cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.sj066
title: Data from: Reduced cellular immune response in social insect lineages

description: Social living poses challenges for individual fitness because of the
 increased risk of disease transmission among conspecifics. Despite this
 challenge, sociality is an evolutionarily successful lifestyle, occurring
 in the most abundant and diverse group of organisms on earth—the social
 insects. Two contrasting hypotheses predict the evolutionary consequences
 of sociality on immune systems. The social group hypothesis posits that
 sociality leads to stronger individual immune systems because of the
 higher risk of disease transmission in social species. By contrast, the
 relaxed selection hypothesis proposes that social species have evolved
 behavioural immune defences that lower disease risk within the group,
 resulting in lower immunity at the individual level. We tested these
 hypotheses by measuring the encapsulation response in 11 eusocial and
 non-eusocial insect lineages. We built phylogenetic mixed linear models to
 investigate the effect of behaviour, colony size and body size on cellular
 immune response. We found a significantly negative effect of colony size
 on encapsulation response (Markov chain Monte Carlo generalized linear
 mixed model (mcmcGLMM) p &lt; 0.05; phylogenetic generalized least
 squares (PGLS) p &lt; 0.05). Our findings suggest that insects living
 in large societies may rely more on behavioural mechanisms, such as
 hygienic behaviours, than on immune function to reduce the risk of disease
 transmission among nest-mates.
description: Seven-gene alignment for
 phylogenetic reconstructionNexus file with
 alignment of seven concatenated genes: NAK, Opsin, PolII, Wg, CAD, COI,
 and EF1 copy 2. Please see annotation of nexus file for gene
 partitions.Lopez-Uribe_SevenGeneAlignment.nexMaximum-likelihood estimated phylogenyThis newick file contains the best tree topology with branch lengths after maximum-likelihood phylogenetic estimation in RAxML.Lopez-Uribe_RAxML_BestTree.treRaw encapsulation dataExcel file with the raw encapsulation dat ('RawEncapsulationData') and metadata.Lopez-Uribe_RawEncapsulationData.xlsx
DOI: 10.5061/dryad.t9r0tf0
title: Data from: Resilience of seed production to a severe El Niño‐induced drought across functional groups and dispersal types

description: More frequent and severe El Niño Southern Oscillations (ENSO) are causing
 episodic periods of decreased rainfall. Although the effects of these
 ENSO-induced droughts on tree growth and mortality have been well studied,
 the impacts on other demographic rates such as reproduction are less well
 known. We use a four-year seed rain dataset encompassing the most severe
 ENSO-induced drought in more than 30 years to assess the resilience (i.e.
 resistance and recovery) of the seed composition and abundance of three
 forest types in a tropical dry forest. We found that forest types showed
 distinct differences in the timing, duration and intensity of drought
 during the ENSO event, which likely mediated seed composition shifts and
 resilience. Drought-deciduous species were particularly sensitive to the
 drought with overall poor resilience of seed production, whereby seed
 abundance of this functional group failed to recover to pre-drought levels
 even two years after the drought. Liana and wind-dispersed species were
 able to maintain seed production both during and after drought suggesting
 that ENSO events promote early successional species or species with a
 colonization strategy. Combined, these results suggest that ENSO-induced
 drought mediates the establishment of functional groups and dispersal
 types suited for early successional conditions with more open canopies and
 reduced competition among plants. The effects of the ENSO-induced drought
 on seed composition and abundance were still evident two years after the
 event suggesting the recovery of seed production requires multiple years
 that may lead to shifts in forest composition and structure in the
 long-term, with potential consequences for higher trophic levels like
 frugivores.
description: Species matrix for
 ordinationMeta data included in
 excel sheetOrdinationData.xlsxMonthly rainfall from 1980Meta data included in excel sheetRainfallData.xlsxMonthly seed fall by plot, functional group and dispersal typeMeta data included in excel sheetSeedAbundanceData.xlsx
DOI: 10.5061/dryad.8c1b6538
title: Data from: Genetic evidence for multiple events of hybridization between wolves and domestic dogs in the Iberian Peninsula

description: Hybridization between wild species and their domestic counterparts may
 represent a major threat to natural populations. However, high genetic
 similarity between the hybridizing taxa makes the detection of hybrids a
 difficult task and may hinder attempts to assess the impact of
 hybridization in conservation biology. In this work, we used a combination
 of 42 autosomal microsatellites together with Y-chromosome
 microsatellite-defined haplotypes and mtDNA sequences to investigate the
 occurrence and dynamics of wolf–dog hybridization in the Iberian
 Peninsula. To do this, we applied a variety of Bayesian analyses and a
 parallel set of simulation studies to evaluate (i) the differences between
 Iberian wolves and dogs, (ii) the frequency and geographical distribution
 of hybridization and (iii) the directionality of hybridization. First, we
 show that Iberian wolves and dogs form two well-differentiated genetic
 entities, suggesting that introgressive hybridization is not a widespread
 phenomenon shaping both gene pools. Second, we found evidence for the
 existence of hybridization that is apparently restricted to more
 peripheral and recently expanded wolf populations. Third, we describe
 compelling evidence suggesting that the dynamics of hybridization in wolf
 populations is mediated by crosses between male dogs and female wolves.
 More importantly, the observation of a population showing the occurrence
 of a continuum of hybrid classes forming mixed packs may indicate that we
 have underestimated hybridization. If future studies confirm this pattern,
 then an intriguing avenue of research is to investigate how introgression
 from free-ranging domestic dogs is enabling wolf populations to adapt to
 the highly humanized habitats of southern Europe while still maintaining
 their genetic differentiation.
description: Wolf&Dog_microsatellite_dataMicrosatellite genotypes at 42 autosomal plus 6 Y-linked loci for the Iberian wolf (L) and dog (C).
DOI: 10.5061/dryad.n04r6
title: Data from: The heritability of chimpanzee and human brain asymmetry

description: Human brains are markedly asymmetric in structure and lateralized in
 function, which suggests a relationship between these two properties. The
 brains of other closely related primates, such as chimpanzees, show
 similar patterns of asymmetry, but to a lesser degree, indicating an
 increase in anatomical and functional asymmetry during hominin evolution.
 We analysed the heritability of cerebral asymmetry in chimpanzees and
 humans using classic morphometrics, geometric morphometrics, and
 quantitative genetic techniques. In our analyses, we separated directional
 asymmetry and fluctuating asymmetry (FA), which is indicative of
 environmental influences during development. We show that directional
 patterns of asymmetry, those that are consistently present in most
 individuals in a population, do not have significant heritability when
 measured through simple linear metrics, but they have marginally
 significant heritability in humans when assessed through three-dimensional
 configurations of landmarks that reflect variation in the size, position,
 and orientation of different cortical regions with respect to each other.
 Furthermore, genetic correlations between left and right hemispheres are
 substantially lower in humans than in chimpanzees, which points to a
 relatively stronger environmental influence on left–right differences in
 humans. We also show that the level of FA has significant heritability in
 both species in some regions of the cerebral cortex. This suggests that
 brain responsiveness to environmental influences, which may reflect neural
 plasticity, has genetic bases in both species. These results have
 implications for the evolvability of brain asymmetry and plasticity among
 humans and our close relatives.
description: Chimpanzee and human
 asymmetry dataFive files including:
 the chimpanzee pedigree, two files listing interlandmark distances (one
 for chimpanzees and one for humans), and two files including asymmetric
 components of shape variation (one file for chimpanzees and one for
 humans).Gomez-Robles_Asymmetry.zip
DOI: 10.5061/dryad.dq4g5
title: Data from: Population size and time since island isolation determine genetic diversity loss in insular frog populations

description: Understanding the factors that contribute to loss of genetic diversity in
 fragmented populations is crucial for conservation measurements.
 Land-bridge archipelagoes offer ideal model systems for identifying the
 long-term effects of these factors on genetic variations in wild
 populations. In this study, we used 9 microsatellite markers to quantify
 genetic diversity and differentiation of 810 pond frogs (Pelophylax
 nigromaculataus) from 24 islands of the Zhoushan Archipelago and 3 sites
 on nearby mainland China and estimated the effects of the island area,
 population size, time since island isolation, distance to the mainland and
 distance to the nearest larger island on reduced genetic diversity of
 insular populations. The mainland populations displayed higher genetic
 diversity than insular populations. Genetic differentiations and no
 obvious gene flow were detected among the frog populations on the islands.
 Hierarchical partitioning analysis showed that only time since island
 isolation (square root transformed) and population size (log transformed)
 significantly contributed to insular genetic diversity. These results
 suggest that decreased genetic diversity and genetic differentiations
 among insular populations may have been caused by random genetic drift
 following isolation by rising sea levels during the Holocene. The results
 provide strong evidence for a relationship between retained genetic
 diversity and population size and time since island isolation for pond
 frogs on the islands, consistent with the prediction of the neutral theory
 for finite populations. Our study highlights the importance of the size
 and estimated isolation time of populations in understanding the
 mechanisms of genetic diversity loss and differentiation in fragmented
 wild populations.
description: Microsatellite
 dataMicrosatellite
 dataRaw
 transectsRaw
 transects
DOI: 10.5061/dryad.73r6j
title: Data from: Climate change alters the structure of arctic marine food webs due to poleward shifts of boreal generalists

description: Climate-driven poleward shifts, leading to changes in species composition
 and relative abundances, have been recently documented in the Arctic.
 Among the fastest moving species are boreal generalist fish which are
 expected to affect arctic marine food web structure and ecosystem
 functioning substantially. Here, we address structural changes at the food
 web level induced by poleward shifts via topological network analysis of
 highly resolved boreal and arctic food webs of the Barents Sea. We
 detected considerable differences in structural properties and link
 configuration between the boreal and the arctic food webs, the latter
 being more modular and less connected. We found that a main characteristic
 of the boreal fish moving poleward into the arctic region of the Barents
 Sea is high generalism, a property that increases connectance and reduces
 modularity in the arctic marine food web. Our results reveal that habitats
 form natural boundaries for food web modules, and that generalists play an
 important functional role in coupling pelagic and benthic modules. We
 posit that these habitat couplers have the potential to promote the
 transfer of energy and matter between habitats, but also the spread of
 pertubations, thereby changing arctic marine food web structure
 considerably with implications for ecosystem dynamics and functioning.
description: Boreal and arctic food
 webs of the Barents SeaThe excel file contains
 the boreal and the arctic food web of the Barents Sea. Sheet 1: boreal
 food web. Sheet 2: arctic food web.The food web networks are represented
 by binary adjacency food web matrices. Each element is equal to 1 if the
 trophospecies in the column (predator) eats the trophospecies in the row
 (prey), and is equal to 0 if no trophic interaction takes
 place.Boreal and Arctic food webs of
 the Barents Sea.xlsx
DOI: 10.5061/dryad.p671ht6
title: Data from: Encephalization and longevity evolved in a correlated fashion in Euarchontoglires but not in other mammals

description: Across mammals, encephalization and longevity show a strong correlation.
 It is not clear, however, whether these traits evolved in a correlated
 fashion within mammalian orders, or when they do, whether one trait drives
 changes in the other. Here, we compare independent and correlated
 evolutionary models to identify instances of correlated evolution within
 six mammalian orders. In cases of correlated evolution, we subsequently
 examined transition patterns between small/large relative brain size and
 short/long lifespan. In four mammalian orders, these traits evolved
 independently. This may reflect constraints related to energy allocation,
 predation avoidance tactics, and reproductive strategies. Within both
 primates and rodents, and their parent clade Euarchontoglires, we found
 evidence for correlated evolution. In primates, transition patterns
 suggest relatively larger brains likely facilitated the evolution of long
 lifespans. Because larger brains prolong development and reduce fertility
 rates, they may be compensated for with longer lifespans. Furthermore,
 encephalization may enable cognitively-complex strategies that reduce
 extrinsic mortality. Rodents show an inverse pattern of correlated
 evolution, whereby long lifespans appear to have facilitated the evolution
 of relatively larger brains. This may be because longer-lived organisms
 have more to gain from investment in encephalization. Together, our
 results provide evidence for the correlated evolution of encephalization
 and longevity, but only in some mammalian orders.
description: Evolution_DeCasien et
 al_Supplementary DataThis excel file contains
 all data used in the manuscript "Encephalization and longevity
 evolved in a correlated fashion in Euarchontoglires but not in other
 mammals". Specifically, this data set contains maximum lifespans,
 species average brain weights, and species average body weights for more
 than 600 mammalian species, including 151 carnivorans (Carnivora), 77
 even-toed ungulates (Artiodactyla), 37 cetaceans (Cetacea), and 54
 chiropterans (Chiroptera) among Laurasiatheria, and 168 rodents
 (Rodentia), 10 lagomorphs (Lagomorpha), 3 tree shrews (Scandentia), and
 144 primates (Primates) among Euarchontoglires.
DOI: 10.5061/dryad.113v0
title: Data from: Does soil moisture availability explain liana seedling distribution across a tropical rainfall gradient?

description: Liana density tends to increase with decreasing rainfall and increasing
 seasonality. However, the pattern of liana distribution may be due to
 differences in soil water retention capacity, not rainfall and seasonality
 per se. We tested the effect of rainfall and soil substrate with respect
 to the distribution of liana seedlings in six sites across a rainfall
 gradient from the wet Atlantic to the dry Pacific in central Panama. Soils
 were either limestone, with low water-holding capacity, or laterite, with
 higher water-holding capacity. We sampled liana seedlings at each site
 using three 1 × 100 m transect. We found that relative liana seedling
 density was higher on limestone soils compared to laterite soils
 regardless of the amount of rainfall. Furthermore, liana community
 composition on limestone soils was more similar to dry forest sites than
 to adjacent wet and moist forest sites. Liana seedling species diversity
 relative to trees was significantly higher in a low-fertility dry forest
 site compared to a high-fertility forest, but did not differ from the
 other sites. Thus, liana seedling density and community structure may be
 driven more by soil type and thus by soil moisture availability than
 strictly by mean annual rainfall and the seasonality of rainfall.
description: LAD1liana seedling census
 and canopy height data for the site LAD1, located in Parque Natural
 MetropolitanoLAD2liana seedling census
 and canopy height data for the site LAD2, located in Cerro Galera, on the
 west side of the Pacific entrance of the Panama CanalLAM1liana seedling census
 and canopy height data for the site LAM1, located in PIPE LINE ROAD,
 Parque Soberania, CTFS site P 15LSM2liana seedling census
 and canopy height data for the site LSM1, located in PARQUE NACIONAL
 CHAGRES, main entranceLAW1liana seedling census
 and canopy height data for the site LAW1, located in Parque Natcional San
 Lorenzo, Road to San Lorenzo Fort, CTFS site P 2LSW2liana seedling census
 and canopy height data for the site LSW1, located in Parque Natcional San
 Lorenzo, Road to San Lorenzo Fort, CTFS site P 1
DOI: 10.5061/dryad.18913
title: Data from: Logging and fire regimes alter plant communities

description: Disturbances are key drivers of plant community composition, structure and
 function. Plant functional traits, including life forms and reproductive
 strategies are critical to the resilience and resistance of plant
 communities in the event of disturbance. Climate change and increasing
 anthropogenic disturbance are altering natural disturbance regimes,
 globally. When these regimes shift beyond the adaptive resilience of plant
 functional traits, local populations and ecosystem functions can become
 compromised. We tested the influence of multiple disturbances, of varying
 intensity and frequency, on the composition and abundance of vascular
 plant communities and their respective functional traits (life forms and
 reproductive strategies) in the wet sclerophyll, Mountain Ash Eucalyptus
 regnans forests of south-eastern Australia. Specifically, we quantified
 the effect of the type and number of disturbances (including fires,
 clearcut logging and salvage logging) on plant community composition. We
 found that clearcut and salvage logging and the number of fires
 significantly influenced plant community composition and functional
 traits. Specifically, multiple fires resulted in lower populations of
 species that depend on on-site seeding for persistence. This includes the
 common tree species, Eucalyptus regnans, Pomaderris aspera and Acacia
 dealbata. In contrast, clearcut and salvage logged sites supported
 abundant on-site seeder species. However, species that depend on
 resprouting by surviving individuals, such as common and keystone ‘tree
 ferns’ Dicksonia antarctica and Cyathea australis declined significantly.
 Our data have important implications for understanding the relationship
 between altered disturbance regimes and plant communities and the
 respective effects on ecosystem function. In a period of rapid global
 environmental change, with disturbances predicted to increase and
 intensify, it is critical to address the impact of altered disturbance
 regimes on biodiversity.
description: Species
 abundanceThe projective foliage
 cover of each plant species/reproductive strategy/lifeform observed within
 each replicate siteAll species abundance
 spreadsheets .xls
DOI: 10.5061/dryad.f1j4s39
title: Data from: Suitability of traits related to aggression and handleability for integration into pig breeding programmes: genetic parameters and comparison between Gaussian and binary trait specifications

description: Changes in husbandry systems as well as consumers' increasing demands
 for animal welfare lead to increasing importance of traits such as
 handleability and aggressiveness in pigs. However, before using such novel
 traits for selection decisions, information on genetic parameters for
 these traits for the specific population is required. Therefore, weight
 gain and behaviour-related traits were recorded in 1004 pigs (814 Pietrain
 x German Landrace crossbred, 190 German Landrace purebred) at different
 ages. Behaviour indicators and tests were assessed and conducted,
 respectively under commercial farm conditions and included scoring of skin
 lesions (twice) and behaviour during backtests (twice), injections (once),
 handling (twice) and weighing (three times). Since behaviour scores often
 exhibit suboptimal statistical properties for parametric analyses,
 variance components were estimated using an animal model assuming a normal
 (Gaussian, GA; all traits) and additionally a binary distribution of
 variables (BI; using a logit-link function for all behaviour traits).
 Heritabilities for behavioural traits ranged from 0.02 ± 0.04 (finishing
 pig handling test; BI) to 0.36 ± 0.08 (backtest 2; GA) suggesting that
 some of the traits are potentially useful for genetic selection (e.g.
 finishing pig weighing test: h² (GA) = 0.20 ± 0.07). Only minor
 differences were observed for results from binary and Gaussian analyses of
 the same traits suggesting that either approach might yield valid results.
 However, four-fold cross-validation using correlations between breeding
 values of a sub-set of animals for the sample trait finishing pig weighing
 score indicated slight superiority of the logit model (r = 0.85 ± 0.04 vs.
 r = 0.77 ± 0.03) Generally, only weak to moderate associations were found
 between behavioural reactions to the same test at different ages (rp ≤
 0.11 for weighing at different ages; rp = 0.30 and but rg (GA) = 0.84 ±
 0.11 for the backtests) as well as between reactions to different tests.
 Therefore, for inclusion of behaviour traits into breeding programmes, and
 considering high labour input required for some tests such as the
 backtest, it is recommended to assess behaviour during situations that are
 relevant and identical to practical conditions, while the use of indicator
 traits generally does not appear to be a very promising alternative.
description: behaviour performance
 pigsvcedat_labelEX1.txtvcepedPedigree