cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1346
title: Data from: AFLP genome scan in the black rat (Rattus rattus) from Madagascar: detecting genetic markers undergoing plague-mediated selection

description: The black rat (Rattus rattus) is the main reservoir of plague (Yersinia
 pestis infection) in Madagascar's rural zones. Black rats are highly
 resistant to plague within the plague focus (central highland), whereas
 they are susceptible where the disease is absent (low altitude zone). To
 better understand plague wildlife circulation and host evolution in
 response to a highly virulent pathogen, we attempted to determine genetic
 markers associated with plague resistance in this species. To this
 purpose, we combined a population genomics approach and an association
 study, both performed on 249 AFLP markers, in Malagasy R. rattus.
 Simulated distributions of genetic differentiation were compared to
 observed data in four independent pairs, each consisting of one population
 from the plague focus and one from the plague-free zone. We found 22 loci
 (9% of 249) with higher differentiation in at least two independent
 population pairs or with combining p-values over the four pairs
 significant. Among the 22 outlier loci, 16 presented significant
 association with plague zone (plague focus vs. plague-free zone).
 Population genetic structure inferred from outlier loci was structured by
 plague zone, whereas the neutral loci dataset revealed structure by
 geography (eastern vs. western populations). A phenotype association study
 revealed that two of the 22 loci were significantly associated with
 differentiation between dying and surviving rats following experimental
 plague challenge. The 22 outlier loci identified in this study may undergo
 plague selective pressure either directly or more probably indirectly due
 to hitchhiking with selected loci.
description: AFLP dataset for
 population analysesAFLP data matrix for the
 239 Malagasy R. rattus individuals genotyped for 249 AFLP markers.The two
 first columns identify the individual (individual name and population) and
 the 249 following columns are AFLP data (marker names are indicated in the
 first line, 1: presence of the peak, 0: absence).dataset_pop.txtAFLP dataset for experimental plague challenge analysesAFLP data matrix for the 249 AFLP markers in 103 Malagasy R. rattus plague-challenged individuals.The first columns identifies the individual (individual name), the second column refers to the experiment (low dose challenge or high dose challenge), the third column refers to the challenge issue (D: dying or S: surviving) and the 249 following columns are AFLP data (marker names are indicated in the first line, 1: presence of the peak, 0: absence).dataset_infect.txt
DOI: 10.5061/dryad.35q01
title: Data from: Resistance of plant–plant networks to biodiversity loss and secondary extinctions following simulated environmental changes

description: 1. Plant interactions are fundamental processes for structuring plant
 communities and are an important mechanism governing the response of plant
 species and communities to environmental changes. Thus, understanding the
 role played by the interaction network in modulating the impact of
 environmental changes on plant community composition and diversity is
 crucial. Here, we aimed to develop a new analytical and conceptual
 framework to evaluate the responses of plant communities to environmental
 changes. 2. This framework uses functional traits as sensitivity measures
 for simulated environmental changes and assesses the consequences of
 microhabitat loss. We show here its application to an alpine plant
 community where we recorded functional traits (specific leaf area [SLA]
 and leaf dry matter content [LDMC]) of all plants associated with three
 foundation species or the surrounding open areas. We then simulated
 primary species loss based on different scenarios of environmental change
 and explored community persistence to the loss of foundation species. 3.
 Generally, plant community responses differed among environmental change
 scenarios. In a scenario of increasing drought alone (i.e. species with
 lower LDMC were lost first) or increasing drought with increasing
 temperature (i.e. species with lower LDMC and higher SLA were lost first),
 the plant community resisted because drought-tolerant foundation species
 tolerated those deteriorating conditions. However, in a scenario with
 increasing nitrogen input (i.e. species having lower SLA were lost
 earlier), foundation species accelerated species loss due to their early
 primary extinctions and the corresponding secondary extinctions of species
 associated to their microhabitat. 4. The resistance of a plant community
 depends on the driver of environmental change, meaning that the prediction
 of the fate of this system is depending on the knowledge of the main
 driver of environmental change. Our framework provides a mechanistic
 understanding of an ecosystem response to such environmental changes
 thanks to the integration of biology-informed criteria of species
 sensitivities to environmental factors into a network of interacting
 species.
description: Plant facilitation
 network simulationThe table (task2)
 contains information about the simulated environmental changes and plant
 network response. scenario: environmental change driver; q: n. step;
 network.size: species richness; prim.ext: primary extinctions; sec.ext:
 secondary extinctions; centr: network centrality; species: 1= present, 0=
 primary extinct, -1= secondary extinct.task2.RData
DOI: 10.5061/dryad.r8f277f
title: Data from: Spatiotemporal use predicts social partitioning of bottlenose dolphins with strong home range overlap

description: Ranging behaviour and temporal patterns of individuals are known to be
 fundamental sources of variation in social networks. Spatiotemporal
 dynamics can both provide and inhibit opportunities for individuals to
 associate, and should therefore be considered in social analysis. This
 study investigated the social structure of a Lahille’s bottlenose dolphin
 (Tursiops truncatus gephyreus) population, which shows different
 spatiotemporal patterns of use and gregariousness between individuals. For
 this we constructed an initial social network using association indices
 corrected for gregariousness and then uncovered affiliations from this
 social network using generalized affiliation indices. The
 association-based social network strongly supported that this dolphin
 population consists of four social units highly correlated to
 spatiotemporal use patterns. Excluding the effects of gregariousness and
 spatiotemporal patterns, the affiliation-based social network suggested an
 additional two social units. Although the affiliation-based social units
 shared a large part of their core areas, space and/or time use by
 individuals of the different units were generally distinct. Four of the
 units were strongly associated with both estuarine and shallow coastal
 areas, while the other two units were restricted to shallow coastal waters
 to the south (SC) and north of the estuary (NC), respectively.
 Interactions between individuals of different social units also occurred,
 but dolphins from the NC were relatively more isolated and mainly
 connected to SC dolphins. From a conservation management perspective, it
 is recommended that information about the dolphin social units should be
 incorporated in modelling intra-population dynamics and viability, as well
 as for investigating patterns of gene flow among them.
description: Individual sightings and
 parameters of Lahille’s bottlenose dolphinsData organized to entry
 in the SocProg program and formulation of maps using Arcmap and estimates
 of home range in the Software R. CMD in the supplemental plan refers to
 Community Division by Modularity.Data for Dryad - Genoves et
 al.xlsx
DOI: 10.5061/dryad.4g200
title: Data from: Living in flowing water increases resistance to ultraviolet B radiation

description: Ultraviolet B radiation (UV-B) is an important environmental driver that
 can affect locomotor performance negatively by inducing production of
 reactive oxygen species (ROS). Prolonged regular exercise increases
 antioxidant activities, which may alleviate the negative effects of
 UV-B-induced ROS. Animals naturally performing exercise, such as humans
 performing regular exercise or fish living in flowing water, may therefore
 be more resilient to the negative effects of UV-B. We tested this
 hypothesis in a fully factorial experiment, where we exposed mosquitofish
 (Gambusia holbrooki) to UV-B and control (no UV-B) conditions in flowing
 and still water. We show that fish exposed to UV-B and kept in flowing
 water had increased sustained swimming performance (Ucrit), increased
 antioxidant defences (catalase activity and glutathione concentrations)
 and reduced cellular damage (lipid peroxidation and protein carbonyl
 concentrations) compared with fish in still water. There was no effect of
 UV-B or water flow on resting or maximal rates of oxygen consumption. Our
 results show that environmental water flow can alleviate the negative
 effects of UV-B-induced ROS by increasing defence mechanisms. The
 resultant reduction in ROS-induced damage may contribute to maintain
 locomotor performance. Hence, the benefits of regular exercise are
 ‘transferred’ to improve resilience to the negative impacts of UV-B.
 Ecologically, the mechanistic link between responses to different habitat
 characteristics can determine the success of animals. These dynamics have
 important ecological connotations when river or stream flow changes as a
 result of weather patterns, climate or human modifications.
description: Ghanizadeh et al_Dryad
 data fileAll data associated with
 this ms.
DOI: 10.5061/dryad.rh67h
title: Data from: Archaeopedological analysis of colluvial deposits in favourable and unfavourable areas: reconstruction of land use dynamics in SW Germany

description: Colluvial deposits, as the correlate sediments of human induced soil
 erosion, depict an excellent archive of land use and landscape history as
 representatives of human-environment interactions. This study establishes
 a chronostratigraphy of colluvial deposits and reconstructs past land use
 dynamics in the Swabian Jura, the Baar and the Black Forest in SW Germany.
 In the agriculturally favourable Baar area multiple main phases of
 colluvial deposition, and thus intensified land use, can be identified
 from the Neolithic to the Modern Times. In the unfavourable Swabian Jura
 increased colluvial deposition began later compared to the more favourable
 areas in the Baar. The same holds true for the unfavourable areas of the
 Black Forest, but intensified land use can only be reconstructed for the
 Middle Ages and Early Modern times instead of for the Bronze and Iron Age
 as in the Swabian Jura. Land use intensity and settlement dynamics
 represented by thick, multi-layered colluvial deposits increase in the
 Baar and the Black Forest during the Middle Ages. In-between those phases
 of geomorphodynamic activity and colluviation, stable phases occur,
 interpreted as phases with sustainable land use or without human presence.
description: Chemical_physical_soil_properties_colluvial_soils_GermanyLab results of soil samples from the SFB1070 B2 Project.Henkner_et_al_2017_Chemical_physical_soil_properties_colluvial_soils_SW_Germany_SFB1070_B02.csvHenkner_et_al_2017_Chemical_physical_soil_properties_colluvial_soils_SW_Germany_SFB1070_B02_README.txt14C_dating_charcoals_colluvial_deposits_pollen_GermanyAMS-14C dating of charcoals sampled from colluvial deposits and of bog peat.Henkner_et_al_2017_AMS14C_dating_charcoals_colluvial_deposits_pollen_SW_Germany_SFB1070_B02.csvHenkner_et_al_2017_AMS14C_dating_charcoals_colluvial_deposits_pollen_SW_Germany_SFB1070_B02_README.txtSoil_profile_descriptions_colluvial_soils_GermanyArchaeopedological analyses of colluvium: A proxy for regional land use history in southwest Germany.Henkner_et_al_ 2017_Soil_profile_descriptions_colluvial_soils_SW_Germany_SFB1070_B02.xlsxHenkner_et_al_ 2017_Soil_profile_descriptions_colluvial_soils_SW_Germany_SFB1070_B02_README.txtOSL_datings_colluvial_deposits_GermanyOSL datings of colluvial deposits in southwestern GermanyFuchs_Henkner_et_al_2017_OSL_datings_colluvial_deposits_SW_Germany_SFB1070_B02.csvFuchs_Henkner_et_al_2017_OSL_datings_colluvial_deposits_SW_Germany_SFB1070_B02_README.txt
DOI: 10.5061/dryad.ct528
title: Data from: More than one genotype: How common is intracolonial genetic variability in scleractinian corals?

description: In recent years, a few colonial marine invertebrates have shown
 intracolonial genetic variability, a previously unreported phenomenon.
 Intracolonial genetic variability describes the occurrence of more than a
 single genotype within an individual colony. This variability can be
 traced back to two underlying processes: chimerism and mosaicism.
 Chimerism is the fusion of two or more individuals, whereas mosaicism
 mostly derives from somatic cell mutations. Until now, it remained unclear
 to what degree the ecologically important group of hermatypic (reef
 building) corals might be affected. We investigate the occurrence of
 intracolonial genetic variability in five scleractinian corals: Acropora
 florida, Acropora hyacinthus, Acropora sarmentosa, Pocillopora species
 complex and Porites australiensis. The main focus was to test different
 genera for the phenomenon via microsatellite markers and to distinguish
 which underlying process caused the genetic heterogeneity. Our results
 show that intracolonial genetic variability was common (between 46.6% for
 A. sarmentosa and 23.8% for P. species complex) in all tested corals. The
 main process was mosaicism (69 cases of 222 tested colonies), but at least
 one chimera existed in every species. This suggests that intracolonial
 genetic variability is widespread in scleractinian corals and could
 challenge the view of a coral colony as an individual and therefore a unit
 of selection. However, it might also hold potential for colony survival
 under rapidly changing environmental conditions.
description: Acropora_Hyacinthus_dryadAcropora_Sarmentosa_dryadAcropora-florida_dryadPocillopora_species_complex_dryadPorites_australiensis_dryad
DOI: 10.5061/dryad.8sb5h
title: Data from: Platelet factor 4 and Duffy antigen required for platelet killing of Plasmodium falciparum

description: Platelets restrict the growth of intraerythrocytic malaria parasites by
 binding to parasitized cells and killing the parasite within. Here, we
 show that the platelet molecule platelet factor 4 (PF4 or CXCL4) and the
 erythrocyte Duffy-antigen receptor (Fy) are necessary for
 platelet-mediated killing of Plasmodium falciparum parasites. PF4 is
 released by platelets on contact with parasitized red cells, and the
 protein directly kills intraerythrocytic parasites. This function for PF4
 is critically dependent on Fy, which binds PF4. Genetic disruption of Fy
 expression inhibits binding of PF4 to parasitized cells and concomitantly
 prevents parasite killing by both human platelets and recombinant human
 PF4. The protective function afforded by platelets during a malarial
 infection may therefore be compromised in Duffy-negative individuals, who
 do not express Fy.
description: McMorran Figure
 1McMorran Figure
 2McMorran Figure
 3McMorran Figure
 4McMorran Figure
 S1McMorran Figure
 S3McMorran Figure
 S4McMorran Figure
 S5McMorran Figure
 S7McMorran Figure
 S8
DOI: 10.5061/dryad.750df
title: Data from: Selection for niche differentiation in mixed plant communities increases biodiversity effects

description: In experimental plant communities, relationships between biodiversity and
 ecosystem functioning have been found to strengthen over time, a fact
 often attributed to increased resource complementarity between species in
 mixtures and negative plant–soil feedbacks in monocultures. Here we show
 that selection for niche differentiation between species can drive this
 increasing biodiversity effect. Growing 12 grassland species in test
 monocultures and mixtures, we found character displacement between species
 and increased biodiversity effects when plants had been selected over 8
 years in species mixtures rather than in monocultures. When grown in
 mixtures, relative differences in height and specific leaf area between
 plant species selected in mixtures (mixture types) were greater than
 between species selected in monocultures (monoculture types). Furthermore,
 net biodiversity and complementarity effects were greater in mixtures of
 mixture types than in mixtures of monoculture types. Our study
 demonstrates a novel mechanism for the increase in biodiversity effects:
 selection for increased niche differentiation through character
 displacement. Selection in diverse mixtures may therefore increase species
 coexistence and ecosystem functioning in natural communities and may also
 allow increased mixture yields in agriculture or forestry. However, loss
 of biodiversity and prolonged selection of crops in monoculture may
 compromise this potential for selection in the longer term.
description: Schmid_2014-06-07391C_Pot_biomassBiomass data for experimental communities for Zuppinger-Dingley et al., Nature http://dx.doi.org/10.1038/nature13869Schmid_2014-06-07391C_Trait_DivergencePlant functional trait divergence (mean and differences in height, specific leaf area, and reproductive biomass) and functional diversity (Petchey & Gaston's FD) for Zuppinger-Dingley et al., Nature http://dx.doi.org/10.1038/nature13869Schmid_2014-06-07391C_Biodiversity_EffectsPartitioned biodiversity effects for Zuppinger-Dingley et al., Nature http://dx.doi.org/10.1038/nature13869
DOI: 10.5061/dryad.ck4h0
title: Data from: Individual, unit, and vocal clan level identity cues in sperm whale codas

description: The ‘social complexity hypothesis’ suggests that complex social structure
 is a driver of diversity in animal communication systems. Sperm whales
 have a hierarchically structured society in which the largest affiliative
 structures, the vocal clans, are marked on ocean-basin scales by
 culturally transmitted dialects of acoustic signals known as ‘codas’. We
 examined variation in coda repertoires among both individual whales and
 social units—the basic element of sperm whale society—using data from nine
 Caribbean social units across six years. Codas were assigned to
 individuals using photo-identification and acoustic size measurement, and
 we calculated similarity between repertoires using both continuous and
 categorical methods. We identified 21 coda types. Two of those (‘1+1+3’
 and ‘5R1’) made up 65% of the codas recorded, were shared across all units
 and have dominated repertoires in this population for at least 30 years.
 Individuals appear to differ in the way they produce ‘5R1’ but not ‘1+1+3’
 coda. Units use distinct 4-click coda types which contribute to making
 unit repertoires distinctive. Our results support the social complexity
 hypothesis in a marine species as different patterns of variation between
 coda types suggest divergent functions, perhaps representing selection for
 identity signals at several levels of social structure.
description: Coda interclick interval
 data from Gero et al Individual, unit, and vocal clan level identity cues
 in sperm whale codas in RSOSEastern Caribbean sperm
 whale coda inter-click interval dataset from Gero et al. Individual, unit,
 and vocal clan level identity cues in sperm whale codas in
 RSOSCoda
 interclick intervals from Gero et al Individual, unit, and vocal clan
 level identity cues in sperm whale codas in
 RSOS.xlsx
DOI: 10.5061/dryad.40sh435
title: Data from: The evolution of fungal substrate specificity in a widespread group of crustose lichens

description: Lichens exhibit varying degrees of specialization with regard to the
 surfaces they colonize, ranging from substrate generalists to strict
 substrate specialists. Though long recognized, the causes and consequences
 of substrate specialization are poorly known. Using a phylogeny of a
 150-200 MYA clade of lichen fungi, we asked whether substrate niche is
 phylogenetically conserved, which substrates are ancestral, whether
 specialists arise from generalists or vice versa, and how specialization
 affects speciation/extinction processes. We found strong phylogenetic
 signal for niche conservatism. Specialists evolved into generalists and
 back again, but transitions from generalism to specialism were more common
 than the reverse. Our models suggest that for this group of fungi,
 “escape” from specialization for soil, rock and bark occurred, but
 specialization for wood foreclosed evolution away from that substrate
 type. In parallel, speciation models showed positive diversification rates
 for soil and rock dwellers but not other specialists. Patterns in the
 studied group suggest that fungal substrate specificity is a key
 determinant of evolutionary trajectory for the entire lichen symbiosis.
description: Data, phylogenetic trees
 and R scripts used to generate resultsThis data package
 accompanies the manuscript "Substrate specificity influences the
 evolutionary trajectory of the constituent fungus in a widespread group of
 crustose lichens" by Philipp Resl, Fernando Fernández-Mendoza, Helmut
 Mayrhofer and Toby Spribille. It includes data, phylogenetic trees and R
 scripts used to generate results.lichen_substrate_evolution_data.zip
DOI: 10.5061/dryad.k5912k6
title: Data from: A continent-scale test of multiple hypotheses on the abundances of Neotropical birds

description: Explaining variation in the abundance of species remains a challenge in
 ecology. We sought to explain variation in abundance of Neotropical forest
 birds using a dataset of population densities of 596 species. We tested a
 priori hypotheses for the roles of species traits, environmental factors,
 and species interactions. Specifically, we focused on four factors: 1)
 body mass (trait); 2) habitat type (environmental factor), 3) net primary
 productivity (NPP; environmental factor); and 4) species richness of
 competitors (species interaction). Body size explained much variation in
 density, although only when analyzed at higher taxonomic levels. Habitat
 type was a strong predictor of density. The relationship between density
 and productivity was weak. Densities were related negatively to the
 species richness of heterospecifics, however – this trend was particularly
 strong within closely related groups. Our results show that the influence
 of energetic factors such as body size and productivity depends on
 phylogeny, and they act through indirect relations with other variables;
 alternative ecological factors such as habitat structure and species
 interactions play a more direct and stronger role in determining abundance
 than previously thought.
description: DataA1Final dataset used to
 generate results of this publication. Note that you must take the medians
 for each taxon to reproduce the results.MetadataA1