cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.pn04m84
title: Data from: Experimental evolution of phytoplankton fatty acid thermal reaction norms

description: Temperature effects on the fatty acid (FA) profiles of phytoplankton,
 major primary producers in the ocean, have been widely studied due to
 their importance as industrial feedstocks and to their indispensable role
 as global producers of long-chain, polyunsaturated FA (PUFA), including
 omega-3 (ω3) FA required by organisms at higher trophic levels. The latter
 is of global ecological concern for marine food webs, as some evidence
 suggests an ongoing decline in global marine-derived ω3 FA due to both a
 global decline in phytoplankton abundance and to a physiological reduction
 in ω3 production by phytoplankton as temperatures rise. Here, we examined
 both short-term (physiological) and long-term (evolutionary) responses of
 FA profiles to temperature by comparing FA thermal reaction norms of the
 marine diatom Thalassiosira pseudonana after ~500 generations (ca. 2.5
 years) of experimental evolution at low (16°C) and high (31°C)
 temperatures. We showed that thermal reaction norms for some key FA
 classes evolved rapidly in response to temperature selection, often in
 ways contrary to our predictions based on prior research. Notably,
 31°C-selected populations showed higher PUFA percentages (including ω3 FA)
 than 16°C-selected populations at the highest assay temperature (31°C,
 above T. pseudonana’s optimum temperature for population growth),
 suggesting that high-temperature selection led to an evolved ability to
 sustain high PUFA production at high temperatures. Rapid evolution may
 therefore mitigate some of the decline in global phytoplankton-derived ω3
 FA production predicted by recent studies. Beyond its implications for
 marine food webs, knowledge of the effects of temperature on fatty acid
 profiles is of fundamental importance to our understanding of the
 mechanistic causes and consequences of thermal adaptation.
description: 1-FattyAcids_total.measured_molar_05182-FattyAcids_mol.biovolume_raw_05183-FattyAcids_percentages_raw_11184-FattyAcids_MCL_WUnSat_raw_0518
DOI: 10.5061/dryad.bn695rf
title: Data from: Resolving coral photoacclimation dynamics through coupled photophysiological and metabolomic profiling

description: Corals continuously adjust to short term variation in light availability
 on shallow reefs. Long-term light alterations can also occur due to
 natural and anthropogenic stressors, as well as management interventions
 such as coral transplantation. Although short term photophysiological
 responses are relatively well-understood in corals, little information is
 available regarding photoacclimation dynamics over weeks of altered light
 availability. We coupled photophysiology and metabolomic profiling to
 explore changes that accompany longer-term photoacclimation in a key Great
 Barrier Reef coral species (Acropora muricata). High (HL) and low light
 (LL) acclimated corals were collected from the reef and reciprocally
 exposed to high and low light ex situ. Rapid light curves using Pulse
 Amplitude Modulation (PAM) fluorometry revealed photophysiological
 acclimation of LL to HL and HL to LL shifted corals within 21 days. A
 subset of colonies sampled at 7 and 21 days for untargeted LC-MS and GC-MS
 metabolomic profiling revealed metabolic reorganization before acclimation
 was detected using PAM fluorometry. Metabolomic shifts were more
 pronounced for LL to HL treated corals than their HL to LL counterparts.
 Compounds driving metabolomic separation between HL-exposed and LL control
 colonies included amino acids, organic acids, fatty acids and sterols.
 Reduced glycerol and campesterol suggest decreased translocation of
 photosynthetic products from symbiont to host in LL to HL shifted corals,
 with concurrent increases in fatty acid abundance indicating reliance on
 stored lipids for energy. We discuss how these data provide novel insight
 into environmental regulation of metabolism and implications for
 management strategies that drive rapid changes in light availability.
description: MS
 filesLCMS and GCMS files in
 .CEF and .CDF format respectively. The processing sequence is detailed in
 README file.
DOI: 10.5061/dryad.3q25r77
title: Data from: Contagious fear: escape behaviour increases with flock size in European gregarious birds

description: Flight initiation distance (FID), the distance at which individuals take
 flight when approached by a potential (human) predator, is a tool for
 understanding predator-prey interactions. Among the factors affecting FID,
 tests of effects of group size (i.e. number of potential prey) on FID have
 yielded contrasting results. Group size or flock size could either affect
 FID negatively (i.e. the dilution effect caused by the presence of many
 individuals) or positively (i.e. increased vigilance due to more eyes
 scanning for predators). These effects may be associated with gregarious
 species, because such species should be better adapted to exploiting
 information from other individuals in the group than non-gregarious
 species. Sociality may explain why earlier findings on group size vs. FID
 have yielded different conclusions. Here, we analyzed how flock size
 affected bird FID in eight European countries. A phylogenetic generalized
 least square regression model was used to investigate changes in escape
 behavior of bird species in relation to number of individuals in the
 flock, starting distance, diet, latitude and type of habitat. Flock size
 of different bird species influenced how species responded to perceived
 threats. We found that gregarious birds reacted to a potential predator
 earlier (longer flight initiation distance) when aggregated in large
 flocks. These results support a higher vigilance arising from many eyes
 scanning in birds, suggesting that sociality may be a key factor in the
 evolution of anti-predator behavior both in urban and rural areas.
 Finally, future studies comparing FID must pay explicit attention to the
 number of individuals in flocks of gregarious species.
description: dataset.fid.gregarious.2019Dataset associated to the article "Contagious fear: Escape behaviour increases with flock size in European gregarious birds" by Morelli et al. 2019. Metadata: Variable Details Species Species latin name FID_mean Flight initiation distance measured in meters (mean value) n No. observations of FID initiation Starting distance species Scientific name diet.specific Type of diet gregariousness gregarious bdm.quant body mass quartile latitude Latitude in decimel degrees habitat Type of habitat: Rural or urban flock Flock size (individuals) bodymass body mass (g)
DOI: 10.5061/dryad.6781kg7
title: Data from: Earthworms affect growth and competition between ectomycorrhizal and arbuscular mycorrhizal plants

description: Previous research showed that during intermediate stages of primary
 succession, when vegetation is dominated by ectomycorrhizal (EcM) shrubs
 and trees, site colonization by earthworms substantially alters plant
 communities. Research has also shown that EcM shrubs and trees suppress
 arbuscular mycorrhizal (AM) plants in the understory. To determine whether
 earthworm activity reduces this asymmetric competition, we conducted a
 full factorial laboratory experiment in which we grew EcM Betula pendula
 and AM Tripleurospermum inodorum, together or apart, in soils affected or
 not affected by earthworms. When both plants were grown together in soil
 unaffected by earthworms, growth of T. inodorum was significantly reduced
 by competition with B. pendula, but B. pendula growth was not reduced by
 T. inodorum. In soil affected by earthworms, the growth of both species
 was increased, and the negative effect of B. pendula on T. inodorum was no
 longer statistically significant (P &lt; 0.05). These data indicate
 that earthworms weaken the asymmetric competition between EcM and AM
 plants. Consistent with this inference, EcM colonization of B. pendula was
 decreased and AM fungal bioassay in soil was increased by earthworms.
description: Data-Frouz et al.,
 2019Codes and relevant data
 are described separately in each excel sheet.
DOI: 10.5061/dryad.7j43s83
title: Data from: Drought soil legacy overrides maternal effects on plant growth

description: 1.Maternal effects (i.e., trans‐generational plasticity) and soil legacies
 generated by drought and plant diversity can affect plant performance and
 alter nutrient cycling and plant community dynamics. However, the relative
 importance and combined effects of these factors on plant growth dynamics
 remain poorly understood. 2.We used soil and seeds from an existing plant
 diversity and drought manipulation field experiment in temperate grassland
 to test maternal, soil drought and diversity legacy effects, and their
 interactions, on offspring plant performance of two grassland species
 (Alopecurus pratensis and Holcus lanatus) under contrasting glasshouse
 conditions. 3.Our results showed that drought soil legacy effects eclipsed
 maternal effects on plant biomass. Drought soil legacy effects were
 attributed to changes in both abiotic (i.e., nutrient availability) and
 biotic soil properties (i.e., microbial carbon, enzyme activity), as well
 as plant root and shoot atom 15N excess. Further, plant tissue nutrient
 concentrations and soil microbial C:N responses to drought legacies varied
 between the two plant species and soils from high and low plant diversity
 treatments. However, these diversity effects did not affect plant root or
 shoot biomass. 4.These findings demonstrate that while maternal effects
 resulting from drought occur in grasslands, their impacts on plant
 performance are likely minor relative to drought legacy effects on soil
 abiotic and biotic properties. This suggests that soil drought legacy
 effects could become increasingly important drivers of plant community
 dynamics and ecosystem functioning as extreme weather events become more
 frequent and intense with climate change.
description: De_Long_maternal_drought_legacy_field_diversity_dataThis file contains data in De Long et al. 2019 “Drought soil legacy overrides maternal effects on plant growth”. These data are the field data collected on plant diversity and the percentage cover of the two target species, Alopecurus pratensis and Holcus lanatus.De_Long_maternal_drought_legacy_field_moisture_dataThis file contains data in De Long et al. 2019 “Drought soil legacy overrides maternal effects on plant growth”. These data are the field data collected on soil moisture.De_Long_maternal_drought_legacy_glasshouse_dataThis file contains data in De Long et al. 2019 “Drought soil legacy overrides maternal effects on plant growth”. These data are the field data collected from the glasshouse on the two target species, Alopecurus pratensis and Holcus lanatus and their soil properties.De_Long_maternal_drought_legacy_seed_dataThis file contains data in De Long et al. 2019 “Drought soil legacy overrides maternal effects on plant growth”. These data are the seed data collected on the two target species, Alopecurus pratensis and Holcus lanatus.
DOI: 10.5061/dryad.n42dd20
title: Data from: Biogeography of plant root-associated fungal communities in the North-Atlantic region mirrors climatic variability

description: Aim Polar and alpine ecosystems appear to be particularly sensitive to
 increasing temperatures and the altered precipitation patterns linked to
 climate change. However, little is currently known about how these
 environmental drivers may affect edaphic organisms within these
 ecosystems. In this study, we examined communities of plant
 root-associated fungi (RAF) over large biogeographic scales and along
 climatic gradients in the North Atlantic region in order to gain insights
 into the potential effects of climate variability on these communities. We
 also investigated whether selected fungal traits were associated with
 particular climates. Locations Austria, Scotland, Mainland Norway,
 Iceland, Jan Mayen and Svalbard Taxa Root fungi associated with the
 ectomycorrhizal and herbaceous plant Bistorta vivipara Methods DNA
 metabarcoding of the ITS1 region was used to characterize the RAF of 302
 whole plant root systems, which were analyzed by means of ordination
 methods and linear modelling. Fungal spore length, width, volume and
 shape, as well as mycelial exploration type of ectomycorrhizal (ECM)
 basidiomycetes were summarized at a community level. Results The RAF
 communities exhibited strong biogeographic structuring, and both
 compositional variation as well as fungal species richness correlated with
 annual temperature and precipitation. In accordance with general island
 biogeography theory, the least speciose RAF communities were found on Jan
 Mayen, a remote and small island in the North Atlantic Ocean. Fungal
 spores tended to be more elongated with increasing latitude. We also
 observed a climate effect on which mycelial exploration type was
 dominating among the ectomycorrhizal fungi. Main conclusions. Both
 geographic and environmental variables were important for shaping root
 associated fungal communities at a North-Atlantic scale, including the
 High Arctic. Fungal OTU richness followed general biogeographical patterns
 and decreased with decreasing size and/or increasing isolation of the host
 plant population. The probability of possessing more elongated spores
 increases with latitude, which may be explained by a selection for greater
 dispersal capacity among more isolated host plant populations in the
 Arctic.
description: New_data_for_this_publDemultiplexed, quality filtered, denoised, inflated data. Needs to be run with ITSx before use.denoised_inflatedN.fasta
DOI: 10.5061/dryad.rm041kb
title: Data from: How stabilizing selection and nongenetic inheritance combine to shape the evolution of phenotypic plasticity

description: Relatively little is known about whether and how nongenetic inheritance
 interacts with selection to impact the evolution of phenotypic plasticity.
 Here, we empirically evaluated how stabilizing selection and a common form
 of nongenetic inheritance––maternal environmental effects––jointly
 influence the evolution of phenotypic plasticity in natural populations of
 spadefoot toads. We compared populations that previous field work has
 shown to have evolved conspicuous plasticity in resource-use phenotypes
 (‘resource polyphenism’) with those that, owing to stabilizing selection
 favouring a narrower range of such phenotypes, appear to have lost this
 plasticity. We show that: 1) this apparent loss of plasticity in nature
 reflects a condition-dependent maternal effect and not a genetic loss of
 plasticity; i.e., ‘genetic assimilation’, and 2) this plasticity is not
 costly. By shielding non-costly plasticity from selection, nongenetic
 inheritance generally, and maternal effects specifically, can preclude
 genetic assimilation from occurring and consequently impede adaptive
 (genetic) evolution.
description: Lab morphology
 dataData from the laboratory
 portion of the experimentlab.experiment.data.csvVariation in field measurementsCoefficients of variation for field datafield.variation.data.csv
DOI: 10.5061/dryad.6h5v2pv
title: Data from: Long-term recovery of the functional community assembly and carbon pools in an African tropical forest succession

description: On the African continent, the population is expected to expand fourfold in
 the next century, which will increasingly impact the global carbon cycle
 and biodiversity conservation. Therefore, it is of vital importance to
 understand how carbon stocks and community assembly recover after
 slash-and-burn events in tropical second-growth forests. We inventoried a
 chronosequence of 15 1-hectare plots in lowland tropical forest of the
 central Congo Basin and evaluated changes in aboveground and soil organic
 carbon stocks and in tree species diversity, functional composition and
 community-weighted functional traits with succession. We aimed to track
 long-term recovery trajectories of species and carbon stocks in secondary
 forests, comparing 5 to 200+ year old secondary forest with reference
 primary forest. Along the successional gradient, the functional
 composition followed a trajectory from resource acquisition to resource
 conservation, except for nitrogen-related leaf traits. Despite a fast
 initial recovery of species diversity and functional composition, there
 were still important structural and carbon stock differences between
 old-growth secondary and pristine forest, which suggests that a full
 recovery of secondary forests might take much longer than currently shown.
 As such, the aboveground carbon stocks of 200+ year old forest were only
 57% of those in the pristine reference forest, which suggests a slow
 recovery of aboveground carbon stocks, although more research is needed to
 confirm this observation. The results of this study highlight the need for
 more in-depth studies on forest recovery in Central Africa, to gain
 insight into the processes that control biodiversity and carbon stock
 recovery.
description: Supplementary
 InformationRaw data underlying the
 analyses in the publication.
DOI: 10.5061/dryad.72gm17m
title: Data from: Playing out Liem's Paradox: opportunistic piscivory across Lake Tanganyikan cichlids

description: Trophic specialization is a key feature of the diversity of cichlid fish
 adaptive radiations. However, Liem (1980) observed that even species with
 highly specialized trophic morphologies have dietary flexibility, enabling
 them to exploit episodic food resources opportunistically. Evidence for
 dietary flexibility comes largely from laboratory studies, and it is
 unclear whether cichlid fishes undergo diet shifts in the wild. We report
 observations of diet switching by multiple cichlid species in Lake
 Tanganyika as a consequence of unusual concentrations of schooling
 juvenile clupeid fishes. Fish species with varying degrees of trophic
 specialization converged on a single prey: juvenile sardines that are also
 endemic to Lake Tanganyika (Stolothrissa tanganicae and Limnothrissa
 miodon). We provide evidence for cichlid species acting as
 jacks-of-all-trades and discuss this evidence in the framework of Liem’s
 classic paradox: that trophic specialization does not preclude dietary
 flexibility.
description: Trait and relative
 abundance data on Lake Tanganyikan cichlids observed at the micro-habitat
 scaleData includes scientific
 names and trait data compiled for Lake Tanganyikan cichlids observed near
 a school of juvenile clupeids near Kigoma, Tanzania.frenzy_jgb19.xlsx
DOI: 10.5061/dryad.1q33s69
title: Data from: Phylogeography and species-limits in the red-shouldered hawk (Buteo lineatus): characterization of the northern Florida suture zone in birds

description: The North American red-shouldered hawk, Buteo lineatus, is comprised of
 two widely allopatric eastern and western populations with an additional
 well-marked subspecies in the Florida peninsula. The two eastern
 populations meet in northern Florida, the location of a well-known suture
 zone in many non-avian organisms. We sequenced the complete mitochondrial
 ND2 gene and two nuclear introns to investigate its genetic population
 structure and species status. No mitochondrial haplotypes were shared
 between the eastern and western populations, and genetic variance among 14
 populations was 0.42; almost all of this (0.40) was distributed among the
 three regions. A clade of haplotypes very common in the Florida peninsula
 decreased in frequency elsewhere and, when modeled as a hybrid zone, had
 an estimated width of 1158km with a center near Ocala, FL. Ecological
 niche modeling suggests the western, eastern, and Florida peninsula
 populations were geographically isolated during the last glacial maximum.
 We consider these to represent three phylogenetic species. A coalescent
 analysis incorporating incomplete lineage sorting and gene tree
 uncertainty also suggested the divergence between the western and eastern
 populations is consistent with species-level divergence. With the addition
 of this hawk, four avian species are now known to hybridize along the Gulf
 Coast of the U.S. in or near the Northern Florida Suture Zone. The widths
 of these avian zones vary substantially (176km-1158km), and appear to
 reflect magnitude of gene flow, rather than extent of genetic
 differentiation. None of these birds was suggested as possible exemplars
 in the original description of the suture zone. Of the six species that
 were so identified, three have been surveyed to date, but none of those
 was found to be genetically differentiated.
description: Comparative-data_HybridZone_correlation_2019-04-04data for correlation analysisButeo_lineatus_Specimen_LatLongdata for MAXENTRsHawk_Specimen_EcoVariable_Correlation_Matrixdata for MAXENTButeo_lineatus_ND2_haps_hybrid_zone_SASdata for SAS logistic regressionMelanerpes_carolinus_ND2_haps_hybrid_zone_SASdata for SAS logistic regressionPoecile_carolinensis_mtDNA-RestrictionSites_SASdata for SAS logistic regressionStrix_varia_mtDNA-ControlRegion_haps_hybrid_zone_SASdata for SAS logistic regressionButeo_3genes_BPPBPP control fileButeo_3genes_BPPBPP geography imap fileButeo_3genes_heredity_BPPBPP heredity file: haploid vs diploid lociButeo_3genes_sequences_BPPBPP DNA sequencesB_lineatus-G3PDH-3groupsButeo lineatus G3PDH DNA script and sequences for ArlequinB_lineatus-ND2-3groupsButeo lineatus ND2 script and sequences for ArlequinB_lineatus-TGFB2-3groupsButeo lineatus TGFB2 DNA sequences and script for ArlequinB_lineatus-ND2-CA_vs_EastButeo lineatus ND2 DNA sequence file for east vs west Arlequin analysis
DOI: 10.5061/dryad.r69v7gp
title: Data from: Insights on the functional composition of specialist and generalist birds throughout continuous and fragmented forests

description: A decline in species number often occurs after forest fragmentation and
 habitat loss, which usually results in the loss of ecological functions
 and a reduction in functional diversity in the forest fragments. However,
 it is uncertain whether these lost ecological functions are consistently
 maintained throughout continuous forests, and so the importance of these
 functions in continuous forests remains unknown. Point counts were used to
 assess both the taxonomic and functional diversity of specialist and
 generalist birds from sampling in a continuous primary forest compared
 with forest fragments in order to investigate the responses of these
 groups to forest fragmentation. We also measured alpha and beta diversity.
 The responses of specialists and generalists were similar when we assessed
 all bird species but were different when only passerines were considered.
 When examining passerines we found lower total taxonomic beta diversity
 for specialists than for generalists in the continuous forest, while
 taxonomic beta diversity was higher in the fragmented forest and similar
 between bird groups. However, total functional beta‐diversity values
 indicated clearly higher trait regularity in continuous forest for
 specialists and higher trait regularity in fragments for generalists.
 Specialists showed significantly higher functional alpha diversity in
 comparison with generalists in the continuous forest, while both groups
 showed similar values in fragments. In passerines, species richness and
 alpha functional diversity of both specialist and generalist were
 explained by forest connectivity; but, only fragment size explained those
 parameters for specialist passerines. We suggest that considering subsets
 of the community with high similarity among species, as passerines,
 provides a better tool for understanding responses to forest
 fragmentation. Due to the regularity of specialists in continuous forest,
 their lost could highly affect functionality in forest fragments.
description: OccurrencesOccurrences of bird species in fragments and continuous forest.LandscapesLandscapes parameters of fragments and continuous forests.