cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.933bs
title: Data from: Log moisture capacity does not predict epixylic bryophyte growth under thinned and unthinned forest canopies

description: 1. Coarse woody debris (CWD) serves as habitat for diverse and rare taxa
 in forest systems. Because the abundance of mosses appears to be
 correlated with log size and stage of decay, many have suggested that CWD
 serves as a moisture reservoir, ensuring a humid microclimate and
 facilitating moss growth, but no one has tested this connection. Intact
 forest canopies are also thought to maintain humid conditions that benefit
 moss growth. If microclimatic regulation is the primary mechanism
 contributing to high moss abundance on CWD, then epixylic moss growth
 should increase with the capacity of the log moisture reservoir, and the
 importance of the reservoir size should increase with canopy opening. 2.
 Three types of synthetic logs, identical in size and shape but differing
 in moisture capacity, and two natural substrates, well-decayed birch and
 Thuja logs, were used to test the effects of log moisture capacity on
 growth of Dicranum flagellare under thinned and intact canopies of a
 spruce plantation over 20 months. 3. Surface humidity was positively
 associated with moisture capacity, but did not reach the water
 compensation point outside of precipitation events. Under a closed forest
 canopy, moss growth was negligible across all log types. Under an open
 forest canopy, moss growth was greater on natural substrates than
 synthetic ones, and negatively related to moisture capacity. CWD
 facilitates a sufficiently humid surface for only a short time after
 precipitation, presumably when a film of liquid water is maintained near
 the surface. 4. For Dicranum flagellare, canopy condition is a more
 accurate predictor of growth than CWD-moisture capacity; any beneficial
 properties of CWD appear to be lessened by a dense forest canopy (as in
 silvicultural plantations), probably because it reduces access to liquid
 water from precipitation. 5. We propose that the surface moisture
 availability of CWD depends on optimal depth of a “resisting layer” below
 the log surface, representing a tradeoff between water retention and loss
 (via percolation or runoff at extremely deep vs. shallow resisting layer
 depth). CWD may possess microclimate-regulating traits that benefit moss
 growth, but it does not appear to act as a moisture capacitor.
description: Haughian&Frego2017_FunctionalEcology_moisture_capacity_&_moss_growth_dataSheet 1 - change in biomass of mosses grown in mesh envelopes over 20 months. Sheet 2 - water potential of air recorded 3-5 mm above the surface of synthetic and natural logs, in the laboratory, under simulated precipitation. Sheet 3 - physical properties of a subset of experimental logs, including porosity, density, and volume. Sheet 4 - ambient moisture availability (water potential) from 9 data loggers in the experimental areas, recorded at 30 minute intervals over the growing season in 2014 (at 1.0 m from the ground).
DOI: 10.5061/dryad.p46n0
title: Data from: Nonselective bottlenecks control the divergence and diversification of phase-variable bacterial populations

description: Phase variation occurs in many pathogenic and commensal bacteria and is a
 major generator of genetic variability. A putative advantage of phase
 variation is to counter reductions in variability imposed by nonselective
 bottlenecks during transmission. Genomes of Campylobacter jejuni, a
 widespread food-borne pathogen, contain multiple phase-variable loci whose
 rapid, stochastic variation is generated by hypermutable simple sequence
 repeat tracts. These loci can occupy a vast number of combinatorial
 expression states (phasotypes) enabling populations to rapidly access
 phenotypic diversity. The imposition of nonselective bottlenecks can
 perturb the relative frequencies of phasotypes, changing both
 within-population diversity and divergence from the initial population.
 Using both in vitro testing of C. jejuni populations and a simple
 stochastic simulation of phasotype change, we observed that single-cell
 bottlenecks produce output populations of low diversity but with bimodal
 patterns of either high or low divergence. Conversely, large bottlenecks
 allow divergence only by accumulation of diversity, while interpolation
 between these extremes is observed in intermediary bottlenecks. These
 patterns are sensitive to the genetic diversity of initial populations but
 stable over a range of mutation rates and number of loci. The qualitative
 similarities of experimental and in silico modeling indicate that the
 observed patterns are robust and applicable to other systems where
 localized hypermutation is a defining feature. We conclude that while
 phase variation will maintain bacterial population diversity in the face
 of intermediate bottlenecks, narrow transmission-associated bottlenecks
 could produce host-to-host variation in bacterial phenotypes and hence
 stochastic variation in colonization and disease outcomes.
description: Aidley_Bayliss_Archive_MapMap of archive. This archive contains the scripts and data files contained within an mBio paper with first author Jack Aidley and last author Chris Bayliss. The scripts are for modelling the effect of non-selective bottlenecks on phase variable genes of Campylobacter jejuni. The data files contains the outputs of the scripts and related experimental data.ExperimentalDataThis folder contains the experimental data on bottlenecks and phase variation.Simulator_Output_FilesThis folder contains the outputs from the simulator on bottlenecks and phase variation.Scripts_for_Figure_PreparationThis folder contains the scripts used for preparation of the figures in the mBio paper.Bottleneck SimulatorThis folder contains the program files for the bottleneck simulator and a readme file that describes how the program works.
DOI: 10.5061/dryad.180nh
title: Data from: Molecular clocks indicate turnover and diversification of modern coleoid cephalopods during the Mesozoic Marine Revolution

description: Coleoid cephalopod molluscs comprise squid, cuttlefish and octopuses, and
 represent nearly the entire diversity of modern cephalopods. Sophisticated
 adaptations such as the use of colour for camouflage and communication,
 jet propulsion and the ink sac highlight the unique nature of the group.
 Despite these striking adaptations, there are clear parallels in ecology
 between coleoids and bony fishes. The coleoid fossil record is limited,
 however, hindering confident analysis of the tempo and pattern of their
 evolution. Here we use a molecular dataset (180 genes, approx. 36 000
 amino acids) of 26 cephalopod species to explore the phylogeny and timing
 of cephalopod evolution. We show that crown cephalopods diverged in the
 Silurian–Devonian, while crown coleoids had origins in the latest
 Palaeozoic. While the deep-sea vampire squid and dumbo octopuses have
 ancient origins extending to the Early Mesozoic Era, 242 ± 38 Ma,
 incirrate octopuses and the decabrachian coleoids (10-armed squid)
 diversified in the Jurassic Period. These divergence estimates highlight
 the modern diversity of coleoid cephalopods emerging in the Mesozoic
 Marine Revolution, a period that also witnessed the radiation of most
 ray-finned fish groups in addition to several other marine vertebrates.
 This suggests that that the origin of modern cephalopod biodiversity was
 contingent on ecological competition with marine vertebrates.
description: aligned_supermatrix_36156_x_52_phylipAligned supermatrix, 180 genes, 36,156 amino acid positions, 52 taxa. Phylip format.ceph_1aug_36156
DOI: 10.5061/dryad.01th0
title: Data from: It's cool to be dominant: social status alters short-term risks of heat stress

description: Climate change has potential to trigger social change. As a first step
 towards understanding mechanisms determining the vulnerability of animal
 societies to rising temperatures, we investigated interactions between
 social rank and thermoregulation in three arid-zone bird species:
 fawn-coloured lark (Mirafra africanoides, territorial); African red-eyed
 bulbul (Pycnonotus nigricans, loosely social) and sociable weaver
 (Philetairus socius, complex cooperative societies). We assessed
 relationships between body temperature (Tb), air temperature (Ta) and
 social rank in captive groups in the Kalahari Desert. Socially dominant
 weavers and bulbuls had lower mean Tb than subordinate conspecifics, and
 dominant individuals of all species maintained more stable Tb as Ta
 increased. Dominant bulbuls and larks tended to monopolise available
 shade, but dominant weavers did not. Nevertheless, dominant weavers
 thermoregulated more precisely, despite expending no more behavioural
 effort on thermoregulation than subordinates. Increasingly unequal risks
 associated with heat stress may have implications for stability of animal
 societies in warmer climates.
description: Table S4: Body
 temperature dataThis .csv file contains
 data used in the analyses of body temperature and thermoregulation in the
 manuscript "It's cool to be dominant". Key to the column
 headings as follows: date: date of collection of data point. time.round:
 time of collection of data point, rounded to the nearest minute.
 time.deci: time.round converted to a decimal. species: bird species
 (common names). bird.id: unique colour-ring code of the bird. Tb: body
 temperature of the bird. soc.rank: social rank of the bird (1 = most
 dominant). Ta: air temperature as recorded by the weather station. tod:
 time of day: day = 6:00am – 7:59pm; night = 8:00pm - 5:59am. mass: capture
 body mass of the bird. sex: sex of the bird, m = male, f= female, u =
 undetermined.Table
 S4.csvTable S5: Behavioural
 dataThis .csv file contains
 data used in the analyses of behavioural thermoregulatory strategies
 shade-seeking, activity, and panting in the manuscript "It's
 cool to be dominant". Key to the column headings as follows: date:
 date of collection of data point. time.round: time of collection of data
 point, rounded to the nearest minute. species: bird species (common
 names). bird.id: unique colour-ring code of the bird. soc.rank: social
 rank of the bird (1 = most dominant). mass: capture body mass of the bird.
 sex: sex of the bird, m = male, f= female, u = undetermined. Ta: air
 temperature as recorded by the weather station. panting: binary behaviour
 variable where 1 = panting, 0 = not panting. active: binary behaviour
 variable where 1 = active, 0 = inactive. shade: binary behaviour variable
 where 1 =in shade, 0 =in sun.Table
 S5.csv
DOI: 10.5061/dryad.2jr8p
title: Data from: Recruitment of reviewers is becoming harder at some journals: a test of the influence of reviewer fatigue at six journals in ecology and evolution

description: Background: It is commonly reported by editors that it has become harder
 to recruit reviewers for peer review and that this is because individuals
 are being asked to review too often and are experiencing reviewer fatigue.
 However, evidence supporting these arguments is largely anecdotal. Main
 body: We examine responses of individuals to review invitations for six
 journals in ecology and evolution. The proportion of invitations that lead
 to a submitted review has been decreasing steadily over 13 years
 (2003–2015) for four of the six journals examined, with a cumulative
 effect that has been quite substantial (average decline from 56% of review
 invitations generating a review in 2003 to just 37% in 2015). The
 likelihood that an invitee agrees to review declines significantly with
 the number of invitations they receive in a year. However, the average
 number of invitations being sent to prospective reviewers and the
 proportion of individuals being invited more than once per year has not
 changed much over these 13 years, despite substantial increases in the
 total number of review invitations being sent by these journals—the
 reviewer base has expanded concomitant with this growth in review
 requests. Conclusions: The proportion of review invitations that lead to a
 review being submitted has been declining steadily for four of the six
 journals examined here, but reviewer fatigue is not likely the primary
 explanation for this decline.
description: Fox et al_reviewer
 burden datasetResponses of peer review
 invitees to invitations for six journals in ecology and evolution
 (Evolution, Functional Ecology, Journal of Animal Ecology, Journal of
 Applied Ecology, Journal of Ecology, and Methods in Ecology and
 Evolution).
DOI: 10.5061/dryad.fs8kv
title: Data from: The Opiliones tree of life: shedding light on harvestmen relationships through transcriptomics

description: Opiliones are iconic arachnids with a Palaeozoic origin and a diversity
 that reflects ancient biogeographic patterns dating back at least to the
 times of Pangea. Owing to interest in harvestman diversity, evolution and
 biogeography, their relationships have been thoroughly studied using
 morphology and PCR-based Sanger approaches to infer their systematic
 relationships. More recently, two studies utilized transcriptomics-based
 phylogenomics to explore their basal relationships and diversification,
 but sampling was limiting for understanding deep evolutionary patterns, as
 they lacked good taxon representation at the family level. Here, we
 analysed a set of the 14 existing transcriptomes with 40 additional ones
 generated for this study, representing approximately 80% of the extant
 familial diversity in Opiliones. Our phylogenetic analyses, including a
 set of data matrices with different gene occupancy and evolutionary rates,
 and using a multitude of methods correcting for a diversity of factors
 affecting phylogenomic data matrices, provide a robust and stable
 Opiliones tree of life, where most families and higher taxa are precisely
 placed. Our dating analyses using alternative calibration points, methods
 and analytical parameters provide well-resolved old divergences,
 consistent with ancient regionalization in Pangea in some groups, and
 Pangean vicariance in others. The integration of state-of-the-art
 molecular techniques and analyses, together with the broadest taxonomic
 sampling to date presented in a phylogenomic study of harvestmen, provide
 new insights into harvestmen interrelationships, as well as an overview of
 the general biogeographic patterns of this ancient arthropod group.
description: Matrix
 IConcatenated matrix of
 the genes with &gt;90% gene occupancy. See Suppl. Mat. for further
 information.opis78.nexMatrix IIConcatenated matrix of the genes with &gt;75% gene occupancy. See Suppl. Mat. for further information.opis305.nexMatrix IIIConcatenated matrix of the genes with &gt;50% gene occupancy. See Suppl. Mat. for further information.opis1550.nexMatrix IVConcatenated matrix of the 100 fastest evolving genes parsed from Matrix I. See Suppl. Mat. for further information.opis100least.nexMatrix VConcatenated matrix of the 100 genes with an evolutionary rate close to the mean parsed from Matrix I. See Suppl. Mat. for further information.opis100middle.nexMatrix VIConcatenated matrix of the 100 slowest evolving genes parsed from Matrix I. See Suppl. Mat. for further information.opis100most.nex
DOI: 10.4228/zalf-68hx-6q27
title: Survey data on farmer mental models and fertilizer management practices in Madagascar

description: This dataset primarily contains mental model data and respondent characteristics from 485 households across five communes in the Irodo watershed (Anketrakabe, Ambolobozobe, Antsoha, Sadjoavato, and Anivorano). Using a stratified proportional sampling design, one adult per household rated how various factors influence fertilizer use decisions using the M-Tool (–3 to +3 scale). The dataset also includes detailed information on respondents and household characteristics (e.g., gender, education, land ownership) as well as household livelihoods, including primary and secondary activities.
DOI: 10.5061/dryad.g89m1
title: Data from: Parasitism drives host genome evolution: insights from the Pasteuria ramosa - Daphnia magna system

description: Because parasitism is thought to play a major role in shaping host
 genomes, it has been predicted that genomic regions associated with
 resistance to parasites should stand out in genome scans, revealing
 signals of selection above the genomic background. To test whether
 parasitism is indeed such a major factor in host evolution and to better
 understand host-parasite interaction at the molecular level, we studied
 genome-wide polymorphisms in 97 genotypes of the planktonic crustacean
 Daphnia magna originating from three localities across Europe. Daphnia
 magna is known to coevolve with the bacterial pathogen Pasteuria ramosa
 for which host genotypes (clonal lines) are either resistant or
 susceptible. Using association mapping, we identified two genomic regions
 involved in resistance to P. ramosa, one of which was already known from a
 previous QTL analysis. We then performed a naïve genome scan to test for
 signatures of positive selection and found that the two regions identified
 with the association mapping further stood out as outliers. Several other
 regions with evidence for selection were also found, but no link between
 these regions and phenotypic variation could be established. Our results
 are consistent with the hypothesis that parasitism is driving host genome
 evolution.
description: SNPs called with
 freebayesThis VCF contains the
 filtered SNPs for studying selection and association with resistance
 phenotypes in european D. magna populations.Input_vcf.recode.vcfSupplementary SNPs obtained from Sanger sequencingThese SNPs were originally part of a sequencing effort to detect association with ephippia production (Roulin et al. 2016, MBE). They were included in the final analysis (total of 7034 SNPs)scaffold1036_supp.vcfResistotypesThis file contains the resistotypes for clones included in the association study (R: resistant ; S: susceptible)
DOI: 10.5061/dryad.v861k
title: Data from: Widespread hybridization and bidirectional introgression in sympatric species of coral reef fish

description: Coral reefs are highly diverse ecosystems, where numerous closely related
 species often coexist. How new species arise and are maintained in these
 high geneflow environments have been long-standing conundrums.
 Hybridization and patterns of introgression between sympatric species
 provide a unique insight into the mechanisms of speciation and the
 maintenance of species boundaries. In this study, we investigate the
 extent of hybridization between two closely related species of coral reef
 fish: the common coral trout (Plectropomus leopardus) and the bar-cheek
 coral trout (Plectropomus maculatus). Using a complementary set of 25
 microsatellite loci, we distinguish pure genotype classes from first- and
 later-generation hybrids, identifying 124 interspecific hybrids from a
 collection of 2,991 coral trout sampled in inshore and mid-shelf reefs of
 the southern Great Barrier Reef. Hybrids were ubiquitous among reefs,
 fertile and spanned multiple generations suggesting both ecological and
 evolutionary processes are acting to maintain species barriers. We
 elaborate on these finding to investigate the extent of genomic
 introgression and admixture from 2,271 SNP loci recovered from a ddRAD
 library of pure and hybrid individuals. An analysis of genomic clines on
 recovered loci indicates that 261 SNP loci deviate from a model of neutral
 introgression, of which 132 indicate a pattern of introgression consistent
 with selection favouring both hybrid and parental genotypes. Our findings
 indicate genome-wide, bidirectional introgression between two sympatric
 species of coral reef fishes and provide further support to a growing body
 of evidence for the role of hybridization in the evolution of coral reef
 fishes.
description: Microsat25_2991Plectropomus25 microsatellite loci for 2991 Plectropomus app collected from the southern Great Barrier Reef, AustraliaMsat25_2991Plectropomus.txtSNP2271_batch_3_filtered_structure2271 SNP loci from 80 Plectropomus spp. including identified hybrids collected from the southern Great Barrier Reef, Australia.
DOI: 10.5061/dryad.vd8tf
title: Data from: Emergence of transformation-tolerant representations of visual objects in rat lateral extrastriate cortex

description: Rodents are emerging as increasingly popular models of visual functions.
 Yet, evidence that rodent visual cortex is capable of advanced visual
 processing, such as object recognition, is limited. Here we investigate
 how neurons located along the progression of extrastriate areas that, in
 the rat brain, run laterally to primary visual cortex, encode object
 information. We found a progressive functional specialization of neural
 responses along these areas, with: (1) a sharp reduction of the amount of
 low-level, energy-related visual information encoded by neuronal firing;
 and (2) a substantial increase in the ability of both single neurons and
 neuronal populations to support discrimination of visual objects under
 identity-preserving transformations (e.g., position and size changes).
 These findings strongly argue for the existence of a rat object-processing
 pathway, and point to the rodents as promising models to dissect the
 neuronal circuitry underlying transformation-tolerant recognition of
 visual objects.
description: Source data file for the
 article authored by Tafazoli and colleagues on invariant object
 representations in rat visual cortexThis data file provides
 the full data set processed in the article “Emergence of
 transformation-tolerant representations of visual objects in rat lateral
 extrastriate cortex” by Sina Tafazoli, Houman Safaai, Gioia De Franceschi,
 Federica Bianca Rosselli, Walter Vanzella, Margherita Riggi, Federica
 Buffolo, Stefano Panzeri and Davide Zoccolan. A detailed description of
 the file is provided in the companion "Readme.pdf"
 file.Tafazoli_et_al_source_data.mat