cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.kj7rh04
title: Data from: Artificial selection on brain size leads to matching changes in overall number of neurons

description: Neurons are the basic computational units of the brain, but brain size is
 the predominant surrogate measure of brain functional capacity in
 comparative and cognitive neuroscience. This approach is based on the
 assumption that larger brains harbour higher numbers of neurons and their
 connections and therefore have a higher information processing capacity.
 However, recent studies have shown that brain mass may be less strongly
 correlated with neuron counts than previously thought. Till now, no
 experimental test has been conducted to examine the relationship between
 evolutionary changes in brain size and the number of brain neurons. Here
 we provide such a test by comparing neuron number in artificial selection
 lines of female guppies (Poecilia reticulata) with &gt;15% difference
 in relative brain mass and numerous previously demonstrated cognitive
 differences. Using the isotropic fractionator, we demonstrate that
 large-brained females have a higher overall number of neurons than
 small-brained females, but similar neuronal densities. Importantly, this
 difference holds also for the telencephalon, a key region for cognition.
 Our study provides the first direct experimental evidence that selection
 for brain mass leads to matching changes in number of neurons and shows
 that brain size evolution is intimately linked to the evolution of neuron
 number and cognition.
description: DATA Electronic
 Supplementary Material
DOI: 10.5061/dryad.805cp7g
title: Data from: Matrix type and landscape attributes modulate avian taxonomic and functional spillover across habitat boundaries in the Brazilian Atlantic Forest

description: Land use intensification drives biodiversity loss worldwide. In
 heterogeneous landscape mosaics, both overall forest area and
 anthropogenic matrix structure induce changes in biological communities in
 primary habitat remnants. However, community changes via cross-habitat
 spillover processes along forest-matrix interfaces remain poorly
 understood. Moreover, information on how landscape attributes affect
 spillover processes across habitat boundaries are embryonic. Here, we
 quantify avian  and β-diversity (as proxies of spillover rates) across
 two dominant types of forest-matrix interfaces (forest-pasture and
 forest-eucalyptus plantation) within the Atlantic Forest biodiversity
 hotspot in southeast Brazil. We also assess the effects of anthropogenic
 matrix type and landscape attributes (forest cover, edge density and
 land-use diversity) on bird taxonomic and functional β-diversity across
 forest-matrix boundaries. Alpha taxonomic richness was higher in forest
 edges than within both matrix types, but between matrix types, it was
 higher in pastures than in eucalyptus plantations. Although significantly
 higher in forests edges than in the adjacent eucalyptus, bird functional
 richness did not differ between forest edges and adjacent pastures.
 Community changes (β-diversity) related to species and functional
 replacements (turnover component) were higher across forest-pasture
 boundaries, whereas changes related to species and functional loss (nested
 component) were higher across forest-eucalyptus boundaries. Forest edges
 adjacent to eucalyptus had significant higher species and functional
 replacements than forest edges adjacent to pastures. Forest cover
 negatively influenced functional β-diversity across both forest-pasture
 and forest-eucalyptus interfaces. We show the importance of matrix type
 and the structure of surrounding landscapes (mainly forest cover) on rates
 of bird assemblage spillover across forest-matrix boundaries, which has
 profound implications to biological fluxes, ecosystem functioning and
 land-use management in human-modified landscapes.
description: Bird occurrence,
 ecological traits and landscape predictors in southeast
 BrazilThis database provide
 data on bird species occurrence in forest edges, pastures and eucalyptus
 plantation across a wide region of fragmented Atlantic Forest,
 southeastern Brazil. Additonally, information on species ecological
 traits, sampling geographical coordinates, and landscape attributes are
 available. Detailed information on how these data were collated are found
 in the Methods section of the manuscript.bird_dataset.xlsx
DOI: 10.5061/dryad.j27h930
title: Data from: On the consequences of the interdependence of stabilizing and equalizing mechanisms

description: We present an overlooked but important property of modern coexistence
 theory (MCT), along with two key new results and their consequences. The
 overlooked property is that stabilizing mechanisms (increasing
 species' niche differences) and equalizing mechanisms (reducing
 species' fitness differences) have two distinct sets of meanings
 within MCT: one in a 2-species, and another in a general multispecies
 context. We demonstrate that the 2-species framework is not a special case
 of the multispecies one, and therefore these two parallel frameworks must
 be studied independently. Our first result is that, using the 2-species
 framework and mechanistic consumer-resource models, stabilizing and
 equalizing mechanisms exhibit complex interdependence, such that changing
 one will simultaneously change the other. Furthermore, the nature and
 direction of this simultaneous change depend sensitively on model
 parameters. The second result states that while MCT is often seen as
 bridging niche and neutral modes of coexistence by building a
 niche-neutrality continuum, the interdependence between stabilizing and
 equalizing mechanisms acts to break this continuum under almost any
 biologically relevant circumstance. We conclude that the complex
 entanglement of stabilizing and equalizing terms makes their impact on
 coexistence difficult to understand, but by seeing them as aggregated
 effects (rather than underlying causes) of coexistence, we may increase
 our understanding of ecological dynamics.
description: code"main text.nb"
 (written in Mathematica) reproduces all five figures in the main text.
 "Supplement 7.R" (written in R) reproduces Supplement
 7.
DOI: 10.5061/dryad.3c45k28
title: Data from: Risk alleles for tuberculosis infection associate with reduced immune reactivity in a wild mammalian host

description: Integrating biological processes across scales remains a central challenge
 in disease ecology. Genetic variation drives differences in host immune
 responses, which, along with environmental factors, generates temporal and
 spatial infection patterns in natural populations that epidemiologists
 seek to predict and control. However, genetics and immunology are
 typically studied in model systems, whereas population-level patterns of
 infection status and susceptibility are uniquely observable in nature.
 Despite obvious causal connections, organizational scales from genes to
 host outcomes to population patterns are rarely linked explicitly. Here we
 identify two loci near genes involved in macrophage (phagocyte) activation
 and pathogen degradation that additively increase risk of bovine
 tuberculosis infection by up to 9-fold in wild African buffalo.
 Furthermore, we observe genotype-specific variation in IL-12 production
 indicative of variation in macrophage activation. Here we provide
 measurable differences in infection resistance at multiple scales by
 characterizing the genetic and inflammatory variation driving patterns of
 infection in a wild mammal.
description: Tavalire_et_al_ProcB_S.caffer_unfiltered_SNPs_n=160_FinalThis file contains unfiltered SNPs obtained by 2bRAD genomic sequencing methods. Each row contains one SNP with marker metadata in the first five columns, followed by animal genotypes in subsequent columns.Tavalire_et_al_ProcB_S.caffer_unfiltered_SNPs_nTavalire_et_al_ProcB_cytokines_and_covariates_n=160_FinalThis file contains the phenotypic data used in Tavalire et al. 2019 for the time to onset of bTB GWAS analysis, final time-to-event multi-locus genotype models, and longitudinal cytokine production models. Each row corresponds to a single capture time point for an animal identified by a unique Animal.ID, followed by month, year, and season of capture and demographic and phenotypic information. Some variables (e.g., bTB status) are repeated across all captures for each animal and can be extracted for single-observation analyses (e.g., time to onset of bTB GWAS analysis). All animals are female.Tavalire_et_al_ProcB_cytokines_and_covariates_n
DOI: 10.5061/dryad.fc75292
title: Data from: Usefulness and limitations of thermal performance curves in predicting ectotherm development under global change

description: 1. Thermal performance curves (TPCs) have been estimated in multiple
 temperate ectotherm species and used to predict the effect of global
 warming. However, TPCs are typically assessed under constant temperature
 regimes, so their reliability for predicting thermal responses in the wild
 where temperature fluctuates diurnally and seasonally remains poorly
 documented. 2. Here we use distant latitudinal populations of five species
 of sepsid flies (Diptera: Sepsidae) from the temperate region (Europe,
 North Africa, North America) to compare estimates derived from constant
 TPCs with observed development rate under fluctuating temperatures in
 laboratory and field conditions. 3. TPCs changed across gradients in that
 flies originating from higher latitudes or altitudes showed accelerated
 development, an adaptive response. TPCs were then used to predict
 development rates observed under fluctuating temperatures; these
 predictions were relatively accurate in the laboratory but not in the
 field. Interestingly, the precision of TPC-predictions depended not only
 on the resolution of temperature data, with diurnal and overall
 temperature summing performing better than hourly temperature summing, but
 also on the frequency of temperatures falling below the estimated critical
 minimum temperature. Hourly temperature resolution most strongly
 underestimated actual development rates, because flies apparently either
 did not stop growing when temperatures dropped below this threshold, or
 they speed up their growth when the temperature rises again, thus most
 severely reflecting this error. 4. We conclude that when flies do not
 encounter cold temperatures, TPC-predictions based on constant
 temperatures can accurately reflect performance under fluctuating
 temperatures if adequately adjusted for non-linearities, but when they
 encounter cold temperatures this method is more error-prone. 5. Our study
 emphasizes the importance of the resolution of temperature data and cold
 temperatures in shaping thermal reaction norms, thus improving predictions
 of the responses of ectotherms to climate change in the age of big data
 and citizen science.
description: Khelifa_et_al_Anim.Ecol.DataTPC Data: Provides the development rates for all temperature treatments and all species Temperature fluctuations: Provides the development rates derived from the temperature fluctuation experiment Predicted vs. observed rate: Provides the data for development rate derived from the TPC (predicted) and observed in the experiment Ratios and chilling: Provides data for the ratio between predicted and observed development rates and the number of days below the critical minimal temperatureAnim.Ecol.Data.rar
DOI: 10.5061/dryad.nh17p1n
title: Data from: Overlooked biodiversity loss in tropical smallholder agriculture

description: Smallholder agriculture is the main driver of deforestation in the western
 Amazon, where terrestrial biodiversity reaches its global maximum.
 Understanding the biodiversity value of the resulting mosaics of
 cultivations and secondary forest is therefore crucial for conservation
 planning. However, Amazonian communities are organized across multiple
 forest‐types that support distinct species assemblages, and little is
 known about smallholder impacts across the range of forest habitats that
 are essential for sustaining biodiversity. We address this issue with a
 large‐scale field inventory of birds and trees in primary forest and
 smallholder agriculture in northern Peru, spanning three key forest‐types
 that structure Amazonian biodiversity. For birds, smallholder agriculture
 supported species richness comparable to primary forest within each
 forest‐type, but biotic homogenization across forest‐types resulted in
 substantial losses of biodiversity overall. These overall losses are
 invisible to studies that focus solely on upland (terra firme) forest. For
 trees, biodiversity losses in upland forests dominated the signal across
 all habitats combined, and homogenization across habitats did not
 exacerbate biodiversity loss. Proximity to forest strongly predicted the
 persistence of forest‐associated bird and tree species in the smallholder
 mosaic, and because intact forest is ubiquitous in our study area, our
 results probably represent a best‐case scenario for biodiversity in
 Amazonian agriculture. Land‐use planning both inside and outside of
 protected areas should recognize that tropical smallholder agriculture has
 pervasive biodiversity impacts that are not apparent in typical
 single‐habitat studies. The full range of forest‐types must be surveyed to
 accurately assess biodiversity losses, and primary forests must be
 protected to prevent landscape‐scale biodiversity loss.
description: Census
 PointsPoint-level
 covariatesCensus_Points.csvBird survey dataCollected and identified by Jacob B. Socolar. Please consider offering co-authorship on any publication that makes extensive use of these data.birds.csvRiver island birds (Rosenberg)Commonness of bird species on river islands, based on Rosenberg (1990)RosenbergCU.csvCensus point data with remote sensingEquivalent to Census_Points.csv, but stored as a spatialpointsdataframe, and includes primary forest cover covariates extracted from Landsat imagery.points_sp_data.rdataTree survey dataData from tree surveys near Iquitos, Peru (one row per stem)trees.csvR script for analysisPerforms the analyses described in Socolar et al 2019 (Conservation Biology)RCode.RReadMEDescriptions of data files
DOI: 10.5061/dryad.8n1n677
title: Data from: Wolbachia acquisition by Drosophila yakuba-clade hosts and transfer of incompatibility loci between distantly related Wolbachia

description: Maternally transmitted Wolbachia infect about half of insect species, yet
 the predominant mode(s) of Wolbachia acquisition remains uncertain.
 Species-specific associations could be old, with Wolbachia and hosts
 co-diversifying (i.e., cladogenic acquisition), or relatively young and
 acquired by horizontal transfer or introgression. The three Drosophila
 yakuba-clade hosts ((D. santomea, D. yakuba), D. teissieri) diverged about
 three million years ago and currently hybridize on Bioko and São Tomé,
 west African islands. Each species is polymorphic for nearly identical
 Wolbachia that cause weak cytoplasmic incompatibility (CI)–reduced egg
 hatch when uninfected females mate with infected males. D. yakuba-clade
 Wolbachia are closely related to wMel, globally polymorphic in D.
 melanogaster. We use draft Wolbachia and mitochondrial genomes to
 demonstrate that D. yakuba-clade phylogenies for Wolbachia and
 mitochondria tend to follow host nuclear phylogenies. However, roughly
 half of D. santomea individuals, sampled both inside and outside of the
 São Tomé hybrid zone, have introgressed D. yakuba mitochondria. Both
 mitochondria and Wolbachia possess far more recent common ancestors than
 the bulk of the host nuclear genomes, precluding cladogenic Wolbachia
 acquisition. General concordance of Wolbachia and mitochondrial
 phylogenies suggests that horizontal transmission is rare, but varying
 relative rates of molecular divergence complicate chronogram-based
 statistical tests. Loci that cause CI in wMel are disrupted in D.
 yakuba-clade Wolbachia; but, a second set of loci predicted to cause CI
 are located in the same WO prophage region. These alternative CI loci seem
 to have been acquired horizontally from distantly related Wolbachia, with
 transfer mediated by flanking Wolbachia-specific ISWpi1 transposons.
description: Code and data for Cooper
 et al. 2019See the readme
 file.cooper_genetics_19_dryad.zip
DOI: 10.5061/dryad.38gk4m6
title: Data from: Genetic divergence outpaces phenotypic evolution among threespine stickleback populations in old freshwater habitats

description: Species such as threespine stickleback fish that are distributed across
 landscapes with divergent selective environments and that have diversified
 on different time scales can be valuable for understanding evolutionary
 processes. Here we synthesize high resolution genotypic and phenotypic
 data to explore a largely unstudied distribution of threespine stickleback
 populations living in marine and freshwater habitats along coastal and
 inland regions of northwestern Oregon. Because many inland aquatic
 habitats of Oregon were not glaciated during the last ice age, we
 hypothesized that some extant Oregon lake and river stickleback are
 descended from freshwater populations that were established long before
 the well-studied, post-glacial freshwater populations of Alaska. Here we
 characterize the major phenotypic and genetic axes of differentiation in
 Oregon stickleback, and compare these patterns to their Alaska
 counterparts currently inhabiting regions that were covered by ice during
 the last glacial maximum. Phenotypic variation in Oregon stickleback is
 predictably partitioned between oceanic and freshwater habitats. However,
 we also found that genetic divergence in Oregon ecotypes is much greater
 than divergence among studied stickleback populations in Alaska.
 Additionally, we report a surprising phenotypic and genetic affinity
 between oceanic stickleback with freshwater populations that live far
 inland in two Oregon river basins.
description: batch_1.structure_Oregon_1100_repeat_2Subset of 1100 loci for individuals from Oregon populations formatted for Structurebatch_1.structure_Oregon_1100_repeat_3Subset of 1100 loci for individuals from Oregon populations formatted for Structurebatch_1.structure_Oregon_1100_repeat_1Subset of 1100 loci for individuals from Oregon populations formatted for Structure.batch_1.structure_Oregon_Alaska_1100_repeat_1Subset of 1100 loci for individuals from Oregon and Alaska populations formatted for Structure.batch_1.structure_Oregon_Alaska_1100_repeat_2Subset of 1100 loci for individuals from Oregon and Alaska populations formatted for Structure.batch_1.structure_Oregon_Alaska_1100_repeat_3Subset of 1100 loci for individuals from Oregon and Alaska populations formatted for Structure.
DOI: 10.5061/dryad.vk15g0c
title: Data from: Bovine tuberculosis disturbs functional trait composition in African buffalo

description: Novel parasites can have wide-ranging impacts, not only on host
 populations, but also on the resident parasite community. Historically,
 impacts of novel parasites have been assessed by examining pairwise
 interactions between parasite species. However, parasite communities are
 complex networks of interacting species. Here, we used multivariate
 taxonomic and trait-based approaches to determine how parasite community
 composition changed when African buffalo (Syncerus caffer) acquired an
 emerging disease, bovine tuberculosis (BTB). Both taxonomic and functional
 parasite richness increased significantly in animals that acquired BTB
 than in those that did not. Thus, the presence of BTB seems to catalyze
 extraordinary shifts in community composition. There were, however, no
 differences in overall parasite taxonomic composition between infected and
 uninfected individuals. The trait-based analysis revealed that
 direct-transmitted, quickly replicating parasites increased following BTB
 infection. This study demonstrates that trait-based approaches provide
 novel insight for understanding parasite community dynamics in the context
 of emerging infections.
description: Parasite Prevalence Data
 by IndividualThis file contains
 information on each disease in each buffalo, including prevalence before
 and after TB diagnostics.Beechler Boersma Data for
 Dryad.csv
DOI: 10.5061/dryad.7sp252q
title: Data from: Nitrogen controls the net primary production of an alpine Kobresia meadow in the northern Qinghai-Tibet Plateau

description: Net primary production (NPP) is a fundamental property of natural
 ecosystems. Understanding the temporal variations of NPP could provide new
 insights into the responses of communities to environmental factors,
 whilst also contributing to a better assessment of regional carbon
 storage. However, few studies based on long-term field biomass
 measurements have directly addressed this subject in the unique
 environment of the Qinghai-Tibet plateau (QTP). we examined the
 interannual variations of NPP during 2008-2015 by monitoring both
 aboveground net primary productivity (ANPP) and belowground net primary
 productivity (BNPP), and identified their relationships with environmental
 factors by adopted the general linear model (GLM)and structural equation
 model (SEM). In addition, the interannual variation of root turnover and
 its controls were also investigated. The results show that the ANPP and
 BNPP increased by rates of 15.01 g/m2 and 143.09 g/m2 per year during
 2008-2015, respectively. BNPP was mainly affected by growing season air
 temperature (GST) and growing season precipitation (GSP) rather than mean
 annual air temperature (MAT) or mean annual precipitation (MAP), while
 ANPP was only controlled by GST. In addition, available nitrogen (AN) was
 significant positively associated with BNPP and ANPP. Root turnover rate
 averaged 30% /yr, increased with soil depth, and was largely controlled by
 GST. Our results suggest that alpine Kobresia meadow was an N-limited
 ecosystem, the NPP on the QTP might increase further in the future in the
 context of global warming and nitrogen deposition.
description: dataThe net primary
 production, climate and soil nutrient data