cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.d67h6
title: Data from: Intraspecific phytochemical variation shapes community and population structure for specialist caterpillars

description: Chemically mediated plant–herbivore interactions contribute to the
 diversity of terrestrial communities and the diversification of plants and
 insects. While our understanding of the processes affecting community
 structure and evolutionary diversification has grown, few studies have
 investigated how trait variation shapes genetic and species diversity
 simultaneously in a tropical ecosystem. We investigated secondary
 metabolite variation among subpopulations of a single plant species, Piper
 kelleyi (Piperaceae), using high-performance liquid chromatography (HPLC),
 to understand associations between plant phytochemistry and
 host-specialized caterpillars in the genus Eois (Geometridae: Larentiinae)
 and associated parasitoid wasps and flies. In addition, we used a
 genotyping-by-sequencing approach to examine the genetic structure of one
 abundant caterpillar species, Eois encina, in relation to host
 phytochemical variation. We found substantive concentration differences
 among three major secondary metabolites, and these differences in
 chemistry predicted caterpillar and parasitoid community structure among
 host plant populations. Furthermore, E. encina populations located at high
 elevations were genetically different from other populations. They fed on
 plants containing high concentrations of prenylated benzoic acid. Thus,
 phytochemistry potentially shapes caterpillar and wasp community
 composition and geographic variation in species interactions, both of
 which can contribute to diversification of plants and insects.
description: eois_glassmire_gprobsThis file contains the genotypes at 20,458 SNPs in 155 Eois encina Dognin individuals.
DOI: 10.5061/dryad.hm23p
title: Data from: Genetic variability, local selection and demographic history: genomic evidence of evolving towards allopatric speciation in Asian seabass

description: Genomewide analysis of genetic divergence is critically important in
 understanding the genetic processes of allopatric speciation. We sequenced
 RAD tags of 131 Asian seabass individuals of six populations from
 South-East Asia and Australia/Papua New Guinea. Using 32 433 SNPs, we
 examined the genetic diversity and patterns of population differentiation
 across all the populations. We found significant evidence of genetic
 heterogeneity between South-East Asian and Australian/Papua New Guinean
 populations. The Australian/Papua New Guinean populations showed a rather
 lower level of genetic diversity. FST and principal components analysis
 revealed striking divergence between South-East Asian and Australian/Papua
 New Guinean populations. Interestingly, no evidence of contemporary gene
 flow was observed. The demographic history was further tested based on the
 folded joint site frequency spectrum. The scenario of ancient migration
 with historical population size changes was suggested to be the best fit
 model to explain the genetic divergence of Asian seabass between
 South-East Asia and Australia/Papua New Guinea. This scenario also
 revealed that Australian/Papua New Guinean populations were founded by
 ancestors from South-East Asia during mid-Pleistocene and were completely
 isolated from the ancestral population after the last glacial retreat. We
 also detected footprints of local selection, which might be related to
 differential ecological adaptation. The ancient gene flow was examined and
 deemed likely insufficient to counteract the genetic differentiation
 caused by genetic drift. The observed genomic pattern of divergence
 conflicted with the ‘genomic islands’ scenario. Altogether, Asian seabass
 have likely been evolving towards allopatric speciation since the split
 from the ancestral population during mid-Pleistocene.
description: SNP genotypes of Asian
 seabassThe genotype dataset
 contains 32433 ddRAD-based SNP loci for 131 individuals across 6 wild
 populations of Asian seabass.All_genotypes.txt
DOI: 10.5061/dryad.6h4t2
title: Data from: Pathways of information transmission amongst wild songbirds follow experimentally imposed changes in social foraging structure

description: Animals regularly use information from others to shape their decisions.
 Yet, determining how changes in social structure affect information flow
 and social learning strategies has remained challenging. We manipulated
 the social structure of a large community of wild songbirds by controlling
 which individuals could feed together at automated feeding stations
 (selective feeders). We then provided novel ephemeral food patches freely
 accessible to all birds and recorded the spread of this new information.
 We demonstrate that the discovery of new food patches followed the
 experimentally imposed social structure and that birds disproportionately
 learnt from those whom they could forage with at the selective feeders.
 The selective feeders reduced the number of conspecific information
 sources available and birds subsequently increased their use of
 information provided by heterospecifics. Our study demonstrates that
 changes to social systems carry over into pathways of information transfer
 and that individuals learn from tutors that provide relevant information
 in other contexts.
description: Data for social
 transmission analysisDescription of Dryad
 Data File The .RData file contains the following objects 1)
 “all.individuals” gives the identity (unique PIT tag number) of all
 detected individuals and which species they belong to 2) “patch.times”
 gives the time of detection of individuals at the ephemeral food patches
 (discovery feeders) along with the unit number and replica number of that
 detection 3) “group_by_individual” gives the matrix denoting which
 individuals were detected in which flocks at the selective feeding
 stations. The columns give the individuals, the rows give the number of
 the group 4) “groups_info” gives information on each detected group (rows
 corresponding to group_by_individual). This includes the start and stop
 times, as well as the unit it was detected at. The “allows.odds” column
 denotes whether or not this unit was programmed to only allow access to
 birds with odd numbered pit tags during the experiment (note: FALSE during
 the experiment means that this feeder only allowed birds with even
 numbered PIT tags). The “experiment.phase” denotes the phrase of the
 experiment (either “pre” manipulation or “during” the
 manipulation).dryad_data.RData
DOI: 10.5061/dryad.c19kb
title: Data from: Measuring stratigraphic congruence across trees, higher taxa, and time

description: The congruence between the order of cladistic branching and the first
 appearance dates of fossil lineages can be quantified using a variety of
 indices. Good matching is a prerequisite for the accurate time calibration
 of trees, while the distribution of congruence across large samples of
 cladograms has underpinned claims about temporal and taxonomic patterns of
 completeness in the fossil record. The most widely used stratigraphic
 congruence indices are the stratigraphic consistency index, the modified
 Manhattan stratigraphic measure, and the gap excess ratio (plus its
 derivatives; the topological gap excess ratio and the modified gap excess
 ratio). Many factors are believed to variously bias these indices, with
 several empirical and simulation studies addressing some subset of the
 putative interactions. This study combines both approaches to quantify the
 effects (on all five indices) of eight variables reasoned to constrain the
 distribution of possible values (the number of taxa, tree balance, tree
 resolution, range of first occurrence dates, center of gravity of first
 occurrence dates, the variability of first occurrence dates, percentage of
 extant taxa, and percentage of taxa with no fossil record). Our empirical
 data set comprised 647 published vertebrate and invertebrate cladograms
 spanning the entire Phanerozoic, and for these data we also modelled the
 effects of mean age of first occurrences (as a proxy for clade age), the
 taxonomic rank of the clade, and the higher taxonomic group to which it
 belonged. The center of gravity of first occurrence dates had not been
 investigated hitherto, and this was found to correlate most strongly with
 some measures of stratigraphic congruence in our empirical study
 (top-heavy clades had better congruence). The modified gap excess ratio
 was the index least susceptible to bias. We found significant differences
 across higher taxa for all indices; arthropods had lower congruence and
 tetrapods higher congruence. Stratigraphic congruence – however measured –
 also varied throughout the Phanerozoic, reflecting the taxonomic
 composition of our sample. Notably, periods containing a high proportion
 of arthropods had poorer congruence overall than those with higher
 proportions of tetrapods.
description: Supplementary
 MaterialsSupplementary figures,
 tables and references, with the exception of Supplementary Table 2, which
 is provided as an xls file.Supplementary Table
 2Summary statistics for
 647 cladograms of animals and plantsGhosts_ScriptsScripts for Ghosts program (calculating indices of stratigraphic congruence and other statistics)Ghosts_data_files_2016_DRYADGhosts data filesnexus_filesSubset of the cladograms for which nexus files were available
DOI: 10.5061/dryad.5b8t8
title: Data from: Coupled range dynamics of brood parasites and their hosts responding to climate and vegetation changes

description: As populations shift their ranges in response to global change, local
 species assemblages can change, setting the stage for new ecological
 interactions, community equilibria, and evolutionary responses. Here we
 focus on the range dynamics of four avian brood parasite species and their
 hosts in southern Africa, in a context of bush encroachment (increase in
 woody vegetation density in places previously occupied by
 savanna-grassland mosaics) favouring some species at the expense of
 others. We first tested whether hosts and parasites constrained each
 other's ability to expand or maintain their ranges. Second, we
 investigated whether range shifts represented an opportunity for new
 host-parasite and parasite-parasite interactions. We used multi-species
 dynamic occupancy models with interactions, fitted to citizen-science
 data, to estimate the contribution of interspecific interactions to range
 shifts and to quantify the change in species co-occurrence probability
 over a 25-year period. Parasites were able to track their hosts’ range
 shifts. We detected no deleterious effect of the parasites’ presence on
 either the local population viability of host species or the hosts’
 ability to colonize newly suitable areas. In the recently diversified
 indigobird radiation (Vidua spp.), following bush encroachment, the new
 assemblages presented more potential opportunities for speciation via host
 switch, but also more potential for hybridization between extant lineages,
 also via host switch. Multi-species dynamic occupancy models with
 interactions brought new insights into the feedbacks between range shifts,
 biotic interactions, and local demography: brood parasitism had little
 detected impact on extinction or colonization processes, but inversely the
 latter processes affected biotic interactions via the modification of
 co-occurrence patterns.
description: Data from
 SABAP1Data from
 SABAP1BroodParasites_dataSABAP1_ForArchivalOnDryad.csvData from SABAP2Data from SABAP2BroodParasites_dataSABAP2_ForArchivalOnDryad.csv
DOI: 10.5061/dryad.nk08s
title: Data from: A map of abstract relational knowledge in the human hippocampal–entorhinal cortex

description: The hippocampal–entorhinal system encodes a map of space that guides
 spatial navigation. Goal-directed behaviour outside of spatial navigation
 similarly requires a representation of abstract forms of relational
 knowledge. This information relies on the same neural system, but it is
 not known whether the organisational principles governing continuous maps
 may extend to the implicit encoding of discrete, non-spatial graphs. Here,
 we show that the human hippocampal–entorhinal system can represent
 relationships between objects using a metric that depends on associative
 strength. We reconstruct a map-like knowledge structure directly from a
 hippocampal–entorhinal functional magnetic resonance imaging adaptation
 signal in a situation where relationships are non-spatial rather than
 spatial, discrete rather than continuous, and unavailable to conscious
 awareness. Notably, the measure that best predicted a behavioural
 signature of implicit knowledge and blood oxygen level-dependent
 adaptation was a weighted sum of future states, akin to the successor
 representation that has been proposed to account for place and grid-cell
 firing patterns.
description: data_and_scriptsThis folder contains the group t-stat brain images, subject-specific parameter estimates extracted from various regions of interest, relevant experimental parameters (e.g. timings between object presentations used in the regression), and Matlab scripts to reproduce all plots in Garvert et al. (2017).
DOI: 10.5061/dryad.p380b
title: Data from: Applying SNP-derived molecular coancestry estimates to captive breeding programs

description: Captive breeding programs for wildlife species typically rely on pedigrees
 to inform genetic management. Although pedigree-based breeding strategies
 are quite effective at retaining long-term genetic variation, management
 of zoo-based breeding programs continues to be hampered when pedigrees are
 poorly known. The objective of this study was to evaluate two options for
 generating single nucleotide polymorphism (SNP) data to resolve unknown
 relationships within captive breeding programs. We generated SNP data for
 a zoo-based population of addax (Addax nasomasculatus) using both the
 Illumina BovineHD BeadChip and double digest restriction site-associated
 DNA (ddRAD) sequencing. Our results demonstrated that estimates of allele
 sharing (AS) between pairs of individuals exhibited low variances. Average
 AS variances were highest when using 50 loci (SNPchipall = 0.00159;
 ddRADall = 0.0249), but fell below 0.0003 for the SNP chip dataset when
 sampling ≥250 loci and below 0.0025 for the ddRAD dataset when sampling
 ≥500 loci. Furthermore, the correlation between the SNPchipall and
 ddRADall AS datasets was 0.88 (95%CI = 0.84 – 0.91) when subsampling 500
 loci. Collectively, our results indicated that both SNP genotyping methods
 produced sufficient data for accurately estimating relationships, even
 within an extremely bottlenecked population. Our results also suggested
 that analytic assumptions historically integrated into the addax pedigree
 are not adversely impacting long-term pedigree-based management; kinships
 calculated from the analytic pedigree were significantly correlated (p
 &gt;&gt;0.001) with AS estimates. Overall, our conclusions are
 intended to serve as both a proof of concept and a model for applying
 molecular data to the genetic management of captive breeding programs.
description: addax_Stacks_filesStacks 1.01 catalog output files with summary statistics. This file must be unzipped.Allele_Sharing_ResultsAverage pair-wise allele sharing estimates in csv format. The zipped file includes allele sharing estimates and the variance using 500 subsampled loci for both ddRAD and SNP chip approaches. One thousand bootstrap replicates with replacement were performed. Results with minor allele filtering (snpCHIP2 and ddRAD2) and without minor allele filtering (snpCHIPall and ddRADall) are included.
DOI: 10.5061/dryad.gt5c0
title: Data from: Novel energy-saving strategies to multiple stressors in birds: the ultradian regulation of body temperature

description: This study aimed to examine thermoregulatory responses in birds facing two
 commonly experienced stressors, cold and fasting. Logging devices allowing
 long-term and precise access to internal body temperature were placed
 within the gizzards of ducklings acclimated to cold (CA) (5°C) or
 thermoneutrality (TN) (25°C). The animals were then examined under three
 equal 4-day periods: ad libitum feeding, fasting and re-feeding. Through
 the analysis of daily as well as short-term, or ultradian, variations of
 body temperature, we showed that while ducklings at TN show only a modest
 decline in daily thermoregulatory parameters when fasted, they exhibit
 reduced surface temperatures from key sites of vascular heat exchange
 during fasting. The CA birds, on the other hand, significantly reduced
 their short-term variations of body temperature while increasing long-term
 variability when fasting. This phenomenon would allow the CA birds to
 reduce the energetic cost of body temperature maintenance under fasting.
 By analysing ultradian regulation of body temperature, we describe a means
 by which an endotherm appears to lower thermoregulatory costs in response
 to the combined stressors of cold and fasting.
description: Data for Repository -
 Tattersall Roussel Voituron TeulierData used to construct
 figures 1, 2, and 3
DOI: 10.5061/dryad.k3479
title: Data from: A global meta-analysis on the ecological drivers of forest restoration success

description: Two billion ha have been identified globally for forest restoration. Our
 meta-analysis encompassing 221 study landscapes worldwide reveals forest
 restoration enhances biodiversity by 15–84% and vegetation structure by
 36–77%, compared with degraded ecosystems. For the first time, we identify
 the main ecological drivers of forest restoration success (defined as a
 return to a reference condition, that is, old-growth forest) at both the
 local and landscape scale. These are as follows: the time elapsed since
 restoration began, disturbance type and landscape context. The time
 elapsed since restoration began strongly drives restoration success in
 secondary forests, but not in selectively logged forests (which are more
 ecologically similar to reference systems). Landscape restoration will be
 most successful when previous disturbance is less intensive and habitat is
 less fragmented in the landscape. Restoration does not result in full
 recovery of biodiversity and vegetation structure, but can complement
 old-growth forests if there is sufficient time for ecological succession.
description: Crouzeilles_et_al_R code
 for Meta-AnalysesCrouzeilles_et_al_R code
 for Model Selection AnalysesMeta_analysisModel_Selection_Landscape_5kmradiusModel_Selection_Landscape_10kmradiusModel_Selection_Landscape_100kmradiusReferences
DOI: 10.5061/dryad.2fp34
title: Data from: Bat trait, genetic and pathogen data from large-scale investigations of African fruit bats (Eidolon helvum)

description: Bats, including African straw-coloured fruit bats (Eidolon helvum), have
 been highlighted as reservoirs of many recently emerged zoonotic viruses.
 This common, widespread and ecologically important species was the focus
 of longitudinal and continent-wide studies of the epidemiological and
 ecology of Lagos bat virus, henipaviruses and Achimota viruses. Here we
 present a spatial, morphological, demographic, genetic and serological
 dataset encompassing 2827 bats from nine countries over an 8-year period.
 Genetic data comprises cytochrome b mitochondrial sequences (n=608) and
 microsatellite genotypes from 18 loci (n=544). Tooth-cementum analyses
 (n=316) provide rare age-specific serologic data for a lyssavirus, a
 henipavirus and two rubulaviruses. This dataset contributes a substantial
 volume of data on the ecology of E. helvum and its viruses and will be
 valuable for a wide range of studies, including viral transmission dynamic
 modelling in age-structured populations, investigation of seasonal
 reproductive asynchrony in wide-ranging species, ecological niche
 modelling, inference of island colonisation history, exploration of
 relationships between island and body size, and various spatial analyses
 of demographic, morphometric or serological data.
description: Eidolon helvum data
 2007-2014Here we present a
 spatial, morphological, demographic, genetic and serological dataset
 encompassing 2827 bats from nine countries over an 8-year period. Genetic
 data comprises cytochrome b mitochondrial sequences (n=608) and
 microsatellite genotypes from 18 loci (n=544). Tooth-cementum analyses
 (n=316) provide rare age-specific serologic data for a lyssavirus, a
 henipavirus and two rubulaviruses. Full details, including descriptors for
 column headings, are available in the associated Scientific Data
 Descriptor manuscript.Eidolon data
 2007_2014_Openaccess.csv
DOI: 10.5061/dryad.58sn8
title: Data from: Genomic data reveal ancient microendemism in forest scorpions across the California Floristic Province

description: The California Floristic Province (CFP) in western North America is a
 globally significant biodiversity hotspot. Elucidating patterns of
 endemism and the historical drivers of this diversity has been an
 important challenge of comparative phylogeography for over two decades. We
 generated phylogenomic data using ddRADseq to examine genetic structure in
 Uroctonus forest scorpions, an ecologically restricted and
 dispersal-limited organism widely distributed across the CFP north to the
 Columbia River. We coupled our genetic data with species distribution
 models (SDMs) to determine climatically suitable areas for Uroctonus both
 now and during the Last Glacial Maximum. Based on our analyses, Uroctonus
 is composed of two major genetic groups that likely diverged over 2
 million years ago. Each of these groups itself contains numerous genetic
 groups that reveal a pattern of vicariance and microendemism across the
 CFP. Migration rates among these populations are low. SDMs suggest forest
 scorpion habitat has remained relatively stable over the last 21 000
 years, consistent with the genetic data. Our results suggest tectonic
 plate rafting, mountain uplift, river drainage formation and
 climate-induced habitat fragmentation have all likely played a role in the
 diversification of Uroctonus. The intricate pattern of genetic
 fragmentation revealed across a temporal continuum highlights the
 potential of low-dispersing species to shed light on small-scale patterns
 of biodiversity and the underlying processes that have generated this
 diversity in biodiversity hotspots.
description: Uroctonus mtDNA data
 setNexus file with aligned
 CO1 sequences generated from 80 samples. See ReadMe file to match sample
 names with species and locality.UroctonusCOI.txtUroctonus RAD loci data setNexus file with concatenated RAD loci sequences generated from 191 samples. See ReadMe file to match sample names with species and locality.UroctonusRADloci.nexUroctonus SNAPP data set all samplesSNAPP input file of unlinked SNPs from 191 samples. See ReadMe file to match sample names with species and locality.ALLscorp50_snapp.nexUroctonus SNAPP input file northern cladeSNAPP input file of unlinked SNPs from all samples in the northern clade. See ReadMe file to match sample names with species and locality.NORTHscorp50_snapp.nexUroctonus SNAPP input file southern cladeSNAPP input file of unlinked SNPs from all samples in the southern clade. See ReadMe file to match sample names with species and locality.SOUTHscorp50_snapp.nexUroctonus STRUCTURE file northern cladeSTRUCTURE input file of unlinked SNPs from all samples in the northern clade. See ReadMe file to match sample names with species and locality.NORTHscorp50.strUroctonus STRUCTURE file southern cladeSTRUCTURE input file of unlinked SNPs from all samples in the southern clade. See ReadMe file to match sample names with species and locality.SOUTHscorp50.str