connectivity in MN areas. However, its impact on volumetric changes across the mentalizing network in brain aging is still unknown. To address this issue, we explored the determinants of volume decrease in MN components including amyloid burden, personality, and APOE genotyping in a previously established cohort of 130 healthy elders with a mean follow-up of 54 months. Personality was assessed with the Neuroticism Extraversion Openness Personality Inventory-Revised. Regression models corrected for multiple comparisons were used to identify predictors of volume loss including time, age, sex, personality, amyloid load, presence of APOE epsilon 4 allele and cognitive evolution. In cases with higher Agreeableness scores, there were lower volume losses in posterior cingulate cortex (PCC), precuneus (PC) and amygdala bilaterally. This was also the case for right medial prefrontal cortex (mPFC) in elders displaying lower Agreeableness and Conscientiousness. In multiple regression models, the effect of Agreeableness was still observed in left PC and right amygdala and that of Conscientiousness in right mPFC volume loss (26.3% of variability, significant age, sex). Several Agreeableness (Modesty) and Conscientiousness (order, dutifulness, achievement striving and self-discipline) facets were positively related to increased volume loss in cortical components of the MN. In conclusion, these data challenge the beneficial role of higher levels of Agreeableness and Conscientiousness in old age showing that they are associated with an increased rate of volume loss within the mentalizing network.</p>
Unsupervised acoustic classification of individual gibbon females and the implications for passive acoustic monitoring
<p>1. Passive acoustic monitoring (PAM) has the potential to greatly improve our ability to monitor cryptic yet vocal animals. Advances in automated signal detection have increased the scope of PAM, but distinguishing between individuals— which is necessary for density estimation— remains a major challenge. When individual identity is known, supervised classification techniques can be used to distinguish between individuals. Supervised methods require labeled training data, whereas unsupervised techniques do not. If the acoustic signals of individuals are sufficiently different, the number of clusters might represent the number of individuals sampled. The majority of applications of unsupervised techniques in animal vocalizations have focused on quantifying species-specific call repertoires. However, with increased interest in PAM applications, unsupervised methods that can distinguish between individuals are needed. <br> 2. Here, we use an existing dataset of Bornean gibbon female calls with known identity from five sites on Malaysian Borneo to test the ability of three different unsupervised clustering algorithms (affinity propagation, K-medoids, and Gaussian mixture model-based clustering) to distinguish between individuals. Calls from different gibbon females are readily distinguishable using supervised techniques. For internal validation of unsupervised cluster solutions, we calculated silhouette coefficients. For external validation, we compared clustering results with female identity labels using a standard metric: normalized mutual information. We also calculated classification accuracy by assigning unsupervised cluster solutions to females based on which cluster had the highest number of calls from a particular female.<br> 3. We found that affinity propagation clustering consistently outperformed the other algorithms for all metrics used. In particular, classification accuracy of affinity propagation clustering was more consistent as the number of females increased, and when we randomly sampled females across sites. <br> 4. We conclude that unsupervised techniques may be useful for providing additional information regarding individual identity for PAM applications. We stress that although we use gibbons as a case study, these methods will be applicable for any individually-distinct vocal animal. <br> </p>
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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.