cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.rd5rn
title: Data from: Are heritability and selection related to population size in nature? Meta-analysis and conservation implications

description: It is widely thought that small populations should have less additive
 genetic variance and respond less efficiently to natural selection than
 large populations. Across taxa, we meta-analytically quantified the
 relationship between adult census population size (N) and additive genetic
 variance (proxy: h2) and found no reduction in h2 with decreasing N;
 surveyed populations ranged from four to one million individuals (1735
 h2estimates, 146 populations, 83 species). In terms of adaptation,
 ecological conditions may systematically differ between populations of
 varying N; the magnitude of selection these populations experience may
 therefore also differ. We thus also meta-analytically tested whether
 selection changes with N, and found little evidence for systematic
 differences in the strength, direction, or form of selection with N across
 different trait types and taxa (7344 selection estimates, 172 populations,
 80 species). Collectively, our results (i) indirectly suggest that genetic
 drift neither overwhelms selection more in small than in large natural
 populations, nor weakens adaptive potential/h2 in small populations, and
 (ii) imply that natural populations of varying sizes experience a variety
 of environmental conditions, without consistently differing habitat
 quality at small N. However, we caution that the data are currently
 insufficient to determine whether some small populations may retain
 adaptive potential definitively. Further study is required into (i)
 selection and genetic variation in completely isolated populations of
 known N, underrepresented taxonomic groups, and non-generalist species,
 (ii) adaptive potential using multidimensional approaches, and (iii) the
 nature of selective pressures for specific traits.
description: Selection
 databaseDatabase of selection
 estimates for four types of selection coefficients with associated
 estimates of population size.Selection_database_DRYAD.xlsxHeritability databaseDatabase of narrow-sense heritability estimates with associated estimates of population size.Heritability_database_DRYAD.xlsxR code for selection analysesMCMCglmm code used in selection meta-analysis and unweighted analysis.Selection_analysis_code.txtR code for heritability analysesMCMCglmm code used for heritability meta-analysis and unweighted analysis.h2_analysis_code.RR code for Variable hypothesis analysisMCMCglmm code used in Variable hypothesis analysis.Variablehyp_analysis_code.R
DOI: 10.5061/dryad.11c40
title: Data from: Inference of Japanese encephalitis virus ecological and evolutionary dynamics from passive and active virus surveillance

description: A comprehensive monitoring strategy is vital for tracking the spread of
 mosquito-borne Japanese encephalitis virus (JEV), the leading cause of
 viral encephalitis in Asia. Virus detection consists of passive
 surveillance of primarily humans and swine, and/or active surveillance in
 mosquitoes, which may be a valuable proxy in providing insights into
 ecological processes underlying the spread and persistence of JEV.
 However, it has not been well characterized whether passive surveillance
 alone can capture the circulating genetic diversity to make reasonable
 inferences. Here, we develop phylogenetic models to infer JEV host
 changes, spatial diffusion patterns, and evolutionary dynamics from data
 collected through active and passive surveillance. We evaluate the
 feasibility of using JEV sequence data collected from mosquitoes to
 estimate the migration histories of genotypes GI and GIII. We show that
 divergence times estimated from this dataset were comparable to estimates
 from all available data. Increasing the amount of data collected from
 active surveillance improved time of most recent common ancestor estimates
 and reduced uncertainty. Phylogenetic estimates using all available data
 and only mosquito data from active surveillance produced similar results,
 showing that GI epidemics were widespread and diffused significantly
 faster between regions than GIII. In contrast, GIII outbreaks were highly
 structured and unlinked suggesting localized, unsampled infectious
 sources. Our results show that active surveillance of mosquitoes can
 sufficiently capture circulating genetic diversity of JEV to confidently
 estimate spatial and evolutionary patterns. While surveillance of other
 hosts could contribute to more detailed disease tracking and evaluation,
 comprehensive JEV surveillance programs should include systematic
 surveillance in mosquitoes to infer the most complete patterns for
 epidemiology, and risk assessment.
description: JEV-AllHosts-PhylogeoThis file contains all sequence data and the discrete character coding used for the ancestral reconstruction of geographic statesJEV_Allspecies_phylogeo_geomask.xml
DOI: 10.5061/dryad.nf981
title: Data from: Metapopulation dominance and genomic-island acquisition of Bradyrhizobium with superior catabolic capabilities

description: Root nodule forming rhizobia exhibit a bipartite lifestyle, replicating in
 soil and also within plant cells where they fix nitrogen for legume hosts.
 Host control models posit that legume hosts act as a predominant selective
 force on rhizobia, but few studies have examined rhizobial fitness in
 natural populations. Here, we genotyped and phenotyped Bradyrhizobium
 isolates across &gt;800km of the native Acmispon strigosus host range.
 We sequenced chromosomal genes expressed under free-living conditions and
 accessory symbiosis loci expressed in planta and encoded on an integrated
 ‘symbiosis island’. We uncovered a massive clonal expansion restricted to
 the Bradyrhizobium chromosome, with a single chromosomal haplotype
 dominating populations, ranging &gt;700km, and acquiring 42 divergent
 symbiosis island haplotypes, none of which were spatially widespread. For
 focal genotypes we quantified utilization of 190 sole-carbon sources
 relevant to soil fitness. Chromosomal haplotypes that were both widespread
 and dominant exhibited superior growth on diverse carbon sources, whereas
 these patterns were not mirrored among symbiosis island haplotypes.
 Abundance, spatial range, and catabolic superiority of chromosomal, but
 not symbiosis genotypes suggests that fitness in the soil environment,
 rather than symbiosis with hosts, might be the key driver of
 Bradyrhizobium dominance.
description: Hollowell_S1Table of all isolates included in analyses and associated accession numbers.Hollowell_S2-S9Supplementary Files S2-S9Hollowell S10 Carbon Utulization AssaysPhenotypic Array data for Carbon UtilizationHollowell_S10.xlsx
DOI: 10.5061/dryad.1p0q9
title: Data from: Polarity of concavo-convex intervertebral joints in the necks and tails of sauropod dinosaurs

description: The highly elongated necks, and often tails, of sauropod dinosaurs were
 composed of concavo-convex vertebrae that provided stability without
 compromising mobility. Polarities of these concavo-convex joints in the
 neck and tail are anatomically opposite one another but mechanically
 equivalent. Opisthocoelous cervical vertebrae and procoelous caudal
 vertebrae have the convex articular face directed away from the body and
 the concave articular face directed toward the body. This “sauropod-type”
 polarity is hypothesized to be (1) more resistant to fracturing of the
 cotylar rim and (2) better stabilized against joint failure by rotation
 than the opposite polarity. We used physical models to test these two
 functional hypotheses. Photoelastic analysis of model centra loaded as
 cantilevers reveals that neither polarity better resists fracture of the
 cotylar rim; strain magnitude and localization are similar in both
 polarities. We assessed the rotational stability of concavo-convex joints
 using pairs of concavo-convex centra loaded near the joint. Sauropod-type
 joints withstood significantly greater weight before failure occurred, a
 pattern we interpret to be dependent on the position of the center of
 rotation, which is always within the convex part of the concavo-convex
 joint. In sauropod-type joints, the free centrum rotates about a center of
 rotation that lies within the more stable proximal centrum. In contrast,
 the opposite polarity results in a free centrum that rotates about an
 internal point; when the condyle rotates down and out of joint, the distal
 end rotates back toward the body, unopposed by ligamentous support.
 Sauropod-type joints remained stable with greater mobility, more
 mechanically advantageous tensile element insertions, and greater distal
 loads than the opposite polarity. The advantages conferred by this joint
 polarity would have facilitated the evolution of hyperelongated necks and
 tails by sauropods. Polarity of concavo-convex joints of the appendicular
 skeleton (e.g., hip, shoulder) is also consistent with the demands of
 rotational stability.
description: FronimosEtAl_Suppl1Reproduction of illustrations from Fick (1890) depicting that author's proposed model for the development of concavo-convex joint polarity.FronimosEtAl_Suppl2Schematic representation of the experimental setup used to test the hypothesis that proximally-concave joints are more resistant to joint failure by rotation than proximally-convex joints. The setup is depicted for a proximally-concave joint with the maximum load applied to the proximal end of the free element.FronimosEtAl_SupplTbl1Raw measurements of the weight (in grams) applied to the proximal end of the free element that is necessary to cause joint failure by rotation. The variables are those presented in Text Figure 5. A + symbol denotes the addition of 20 g of weight to the distal end of the free element, representing the presence of additional vertebrae in series.
DOI: 10.5061/dryad.4ch2c
title: Data from: Individual variation in winter supplementary food consumption and its consequences for reproduction in wild birds.

description: The provision of wild birds with supplementary food has increased
 substantially over recent decades. While it is assumed that provisioning
 birds is beneficial, supplementary feeding can have detrimental
 ‘carry-over’ effects on reproductive traits. Due to difficulties in
 monitoring individual feeding behaviour, assessing how individuals within
 a population vary in their exploitation of supplementary food resources
 has been limited. Quantifying individual consumption of supplementary food
 is necessary to understand the operation of carry-over effects at the
 individual level. We used Radio Frequency Identification (RFID) technology
 and automated feeders to estimate individual consumption of supplementary
 winter food in a large wild population of great tits Parus major and blue
 tits Cyanistes caeruleus. Using these data, we identified demographic
 factors that explained individual variation in levels of supplementary
 food consumption. We also tested for carry-over effects of supplementary
 food consumption on recruitment, reproductive success and a measure of
 survival. Individual variation in consumption of supplementary food was
 explained by differences between species, ages, sexes and years.
 Individuals were consistent across time in their usage of supplementary
 resources. We found no strong evidence that the extent of supplementary
 food consumption directly influenced subsequent fitness parameters. Such
 effects may instead result from supplementary food influencing population
 demographics by enhancing the survival and subsequent breeding of less
 competitive individuals, which reduce average breeding parameters and
 increase density-dependent competition. Carry-over effects of
 supplementary feeding are not universal and may depend upon the temporal
 availability of the food provided. Our study demonstrates how RFID systems
 can be used to examine individual-level behaviour with minimal effects on
 fitness.
description: Final_seed_datathe data is divided into 5 spreadsheets, for different analyses. See attached user guidance for further descriptions of column headers
DOI: 10.5061/dryad.1mc01
title: Data from: Rapid adaptive evolution of colour vision in the threespine stickleback radiation

description: Vision is a sensory modality of fundamental importance for many animals,
 aiding in foraging, detection of predators, and mate choice. Adaptation to
 local ambient light conditions is thought to be commonplace, and a match
 between spectral sensitivity and light spectrum is predicted. We use opsin
 gene expression to test for local adaptation and matching of spectral
 sensitivity in multiple independent lake populations of threespine
 stickleback populations derived since the last ice age from an ancestral
 marine form. We show that sensitivity across the visual spectrum is
 shifted repeatedly towards longer wavelengths in freshwater compared with
 the ancestral marine form. Laboratory rearing suggests this shift is
 largely genetically based. Using a new metric, we found that the magnitude
 of shift in spectral sensitivity in each population corresponds strongly
 to the transition in the availability of different wavelengths of light
 between the marine and lake environment. We also found evidence of local
 adaptation by sympatric benthic and limnetic ecotypes to different light
 environments within lakes. Our findings indicate rapid parallel evolution
 of the visual system to altered light conditions. The changes have not,
 however, yielded a close matching of spectrum-wide sensitivity to
 wavelength availability, for reasons we discuss.
description: read me file
 descriptionThis file outlines the
 contents of the data files and provides a key for column
 headings.file_metadata_read_meraw irradiance dataContains subfolders with raw individual irradiance measuresSite.meta.dataContains meta data from sample sitesProportional.Opsin.ExpressionOpsin Expression data converted to cone proportionsRaw.Opsin.ExpressionContains raw opsin expression dataIrridanceContains irradiance data used in the studyTransmissionContains transmission data used in the study
DOI: 10.5061/dryad.p52sq
title: Data from: De novo transcriptome analysis of the common New Zealand stick insect Clitarchus hookeri (Phasmatodea) reveals genes involved in olfaction, digestion and sexual reproduction

description: Phasmatodea, more commonly known as stick insects, have been poorly
 studied at the molecular level for several key traits, such as components
 of the sensory system and regulators of reproduction and development,
 impeding a deeper understanding of their functional biology. Here, we
 employ de novo transcriptome analysis to identify genes with primary
 functions related to female odour reception, digestion, and male sexual
 traits in the New Zealand common stick insect Clitarchus hookeri (White).
 The female olfactory gene repertoire revealed ten odorant binding proteins
 with three recently duplicated, 12 chemosensory proteins, 16 odorant
 receptors, and 17 ionotropic receptors. The majority of these olfactory
 genes were over-expressed in female antennae and have the inferred
 function of odorant reception. Others that were predominantly expressed in
 male terminalia (n = 3) and female midgut (n = 1) suggest they have a role
 in sexual reproduction and digestion, respectively. Over-represented
 transcripts in the midgut were enriched with digestive enzyme gene
 families. Clitarchus hookeri is likely to harbour nine members of an
 endogenous cellulase family (glycoside hydrolase family 9), two of which
 appear to be specific to the C. hookeri lineage. All of these cellulase
 sequences fall into four main phasmid clades and show gene duplication
 events occurred early in the diversification of Phasmatodea. In addition,
 C. hookeri genome is likely to express γ-proteobacteria pectinase
 transcripts that have recently been shown to be the result of horizontal
 transfer. We also predicted 711 male terminalia-enriched transcripts that
 are candidate accessory gland proteins, 28 of which were annotated to have
 molecular functions of peptidase activity and peptidase inhibitor
 activity, two groups being widely reported to regulate female reproduction
 through proteolytic cascades. Our study has yielded new insights into the
 genetic basis of odour detection, nutrient digestion, and male sexual
 traits in stick insects. The C. hookeri reference transcriptome, together
 with identified gene families, provides a comprehensive resource for
 studying the evolution of sensory perception, digestive systems, and
 reproductive success in phasmids.
description: Clitarchus transcriptome
 assembly from five different tissuesTranscriptome assembly
 constructed from C. hookeri female antennae, head and prothorax, midgut,
 leg and male terminalia. More details are shown in ReadMe
 file.Choo_5tissues_transcriptome.fasta.gzClitarchus four genomic scaffoldsGenomic scaffolds were obtained from Chen Wu's unpublished data. Scaffold1029 contains OBP4, OBP5 and OBP6. The other scaffolds contain the nine GH9 cellulase genes.Choo_scaffolds.fasta
DOI: 10.5061/dryad.73qf0
title: Data from: Re-evaluating the distribution of cooperative breeding in birds: is it tightly linked with altriciality?

description: The evolution of cooperative breeding (CB) in birds has aroused intensive
 interest for decades, largely due to the paradox that some adults forgo
 independent breeding to help others. While much effort has been directed
 at understanding the adaptive significance of CB behavior, much less
 effort has been spent on understanding its origin. Ligon and Burt argued
 that the evolution of altriciality played a key role in the origin of CB
 since CB occurs more frequently in altricial lineages than expected if
 developmental mode and CB evolved independently and that both traits arose
 early in the avian tree of life. We mapped presence or absence of CB, and
 precocial or altricial development on a recent phylogeny of all birds to
 re-evaluate their conclusions. Our results suggest altriciality may be
 more recently derived than previously thought, and that CB species
 clustered in a derived land bird clade (especially within Passeriformes)
 where we reconstructed many gains and losses. We did find a link between
 cooperative breeding and altriciality. However, since CB also occurs in
 precocial species, has not evolved in many altricial clades, and may have
 evolved prior to altriciality (based on some classifications of which
 species have CB), it is not clear whether altriciality is linked to other
 factors, such as benefits to group living, that are necessary for the
 acquisition of CB behavior, or whether altriciality may have been a
 driving force in the evolution of CB itself. The relative importance of
 these other factors versus altriciality for the origin of CB needs to be
 considered.
description: Appendix and data
 filesAppendix 1 and 2 were
 used in the main text. Four original data files were used to conduct the
 analyses.Phylogenetic distribution of
 cooperative breeding in birds_data.zip
DOI: 10.5061/dryad.5c820
title: Data from: International collaboration and spatial dynamics of US patenting in Central and Eastern Europe 1981-2010

description: How did post-socialist transition and a parallel shift in international
 labor division restructure regional innovation systems in Central and
 Eastern Europe? This question is increasingly important, because current
 EU innovation policy is combined with regional development in Smart
 Specialization Strategies; however, spatial trends of innovation in
 Central and Eastern Europe are not fully understood which might lead to
 less than perfectly efficient policy. In this paper we describe the
 spatial dynamics of inventor activity in the Czech Republic, Hungary,
 Poland and Slovakia between 1981 and 2010 –a period that covers both the
 late socialist era and the post-socialist transition. Cleaning and
 analyzing the publicly available data from the United States Patent and
 Trademark Office we illustrate that Central and Eastern European patents
 made in international co-operations with partners outside the region
 receive more citations than those Central and Eastern European patents
 that lack international co-operation. Furthermore, the technological
 portfolio of the former patents has become increasingly independent from
 the technological portfolio of the latter class. A town-level analysis of
 the applicant-inventor ties reveals that inventors have started to work
 for foreign assignees in those towns where no innovation activity had been
 recorded before. However, the positive effect does not last long and
 patenting seems to be only periodic in the majority of these towns.
 Therefore, innovation policy in Central and Eastern European countries, as
 well as in other less developed regions, shall foster synergies between
 international and domestic collaborations in order to decrease regional
 disparities in patenting.
description: USPTO_patents_in_CEE_1981-2010This file contains publicly available and cleaned data of USPTO patents with at least one inventor from the Czech Republic, Hungary, Poland and Slovakia in the period 1981-2010. As an addition to the original data file submitted to the article, we added the NUTS 3 region and population size to every town in the above countries.
DOI: 10.5061/dryad.1fp80
title: Data from: How do cold-adapted plants respond to climatic cycles? interglacial expansion explains current distribution and genomic diversity in Primula farinosa L.

description: Understanding the effects of past climatic fluctuations on the
 distribution and population-size dynamics of cold-adapted species is
 essential for predicting their responses to ongoing global climate change.
 In spite of the heterogeneity of cold-adapted species, two main
 contrasting hypotheses have been proposed to explain their responses to
 Late Quaternary glacial cycles, namely, the interglacial contraction
 versus the interglacial expansion hypotheses. Here, we use the
 cold-adapted plant Primula farinosa to test two demographic models under
 each of the two alternative hypotheses and a fifth, null model. We first
 approximate the time and extent of demographic contractions and expansions
 during the Late Quaternary by projecting species distribution models
 across the last 72 ka. We also generate genome-wide sequence data using a
 Reduced Representation Library approach to reconstruct the spatial
 structure, genetic diversity, and phylogenetic relationships of lineages
 within P. farinosa. Finally, by integrating the results of climatic and
 genomic analyses in an Approximate Bayesian Computation framework, we
 propose the most likely model for the extent and direction of
 population-size changes in P. farinosa through the Late Quaternary. Our
 results support the interglacial expansion of P. farinosa, differing from
 the prevailing paradigm that the observed distribution of cold-adapted
 species currently fragmented in high altitude and latitude regions
 reflects the consequences of postglacial contraction processes.
description: Ingroup
 DatasetFasta file as exported
 from STACKS software. This file includes sequences for all populations of
 Primula farinosa and was used for all subsequent molecular analysis except
 for the phylogenomic (RAxML) analysis.IngroupDataset.fa.zipOutgroup DatasetFasta file as exported from STACKS software. This file includes sequences for all populations of Primula farinosa, P. frondosa, and P. exigua and was used for the phylogenomic (RAxML) analysis.OutgroupDataSet.fa.zipAllelic_Richness_ScriptThe python programm that was used for calculating the allelic richness and private allelic richness for each lineage of P. farinosaSupplementary MaterialFigures S1-S3, Tables S1-S7Theodoridis_et_al_SuppFigsTables.docx