cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.9p8cz8whm
title: Data from: Interindividual variation in the use of social information during learning in honeybees

description: Slow-fast differences in cognition among individuals have been proposed to
 be an outcome of the speed-accuracy trade-off in decision-making. Based on
 the different costs associated with acquiring information via individual
 and social learning, we hypothesized that slow-fast cognitive differences
 would also be tied to the adoption of these different learning modes.
 Since foragers in honeybee colonies likely have both these information
 acquisition modes available to them, we chose to test them for
 inter-individual differences in individual and social learning. Individual
 honeybees foragers were presented with a learning task: making a choice
 between two types of flowers one rewarding (offering sucrose) and one
 unrewarding (offering water). This task was presented twice: 1) the bee
 was alone (individual learning) and 2) there was a social cue (model bee)
 on the correct color. For every individual, the raw data
 consisted of 20 successive choices between rewarding and unrewarding
 flowers in each of the two learning tasks. From these data, learning
 curves were constructed by calculating an accuracy index as the proportion
 of correct choices for rewarding in the 4 visits up to and including that
 visit, and a logisitc function was fit to the accuracy index. From this
 logistic function we calculated individual learning parameters: maximum
 individual learning score, individual learning rate, maximum social
 learning score, social learning rate.  Our results
 support the existence of a speed-accuracy trade-off in both the individual
 and the social learning contexts. However, the trade-off is steeper during
 individual learning, which was slower than social learning but led to
 higher accuracy. Most importantly, our results also show that bees which
 attained high accuracy on the individual learning task had low accuracy on
 the social learning task and vice versa.
description: Individual foragers were measured for both indivdual and social
 learning ability. The learning task consisted of presenting foragers with
 two different colored flowers: one rewarding and one non-rewarding.
 Individual decisions (correct or incorred) were recorded for a total of 20
 deceisions. During the individual task, foragers completed the learning
 task alone, while during the social learning task, a social cue (model
 bee) was placed on the correct color morph. Scores were then fit to a
 logisitc function to extract two parameters: learning rate (the slope) and
 maximum accuracy (asymptote) in both contexts. This data set includes
 indivdual scores (learning rate and maximum accuracy), age and colony of
 origin.
DOI: 10.5061/dryad.s1rn8pk8z
title: Spatial structure within root systems moderates stability of Arbuscular Mycorrhizal mutualism and plant-soil feedbacks

description: The persistence of mutualisms is paradoxical, as there are fitness
 incentives for exploitation.  This is particularly true for
 plant-microbe mutualisms like arbuscular mycorrhizae (AM), which are
 promiscuously, horizontally-transmitted.  Preferential allocation
 by hosts to the best mutualist can stabilize horizontal mutualisms,
 however preferential allocation is imperfect, with its fidelity likely
 depending upon the spatial structure of symbionts in plant
 roots.  In this study, we tested AM mutualisms’ dependence on two
 dimensions of spatial structure: the initial dispersion of fungi and the
 ease of fungal dispersal, through three complementary experiments. We
 found that fitness of the beneficial AM fungus increased when fungi were
 initially separate, while initial spatial mixing benefited the fitness of
 the non-beneficial fungus. These effects were strongest when dispersal was
 limited, and hosts could discriminate.  Additionally, we found
 that spatial structure moderated changes in AM fungal composition produced
 differential feedbacks on plant growth.  Our results identify
 symbiont spatial structure within plant roots as an important modifier of
 plant preferential allocation and the dynamics of  mycorrhizal
 mutualisms, with cascading effects on plant communities.
DOI: 10.5061/dryad.6m905qg17
title: Comparative riverscape genomics of the rainbow darter (Etheostoma caeruleum) in glaciated and unglaciated environments

description: Periodic glaciation during the Quaternary period shaped the contemporary
 riverscape and distribution of freshwater fishes in the Mississippi River
 drainage of central North America. The rainbow darter (Etheostoma
 caeruleum) is a member of this ichthyofauna and has a disjunct
 distribution in glaciated and unglaciated environments west of the
 Mississippi River. Based on glacial history of the region there are
 different expectations on the observed spatial genetic structure of
 populations in these environments. The aim of this study was to utilize
 genome-wide SNP data to compare the population genomic structure of the
 rainbow darter in river networks with disparate glacial histories; the
 Volga River in the glaciated upper Mississippi River basin and the Meramec
 River in the unglaciated Ozark Plateau. Individuals were sampled from
 localities within each river system at distances dictated by the
 organismal life history and habitat preferences. Riverscape analyses were
 performed on three datasets: total combined localities of both rivers and
 one for each river independently. The results revealed a lasting influence
 of historic glaciation on the population genomic structure of rainbow
 darter populations. There was evidence of population expansion into the
 glaciated northern region following glacial retreat. The population
 genetic signature within the Volga River did not fit expectations of the
 stream hierarchy model, but revealed a pattern of repeated colonization
 and extirpation due to cyclic glaciation. The population within the
 unglaciated Meramec River adhered to the stream hierarchy model, with a
 directional order of genetic diversity based on the life history and
 habitat preferences of the species. These results demonstrate the
 importance of considering the geologic and climatic history of a region as
 well as the life history of an organism when interpreting spatial genetic
 patterns.
description: This is a dataset generated through the use of Restriction
 Site-Assocated DNA Sequencing (RADseq) with the Illumina HiSeq 4000 and
 NovaSeq 6000 platforms. Raw read data was processed for the appropriate
 barcode sequences for individual organisms and assembled de novo using
 Stacks (v.2.59). This data was processed further with the populations
 function within Stacks to generate three separate data groupings for the
 Volga River of NE Iowa, the Meramec River of Missouri, as well as a
 combined set.
description: To use this data, one would need a familiarity with the following
 software packages; fastStructure, R (adegenet, ade4, hierfstat), Arlequin,
 PGDSpider. A spreadsheet with the sample IDs, locality IDs, MID sequences
 used, as well as geographic locations is included, as well as a text
 ReadMe file describing archive contents.
DOI: 10.5061/dryad.zgmsbcccs
title: Task-induced modulations of neuronal activity along the auditory pathway

description: Sensory processing varies depending on behavioral context. Here, we ask
 how task-engagement modulates neurons in the auditory system. We train
 mice in a simple tone-detection task, and compare their neuronal activity
 during passive hearing and active listening. Electrophysiological
 extracellular recordings in the inferior colliculus, medial geniculate
 body, primary auditory cortex and anterior auditory field reveals
 widespread modulations across all regions and cortical layers, and in both
 putative regular and fast-spiking cortical neurons. Clustering analysis
 unveils ten distinct modulation patterns that can either enhance or
 suppress neuronal activity. Task-engagement changes the tone-onset
 response in most neurons. Such modulations first emerge in subcortical
 areas, ruling out cortical feedback as the only mechanism underlying
 subcortical modulations. Half the neurons additionally display late
 modulations associated with licking, arousal or reward. Our results reveal
 the presence of functionally distinct subclasses of neurons,
 differentially sensitive to specific task-related variables but
 anatomically distributed along the auditory pathway.
DOI: 10.5061/dryad.kkwh70s5x
title: Poa arachnifera demography and sex ratio surveys

description: Understanding the mechanisms that generate biogeographic range limits is a
 long-standing goal of ecology. It is widely hypothesized that
 distributional limits reflect the environmental niche, but this hypothesis
 is complicated by widespread potential for intra-specific niche
 heterogeneity. In dioecious species, sexual niche differentiation
 may cause divergence between the sexes in their limits of environmental
 suitability. We studied range boundary formation in Texas
 bluegrass ( Poa arachnifera ), a perennial dioecious
 plant, testing the alternative hypotheses that range limits reflect the
 niche limits of females only versus the combined contributions of females
 and males, including their inter-dependence via mating. Common
 garden experiments across a longitudinal aridity gradient revealed
 female-biased flowering approaching eastern range limits, suggesting that
 mate limitation may constrain the species'
 distribution. However, a demographic model showed that declines
 in λ approaching range limits were driven almost entirely by female vital
 rates. The dominant role of females was attributable to seed
 viability being robust to sex ratio variation and to low sensitivity of λ
 to reproductive transitions. We suggest that female-dominant range limits
 may be common to long-lived species with polygamous mating systems, and
 that female responses to environmental drivers may often be sufficient for
 predicting range shifts in response to environmental change.
DOI: 10.5061/dryad.ns1rn8pv7
title: Salmonberry stomatal density

description: Triangle Island on Canada’s Pacific coast is home to a large, globally
 important seabird breeding colony. The shrub Salmonberry Rubus spectabilis
 and tussock-forming Tufted Hairgrass Deschampsia cespitosa together form
 ~70% of vegetation coverage, and contain the vast majority (~90%) of
 seabird nesting burrows. Salmonberry has in recent decades greatly
 expanded its coverage, while that of Tufted Hairgrass has receded.
 Seabirds prefer not to burrow under Salmonberry, making its ongoing
 expansion a potential conservation issue. We investigated three hypotheses
 proposed to explain Salmonberry’s expansion (climate change,
 biopedturbation, nutrient input), using comparisons of stomatal density of
 Salmonberry leaves sampled from Triangle Island, other seabird colonies,
 other coastal locations, and from historical specimens in herbaria.
 Stomatal density helps regulate photosynthetic gain and control water
 loss, and responds to light, nutrient, carbon dioxide and water
 availability. Differing patterns of stomatal density are expected among
 sample locations depending on which of the hypothesized factors most
 strongly affects Salmonberry’s performance. Our data are most consistent
 with the nutrient input hypothesis. We discuss possible reasons why
 Salmonberry has expanded so recently, even though Triangle has been a
 large seabird colony for at least a century and likely much longer.
description: Described in detail in the paper, ECE-06-00902.
description: Notes on the data file for Ydenberg et al. ‘Century-long stomatal
 density record of the nitrophyte, <i>Rubus spectabilis</i> L.,
 from the Pacific northwest indicates no effect of changing atmospheric
 carbon dioxide but a strong response to nutrient subsidy.’
 ECE-2021-06-00902. The file contains for each
 salmonberry specimen the sample identifier from the various herbaria, or
 from my own collection (Column A), the date collected (if available,
 Column B) and its Julian date equivalent (Column C), the year (Column D),
 the stomatal density (Column E, in mm<sup>-2</sup>), and the
 location, altitide, latitude and longitude (Columns F, G, H, and I,
 respectively) when this information was noted with the specimen.
DOI: 10.5061/dryad.5dv41ns74
title: Data from: Inter-specific variation in the potential for upland rush management advocated by agri-environment schemes to increase breeding wader densities

description: Encroachment of rush Juncus spp. in the United Kingdom uplands poses a
 threat to declining wader populations due to taller, denser
 swards that can limit foraging and breeding habitat quality for some
 species. Rush management via cutting, implemented through agri-environment
 schemes (AESs), could thus increase wader abundance, but there is
 insufficient assessment and understanding of how rush management
 influences upland waders. Across two upland regions of England
 [South West Peak (SWP) and Geltsdale nature reserve, Cumbria], we surveyed
 waders over four visits in fields where rush was managed
 according to AES prescriptions (treatment; n = 21) and fields without rush
 management that were otherwise ecologically similar (control; n = 22)
 to assess how the densities of breeding wader pairs respond to
 rush management in the short-term. We find evidence for regional variation
 in the response of waders to rush management, with densities of
 Common Snipe Gallinago gallinago significantly higher in treatment than
 control fields in the SWP, but not Geltsdale. There were no
 statistically significant responses to treatment on densities of
 Eurasian Curlew Numenius arquata or Northern Lapwing Vanellus vanellus.
 The 95% confidence intervals for the treatment parameter
 estimates suggest that this may be due to limited statistical power in the
 case of Lapwing. For Curlew, however, any potential increases in densities
 are negligible. There was no evidence that variation in rush
 cover, which ranged from 10 to 70%, influenced densities of any of our
 three focal species. Our results suggest that rush management
 through AES prescriptions delivered in isolation of other interventions
 may not lead to general increases in breeding wader densities in the
 short-term, but benefits may arise in some situations due to
 regional and inter-specific variation in effectiveness. Rush management
 supported with interventions that improve soil conditions and
 thus food availability, or reduce predation pressure, may enable
 AES rush management to generate benefits. Additional research is required
 to maximise the potential benefits of rush management for each
 species through the development of prescriptions that tailor to individual
 species’ optimum sward structure.
description: WaderPairsData.xlsx Dataset for analyses of
 breeding wader pair densities in treatment fields with rush management and
 control fields without rush management. Each row is a field. Metadata is
 available in the second sheet of the WaderPairsData.xlsx file and in the
 README_WaderPairsData.txt file.
DOI: 10.5061/dryad.c866t1g84
title: Light and thermal niches of ground-foraging Amazonian insectivorous birds

description: Insectivores of the tropical rainforest floor are consistently among the
 most vulnerable birds to forest clearing and fragmentation. Several
 hypotheses attempt to explain this pattern, including sensitivity to
 extreme microclimates found near forest borders—particularly brighter and
 warmer conditions. Importantly, this “microclimate hypothesis” has
 additional implications for intact forest under global climate change that
 could be evaluated through direct assessment of the light and temperature
 environment of terrestrial insectivores. In this study, we harness novel
 technology to directly quantify the light and thermal niches of 10 species
 of terrestrial insectivores in undisturbed Amazonian rainforest. Loggers
 placed on birds (N = 33) and their environment (N = 9) recorded nearly
 continuous microclimate data from 2017–2019, amassing &gt;5 million
 measurements. We found that midday light intensity in treefall gaps
 (~39,000 lux) was &gt;40 times higher than at the ground level of
 forest interior (950 lux). Light intensity registered by sensors placed on
 birds averaged 17.4 (range 3.9–41.5) lux, with species using only 4.3
 (0.9–10.4) % of available light on the forest floor. Birds thus selected
 very dark microhabitats—the light environment was &gt;2,200 times
 brighter in treefall gaps. Bird thermal niche was a function of ambient
 temperature as well as body temperature, which averaged &gt;40.5 °C
 but varied among species. Forest floor temperature peaked daily at 27.0
 °C, while bird loggers averaged 35.1 (34.5–35.7) °C at midday. The
 antpitta Myrmothera campanisona and the antthrush Formicarius colma used
 thermal conditions closest to their body temperatures, whereas leaftossers
 (Sclerurus spp.) and Myrmornis torquata occupied relatively cool
 microclimates. We found no general link between abundance trends and
 variation in species-specific light and thermal niches. Rather, all
 species occupied remarkably dim and cool microclimates. Because such
 conditions are rare outside of the interior of primary forest, these
 results support the microclimate hypothesis in disturbed landscapes.
 Moreover, strong avoidance to conditions that are becoming more common
 under climate change highlights the vulnerability of terrestrial
 insectivores even in the absence of disturbance and may be the reason for
 enigmatic declines in Amazonia and elsewhere.
description: Please see the associated publication for methods on data
 collection and processing.
DOI: 10.7291/d17h67
title: Population structure and genetic differentiation in extant alligator snapping turtles (genus Macrochelys) with implications for taxonomy and conservation

description: Historically believed to harbor unrecognized diversity, the taxonomy of
 the declining Alligator Snapping Turtle (genus Macrochelys) is debated.
 The original species, M. temminckii, was recently split into M.
 temminckii, M. apalachicolae, and M. suwanniensis. However, authors
 contest the status of M. apalachicolae. In this study, we generated
 thousands of genome-wide loci to quantify population structure and genetic
 differentiation across the range of Macrochelys spp. Our data indicate
 that M. apalachicolae is genetically distinct, with little gene flow
 between M. apalachicolae and other species, thus adding evidence that M.
 apalachicolae may be a distinct species. We also find genetic variation
 partitioned among river drainages, with very high intra- and interspecific
 genetic divergence among-river drainages. We suggest that translocations
 and re-introductions only move turtles in this genus within their natal
 river drainages to preserve existing patterns of genetic diversity.
description: These are raw SNPs that passed all filters from ipyrad.
description: Note: use population assignment file to assign individuals in the
 VCF to assemblages described in the manuscript.
DOI: 10.5061/dryad.wdbrv15qd
title: Impact of model assumptions on the inference of the evolution of ectomycorrhizal symbiosis in fungi

description: Ectomycorrhiza (ECM) is a symbiotic relation between plant and fungi that
 is essential for nutrient uptake of many stand forming trees. There are
 two conflicting views about the evolution of ECM in fungi suggesting (1)
 relatively few transitions to ECM followed by reversals to non-ECM, or (2)
 many independent origins of ECM and no reversals. In this study, we
 compare these, and other, hypotheses and test the impact of different
 models on inference. We assembled a dataset of five marker gene sequences
 (nuc58, nucLSU, nucSSU, rpb1, and rpb2) and 2,174 fungal taxa covering the
 three subphyla: Agaricomycotina, Mucoromycotina and Pezizomycotina. The
 fit of different models, including models with variable rates in clades or
 through time, to the pattern of ECM fungal taxa was tested in a Bayesian
 framework, and using AIC and simulations. We find that models implementing
 variable rates are a better fit than models without rate shift, and that
 the conclusion about the relative rate between ECM and non-ECM depend
 largely on whether rate shifts are allowed or not. We conclude that
 standard constant-rate ancestral state reconstruction models are not
 adequate for the analysis of the evolution of ECM fungi, and may give
 contradictory results to more extensive analyses.
DOI: 10.5061/dryad.sj3tx9662
title: Data for: Population structure of a grassland songbird (Dolichonyx oryzivorus) to inform conservation units

description: Understanding the patterns and processes driving population structure is
 crucial for conservation planning. Spatial conservation units
 (CUs) for one or more species have been defined using similarities in
 communities, habitats, and resource management concerns. Additionally, CU
 boundaries can be informed by population genetic structure. Here, we
 determined the population structure of the Bobolink (Dolichonyx
 oryzivorus), a migratory grassland bird. Its breeding range spans
 longitudinally across most of North America in the northern U.S. and
 southern Canada, and its population has declined by 59% from 1971 to 2014.
 We sampled blood from Bobolinks at seven breeding sites and used a ddRAD
 sequencing approach to identify 3236 SNPs for population genetic analyses.
 Using the Bayesian clustering approach, STRUCTURE, we found low levels of
 genetic differentiation across the breeding range. F st values ranged from
 0.002 to 0.036 among all population pairs, and genetic structure followed
 an isolation-by-distance model. Despite low levels of genetic
 differentiation, we found evidence for four genetic groupings— breeding
 populations in Oregon and British Columbia were distinct from each other
 as well as from Central and eastern North American breeding populations.
 Investigating the demographic history of the populations using approximate
 Bayesian computation, we found evidence that western Bobolink populations
 are not relict populations but instead were founded during a recent
 westward range expansion, possibly enabled by agricultural expansion. We
 identify four genetics-based CUs that may serve as a complementary spatial
 framework, broader in scale compared to the commonly-used Bird
 Conservation Regions, for defining and achieving population objectives.
description: Blood samples were taken from 174 individuals captured with mist
 nets. SNP genotypes were obtained from ddRAD sequencing. After processing
 with the Stacks pipeline, genotypes were called from a panel of 3226 SNPs.
 These genotypes are collated for the 174 birds across 7 sampling
 locations.
description: This SNP genotype file is formatted in the STRUCTURE data
 format.