cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.6wwpzgmxh
title: Data from: Temporal stability of chimpanzee social culture

description: Culture is a hallmark of the human species, both in terms of the
 transmission of material inventions (e.g., tool manufacturing) and the
 adherence to social conventions (e.g., greeting mannerisms). While
 material culture has been reported across the animal kingdom, indications
 of social culture in animals are limited. Moreover, there is a paucity in
 evidencing cultural stability in animals. Here, based on a large dataset
 spanning 12 years, I show that chimpanzees adhere to arbitrary
 group-specific handclasp preferences that cannot be explained by genetics
 or the ecological environment. Despite substantial changes in group
 compositions across the study period, and all chimpanzees having several
 behavioral variants in their repertoires, chimpanzees showed and
 maintained the within-group homogeneity and between-group heterogeneity
 that is so characteristic of the cultural phenomenon in the human species.
 These findings indicate that human culture, including its arbitrary social
 conventions and long-term stability, is rooted in our evolutionary
 history.
description: Observational, all-occurrence data.
DOI: 10.5061/dryad.5mkkwh74q
title: Precipitation, water level and descriptive statistics

description: Extreme weather events and the presence of mega-hydroelectric dams, when
 combined, present an emerging threat to natural habitats in the Amazon
 region. To understand the magnitude of these impacts, we used remote
 sensing data to assess forest loss in areas affected by the extreme 2014
 flood in the entire Madeira River basin, the location of two mega-dams. In
 addition, forest plots (26 ha) were monitored between 2011 and 2015
 (14,328 trees) in order to evaluate changes in tree mortality, aboveground
 biomass (AGB), species composition and community structure around the
 Jirau reservoir (distance between plots varies from 1 to 80 km). We showed
 that the mega-dams were the main driver of tree mortality in Madeira basin
 forests after the 2014 extreme flood. Forest loss in the areas surrounding
 the reservoirs was 56 km² in Santo Antônio, 190 km² in Jirau (7.4-9.2% of
 the forest cover before flooding), and 79.9% above that predicted in
 environmental impact assessments. We also show that climatic anomalies,
 albeit with much smaller impact than that created by the mega-dams,
 resulted in forest loss along different Madeira sub-basins not affected by
 dams (34-173 km²; 0.5-1.7%). The impact of flooding was greater in várzea
 and transitional forests, resulting in high rates of tree mortality
 (88-100%), AGB decrease (89-100%), and reduction of species richness
 (78-100%). Conversely, campinarana forests were more flood-tolerant with a
 slight decrease in species richness (6%) and similar AGB after flooding.
 Taking together satellite and field measurements, we estimate that the
 2014 flood event in the Madeira basin resulted in 8.81-12.47 ∙ 106 tons of
 dead biomass. Environmental impact studies required for environmental
 licensing of mega-dams by governmental agencies should consider the
 increasing trend of climatic anomalies and the high vulnerability of
 different habitats to minimize the serious impacts of dams on Amazonian
 biodiversity and carbon stocks.
DOI: 10.5061/dryad.cjsxksn58
title: Novel laboratory index, based on fasting blood parameters, accurately reflects insulin sensitivity

description: Simple and reliable measurement of insulin sensitivity may be important
 for the prevention of insulin-resistance related diseases. Surrogate
 indices of insulin sensitivity are of limited utility in population
 without signs of metabolic syndrome. The aim of our study was to provide
 simple and accurate index of insulin sensitivity. The study group
 comprised 150 young healthy participants. Hyperinsulinemic-euglycemic
 clamp was performed. Regression models with different laboratory
 parameters were constructed. Validation cohort 1 comprised independent
 group of 110 subjects, including individuals with prediabetes and newly
 diagnosed type 2 diabetes. Validation cohort 2 comprised 38 obese subjects
 before and after diet-induced weight loss. Validation cohort 3 comprised
 60 nondiabetic subjects from an independent center. The supervised
 principal component model established optimal set of variables correlated
 with insulin sensitivity. This model (Fasting Laboratory Assessment of
 Insulin Sensitivity, FLAIS) used red blood cell count, alanine
 aminotransferase activity, serum C-peptide, SHBG, IGF-binding protein 1
 and adiponectin concentrations. FLAIS exhibited strong correlation with
 clamp-derived insulin sensitivity. The sensitivity of the model was 90%
 and the specificity was 68%. In the validation cohort 1, differences in
 FLAIS among the groups paralleled those observed with the clamp, with the
 lowest values in prediabetes and diabetes. In the validation cohort 2,
 FLAIS reflected the change in insulin sensitivity after weight loss. The
 main findings were confirmed in the validation cohort 3. We provide simple
 and accurate method of assessing insulin sensitivity, which allows to
 identify insulin resistance even in the population without overt metabolic
 disturbances.
DOI: 10.5061/dryad.qnk98sffj
title: The genetic architecture and evolution of life history divergence among perennials in the Mimulus guttatus species complex

description: Ecological divergence is a main source of trait divergence between closely
 related species. Despite its importance in generating phenotypic
 diversity, the genetic architecture of most ecologically relevant traits
 is poorly understood. Differences in elevation can impose substantial
 selection for phenotypic divergence of both complex, correlated suites of
 traits (such as life history), as well as novel adaptations. Here, we use
 the Mimulus guttatus species complex to assess if divergence in elevation
 is accompanied by trait divergence in a group of closely related perennial
 species, and determine the genetic architecture of this divergence. We
 find that divergence in elevation is associated with differences in
 multivariate quantitative life history traits, as well as a unique trait;
 the production of rhizomes, which may play an important role in
 overwintering survival. However, the extent of phenotypic divergence among
 species depended on ontogeny, suggesting that species also diverged in
 investment strategies across development. Lastly, we show that the genetic
 architecture of life history divergence between two species is simple,
 involving few mid to large effect Quantitative Trait Loci (QTLs), and that
 the genetic architecture of the ability to produce rhizomes changes
 through development, which has potential implications for hybrid fitness
 in the wild.
description: Occurrence+PredictedOccurrence Dataset: Maxent models were run
 for 5 perennial taxa of the M. guttatus species complex based on herbarium
 records from GBIF. Models were run using 4 bioclim variables (temperature
 and precipitation seasonality, mean temperature of the warmest quarter,
 and mean precipitation of the warmest quarter) plus elevation downloaded
 to 2.5 arc degrees. This dataset represents a subset of 500 suitable
 locales for each taxa from the predicted ranges concatenated with true
 herbarium records, plus affiliated ecological data from those locales (all
 climate variables from WorldClim, plus elevation, plus the PCs from a PCA
 of these variables). PopulationPhenotypicSurvey: plants
 of 5 perennial taxa were grown in the Duke Greenhouses under long day warm
 conditions (18h, 22 degrees C) and surveyed at 3 developmental stages (3
 weeks post germination, day of first flower, 3 weeks post first flower)
 for several life history traits. Phenotypic data for each developmental
 stage, plus information regarding the geographic locale of origin for each
 population RqtlFormatedGenotype+Phenotype: Genotype and
 phenotype information for 213 F2 individuals across 1,311 markers inferred
 from a modified Andolfatto shotgun sequencing approach using the Csp6I
 enzyme. Hybrids+pars_PhenotypesAcrossDev: phenotypes
 for all F1s, F2s, and inbred line replicates across three developmental
 stages.
DOI: 10.5061/dryad.ncjsxkstd
title: Audio recordings of Atelpus varius calls from Panama

description: Anurans (frogs and toads) are among the most globally threatened taxonomic
 groups. Successful conservation of anurans will rely on improved data on
 the status and changes in local populations, particularly for rare and
 threatened species. Automated sensors, such as acoustic recorders, have
 the potential to provide such data by massively increasing the spatial and
 temporal scale of population sampling efforts. We used AudioMoth
 autonomous recorders to survey for the critically endangered Harlequin
 toad (Atelopus varius) in Panama. This sampling effort generated
 thousands of hours of audio recordings from stream-side transects.
 Atelopus varius has a distinctive call with fast amplitude
 modulation of about 120 pulses per second.  We used the
 opens-source Repeat Interval-Based Bioacoustic Identification Tool
 (RIBBIT), which classifies anuran vocalizations in audio recordings based
 on their periodic structure, to detect A. varius vocalizations in the
 data. Here we provide 70 detected recordings of A. varius. These
 recordings represent a dramatic increase in the total number of openly
 available audio recordings of A.
 varius vocalizations. 
description: These files were extracted from recordings taken by AudioMoth
 autonomous recording units in Panama in 2019. We used an automated
 detection method (the Repeat Interval-Based Bioacoustic Identification
 Tool, ie RIBBIT) to search for vocalizations of Atelopus varius in a large
 audio dataset. This dataset contains 70 60-second audio files which all
 contain vocalizations of Atelopus varius - all are from one stationary
 recorder during a three-day period, and possibly originate from a single
 individual frog. All 70 of these files were ranked by RIBBIT in the 72
 top-scoring files out of several million inputs.
description: This dataset contains 70 audio files in .wav format, each 60
 seconds long. The audio was recorded using AudioMoth acoustic
 recorders.
DOI: 10.5061/dryad.crjdfn338
title: CT-informed skull osteology of Palaeolagus haydeni (Mammalia: Lagomorpha)

description: Lagomorpha is a clade of herbivorous mammals nested within
 Euarchontoglires, one of the major placental groups represented today. It
 comprises two extant families with markedly different body plans: the
 long-eared and long-limbed Leporidae (hares and rabbits) and the
 short-eared and short-limbed Ochotonidae (pikas). These two lagomorph
 lineages diverged probably during the latest Eocene/early Oligocene, but
 it is unclear whether the last common ancestor of crown lagomorphs was
 more leporid- or more ochotonid-like in morphology. Palaeolagus, an early
 lagomorph dominant in western North America from the late Eocene to
 Oligocene is of particular importance for addressing this controversy.
 Here, we present new and comprehensive data on the cranial anatomy of
 Palaeolagus haydeni, the type species for the genus, based on
 micro-computed tomography (μCT). Our μCT data allow us to confirm, revise
 and score for the very first time the states of several leporid-like and
 ochotonid-like characters in the skull of Palaeolagus. This mixed cranial
 architecture differentiates Palaeolagus from the crown groups of
 Lagomorpha and supports its phylogenetic status as a stem taxon.
description: This study is based on CT-scan data from an almost complete
 cranium with mandible in occlusion of <i>Palaeolagus
 haydeni</i> (FMNH PM9476) from the early Oligocene of the Brule
 Formation, Nebraska, USA. The skull roof is partially missing in this
 specimen, the anterior nasals and the left zygomatic arch are also largely
 damaged. FMNH PM9476 was CT-scanned in a
 high-resolution Phoenix v|tome|x L 240 scanner (GE Measurement &
 Control Solutions) at the AMNH. The specimen was scanned in a single scan
 with the following parameters: voltage 170kV, current 170 µA and a 0.1 mm
 Cu filter to minimize beam hardening. The CT-data were reconstructed with
 Phoenix datos|x 2.0 software obtaining a total of 1401 images at a
 resolution of 0.0365 mm (isometric voxels). The reconstruction of the raw
 data generated a 16-bit TIFF image stack comprising 980 slices (570 x 515
 pixels). The original image stack was first uploaded into ImageJ 1.52a to
 remove beam hardening artefacts and increase the contrast between
 fossilized bone and rock matrix using the Brightness and Contrast tool
 (Image -&gt;Adjust -&gt; Brightness/Contrast). The adjusted images
 were then saved as an 8-bit TIFF image stack and uploaded into AvizoLite
 2019.4 (Thermo Fischer Scientific 1995–2019) installed on a FUJITSU
 Celsius M740 workstation (processor: Intel Xeon CPU E5-2620 v4 2.10 GHz,
 RAM: 128 GB, graphics card: GeForce GTX 1050 Ti, hard drive: Samsung SSD
 860 EVO 500 GB) operating on Windows 10 Pro (Microsoft 2019). Manual
 segmentation involved using the Lasso and Magic Wand tools. 3D models of
 individual bones and bone complexes were generated using the Unconstrained
 Smoothing option (smoothing extent = 2.5).
 Institutional Abbreviation: FMNH, Field Museum of Natural
 History, Chicago, IL, USA
description: All files are in the PLY format.
DOI: 10.5061/dryad.547d7wm7d
title: Interspecific and intraspecific comparisons reveal the importance of evolutionary context in sunfish brain form divergence

description: Habitats can select for specialized phenotypic characteristics in animals.
 However, the consistency of evolutionary responses to particular
 environmental conditions remains difficult to predict. One trait of great
 ecological importance is brain form, which is expected to vary between
 habitats that differ in their cognitive requirements. Here we compared
 divergence in brain form and oral jaw size across a common
 littoral-pelagic ecological axis in two sunfishes at both the
 intraspecific and interspecific levels. Brain form differed between
 habitats at every level of comparison, however divergence was
 inconsistent, despite consistent differences in oral jaw size. Pumpkinseed
 and bluegill species differed in cerebellum, optic tectum, and olfactory
 bulb size. These differences are consistent with a historical ecological
 divergence because they did not manifest between littoral and pelagic
 ecotypes within either species, suggesting constraints on changes to these
 regions over short evolutionary time scales. There were also differences
 in brain form between conspecific ecotypes, but they were inconsistent
 between species. Littoral pumpkinseed had larger brains than their pelagic
 counterpart, and littoral bluegill had smaller telencephalons than their
 pelagic counterpart. Inconsistent brain form divergence between
 conspecific ecotypes of pumpkinseed and bluegill sharing a common
 littoral-pelagic habitat axis suggests that contemporary ecological
 conditions and historic evolutionary context interact to influence
 evolutionary changes in brain form in fishes.
DOI: 10.5061/dryad.mkkwh70zk
title: Bumble bee demographic data for functional linear models

description: 1. Behavior and organization of social groups is thought to be vital to
 the functioning of societies, yet the contributions of various roles
 within social groups towards population growth and dynamics have been
 difficult to quantify. A common approach to quantifying these role-based
 contributions is evaluating the number of individuals conducting certain
 roles, which ignores how behavior might scale up to effects at
 the population-level. Manipulative experiments are another common
 approach to determine population-level effects, but they often
 ignore potential feedbacks associated with these various roles.
 2. Here, we evaluate the effects of worker size distribution in bumblebee
 colonies on worker production in 24 observational colonies across three
 environments, using functional linear models. Functional linear
 models are an underused correlative technique that has been used
 to assess lag effects of environmental drivers on plant
 performance. We demonstrate potential applications of this
 technique for exploring high-dimensional ecological systems, such as
 the contributions of individuals with different traits to colony
 dynamics. 3. We found that more larger workers had mostly positive effects
 and more smaller workers had negative effects on worker
 production. Most of these effects were only detected under low
 or fluctuating resource environments suggesting that the
 advantage of colonies with larger-bodied workers becomes more
 apparent under stressful conditions. 4. We also demonstrate the wider
 ecological application of functional linear models. We highlight
 the advantages and limitations when considering these models, and how they
 are a valuable complement to many of these performance-based and
 manipulative experiments.
DOI: 10.5061/dryad.n5tb2rbv1
title: Temporal dynamics and biocontrol potential of a hyperparasite on coffee leaf rust across a landscape in Arabica coffee’s native range

description: Agroforestry systems can provide habitats for rich biodiversity including
 multitrophic interactions, which presents opportunities to develop natural
 pest control. Shade coffee systems in several coffee-growing areas of the
 world host such unique habitats where pests and their natural enemies
 interact. One of the major global challenges for coffee production, coffee
 leaf rust caused by the fungal pathogen Hemileia vastatrix is attacked by
 the fungal hyperparasite, Lecanicillium lecanii. However, we lack insights
 in the dynamics and biocontrol potential of the hyperparasite on coffee
 leaf rust from landscapes in Arabica coffee’s native range. To understand
 the temporal dynamics across landscapes and environmental drivers of the
 rust and hyperparasite, and the potential for biocontrol of the rust by
 the hyperparasite, we studied the rust and hyperparasite during the dry
 and wet seasons for three consecutive years at 60 sites across a gradient
 of coffee management in southwestern Ethiopia. We found that coffee leaf
 rust was more severe during the dry season, whereas the hyperparasite was
 more severe during the wet season in two out of three years. The rust
 growth rate from the wet to the dry season transition was negatively
 related to the hyperparasite index during the wet season, implying a
 potential top-down control. Coffee leaf rust was generally more severe at
 lower altitudes in the dry season, whereas the hyperparasite was more
 severe at high altitude. The rust incidence increased with management
 intensity, while the hyperparasite was more common under less intensive
 management. This study could be interesting in that it represents a
 landscape where Arabica coffee originated and the rust and hyperparasite
 might have a long co-evolutionary history. Our findings highlight the
 potential of the hyperparasite to suppress the rust’s growth rate from the
 wet to dry season transition when the rust severity could otherwise be at
 its peak. We show that less intensively managed landscapes with dense
 shade levels are likely to increase hyperparasite abundance and result in
 an improved top-down control of the rust. However, more detailed knowledge
 is needed on the interaction of these species to assess its importance for
 reducing rust induced yield losses or the risk of rust outbreaks.
DOI: 10.5061/dryad.3bk3j9kj6
title: Data from: Nutrient dominance governs the assembly of microbial communities in mixed nutrient environments

description: A major open question in microbial community ecology is whether we can
 predict how the components of a diet collectively determine the taxonomic
 composition of microbial communities. Motivated by this challenge, we
 investigate whether communities assembled in pairs of nutrients can be
 predicted from those assembled in every single nutrient alone. We first
 find that although the null, naturally additive model generally predicts
 well the family-level community composition, there exist systematic
 deviations from the additive predictions that reflect generic patterns of
 nutrient dominance at the family-level. Pairs of more similar nutrients
 (e.g. two sugars) are on average more additive than pairs of more
 dissimilar nutrients (one sugar- one organic acid). Second, a simple
 dominance rule emerges: sugars generally dominate organic acids. These
 findings may be explained by family-level asymmetries in nutrient
 benefits. Overall, our results suggest that regularities in how nutrients
 interact may help predict communities responses to dietary changes.
description: This dataset contains 1) the taxonomy and relative abundance of
 each ESV in each community, and 2) the community biomass (OD620) of each
 community. The community composition was determined using 16S rRNA
 amplicon sequencing. DADA2 (version 1.6.0) was used to infer exact
 sequence variants (ESVs) from each sample, and the taxonomy was assigned
 using the SILVA reference database.
DOI: 10.5061/dryad.59zw3r267
title: Genetic, anatomical, and environmental patterns related to pod shattering resistance in domesticated cowpea Vigna unguiculata [L.] Walp

description: Pod shattering, which causes the explosive release of the seeds from the
 pod, is one of the main sources of yield losses in cowpea in arid and
 semi-arid areas. Reduction of shattering has therefore been a primary
 target for selection in the domestication process of the species. Using a
 mini-core diversity panel of 368 cowpea accessions, four regions with a
 significant association with pod shattering were identified. Two genes
 (Vigun03g321100 and Vigun11g100600) involved in cell wall biosynthesis
 were identified as strong candidates for pod shattering. Microscopical
 analysis was conducted on a subset of accessions representing the full
 spectrum of shattering phenotypes. This analysis indicated that the extent
 of wall fiber deposition was highly correlated with shattering. The
 results from this study also confirm that pod shattering in cowpea is
 exacerbated by arid environmental conditions. Finally, using a subset of
 West African landraces, patterns of historical selection for shattering
 resistance related to precipitation in the environment of origin were
 identified. Together, these results shed light on sources of resistance to
 pod shattering, which will, in turn, improve climate resilience of a major
 global nutritional staple.