cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.k30v3
title: Data from: Relation between stability and resilience determines the performance of early warning signals under different environmental drivers

description: Shifting patterns of temporal fluctuations have been found to signal
 critical transitions in a variety of systems, from ecological communities
 to human physiology. However, failure of these early warning signals in
 some systems calls for a better understanding of their limitations. In
 particular, little is known about the generality of early warning signals
 in different deteriorating environments. In this study, we characterized
 how multiple environmental drivers influence the dynamics of laboratory
 yeast populations, which was previously shown to display alternative
 stable states [Dai et al., Science, 2012]. We observed that both the
 coefficient of variation and autocorrelation increased before population
 collapse in two slowly deteriorating environments, one with a rising death
 rate and the other one with decreasing nutrient availability. We compared
 the performance of early warning signals across multiple environments as
 “indicators for loss of resilience.” We find that the varying performance
 is determined by how a system responds to changes in a specific driver,
 which can be captured by a relation between stability (recovery rate) and
 resilience (size of the basin of attraction). Furthermore, we demonstrate
 that the positive correlation between stability and resilience, as the
 essential assumption of indicators based on critical slowing down, can
 break down in this system when multiple environmental drivers are changed
 simultaneously. Our results suggest that the stability–resilience relation
 needs to be better understood for the application of early warning signals
 in different scenarios.
description: data_deteriorationdata_SUCbifurcationdata_SUCindicator
DOI: 10.5061/dryad.65cq4
title: Data from: Roles of pathogens on replacement of tree seedlings in heterogeneous light environments in a temperate forest: a reciprocal seed sowing experiment

description: 1. In forest communities, the Janzen–Connell (J-C) hypothesis proposes
 that species diversity is maintained by non-competitive distance- and/or
 density-dependent seedling mortality caused by host-specific natural
 enemies. However, the effects of pathogen associations from nearby
 conspecifics vs. heterospecifics remain unknown in spatially heterogeneous
 light environments. 2. Seeds of hardwood species Cornus controversa
 (Cornus) and Prunus grayana (Prunus) were sown beneath 6–7 Cornus and
 Prunus adults in both the forest understory (FU) and in gaps (Gap) created
 by felling all woody vegetation near the focal adults. Seedling growth,
 mortality, killing agents (e.g. pathogens that cause damping-off and leaf
 diseases), and root infection by arbuscular mycorrhizal fungi (AMF) were
 investigated. 3. We found strong habitat effects on the expression of soil
 fungi beneath both tree species. Seedling mortality caused by soil-borne
 damping-off pathogens was greater in FU than in Gap, and AMF infection,
 which enhanced relative seedling growth rate, was greater in Gap than in
 FU. Seedling mortality caused by damping-off pathogens did not differ
 between Cornus and Prunus seedlings beneath the adults of conspecific or
 heterospecific adults in both FU and Gap, suggesting little
 distance-dependence or host preference in the fungus. 4. Beneath the
 adults of Cornus and Prunus, the most prevalent leaf diseases were zonate
 leaf blight and angular leaf spot caused by the airborne pathogenic fungi
 Haradamyces foliicola and Phaeoisariopsis pruni-grayanae, respectively.
 Although these pathogens attacked the seedlings of both species,
 conspecific seedlings (i.e. home) showed more severe leaf damage, earlier
 leaf shedding and/or less defensive behaviour (cell wall defence) relative
 to heterospecific seedlings (i.e. away), suggesting negative
 distance-dependent attack (i.e. host preference) for these leaf diseases.
 As a result, greater seedling mortality was observed for conspecific
 seedlings under both FU and Gap treatments. 5. Synthesis. In the temperate
 forest, the J-C hypothesis is largely mediated through the strong negative
 influence of airborne leaf diseases rather than through soil-borne
 damping-off pathogens. We found that airborne diseases demonstrated
 distance-dependent host preferences, which led to greater conspecific
 seedling damage regardless of environmental light conditions.
description: Bayandala_JEcol_rawdata
DOI: 10.5061/dryad.rq8n5
title: Data from: Competition is a strong driving factor in wetlands, peaking during drying out periods

description: The aim of the study is to investigate the relative importance of
 plant-plant interactions with regard to flooding and drought effect on
 perennial plant performances in wetlands. Flooding is expected to be the
 major driver and, accordingly, the importance of drought is hardly if ever
 taken into account. Focusing on five widespread species, the growth, the
 survival and the competitive ability of plants were monitored on permanent
 plots spread along two elevation gradients. Flooding duration and drought
 intensity were found to vary substantially along the ~ 0.5 meter range
 elevation gradient. Flooding and drought alternate over the hydrological
 year and the pin-point surveys were thus conducted over the course of one
 year. The data were modeled taking into account survival, recruitment and
 competitive growth throughout flooding and drying out periods. Flooding
 and drought both directly impacted the plant performances and their
 competitive effect, with the effect of drought being much more general
 among species and of higher magnitude than flooding. The importance of
 competition was found to be high for all species, particularly during the
 drying out period. It varied more along the flooding gradient than along
 the drought gradient. The higher flooding tolerance shown by the studied
 species compared to drought may be related to species specific growth
 timing together with efficient response traits. These results offer new
 insights into the filters operating over the species pools. This suggests
 that the drying out period and drought conditions may be even more
 important for species’ relative success and the importance of competition
 than the flooding pattern. The general applicability of this result,
 obtained in mild Atlantic climate and fertile wetlands, remains to be
 studied.
description: pin points reading along
 elevation gradients in wetlandsThis data corresponds to
 the reading of plant vegetation surveys conducted on plots 25x25 cm large,
 with 18 readings (R1 to R18) on each plot. Each count is the number of
 hits per species. They were recorded on 70 plots, 25 x 25cm large, placed
 every 20 cm along two elevation transects used as replicates (35 plots per
 sequence). Plots were proteted from grazing by cattle and horses. On each
 plot, vegetation relevés were performed along both diagonals using the
 pinpoint method, with a record every 4 cm. Three readings were made: on
 the 23-29 October, 2008 (Year 1, period 2), on the 3-12 June, 2009 (Year
 2, period 1) and on the 19-20 October, 2009 (Year 2, period 2). Aeration
 Sum Exceedance values were measured based on water table field monitoring,
 and foflowing Gowing et al. 1998. Predicting the effect of change in water
 regime on plant communities. In: Wheater H, Kirby C, editors. Hydrology in
 a Changing Environment vol. I. John Wiley, Chichester: pp.
 473–483pinpointMP.xlsx
DOI: 10.5061/dryad.28fb0
title: Data from: Reconstructing the origin and dispersal patterns of village chickens across East Africa: insights from autosomal markers

description: Unravelling the genetic history of any livestock species is central to
 understanding the origin, development and expansion of agricultural
 societies and economies. Domestic village chickens are widespread in
 Africa. Their close association with, and reliance on, humans for long
 range dispersal makes the species an important biological marker in
 tracking cultural and trading contacts between human societies and
 civilisations across time. Archaezoological and linguistic evidences
 suggest a complex history of arrival and dispersion of the species on the
 continent, with mitochondrial DNA (mtDNA) D-loop analysis revealing the
 presence of five distinct haplogroups in East African village chicken,
 supporting the importance of the region in understanding the history of
 the species and indirectly, of human interactions. Here, through a
 detailed analysis of 30 autosomal microsatellite markers genotyped in 657
 village chickens from four East African countries (Kenya, Uganda, Ethiopia
 and Sudan), we identify three distinct autosomal gene pools (I, II and
 III). Gene pool I is predominantly found in Ethiopia and Sudan, while II
 and III occur both in Kenya and Uganda. A gradient of admixture for gene
 pools II and III between the Kenyan coast and Uganda’s hinterland (P =
 0.001) is observed, while gene pool I is clearly separated from the other
 two. We propose that these three gene pools represent genetic signatures
 of separate events in the history of the continent that relate to the
 arrival and dispersal of village chicken and humans across the region. Our
 results provide new insights on the history of chicken husbandry which has
 been shaped by terrestrial and maritime contacts between ancient and
 modern civilisations in Asia and East Africa.
description: Genotypes of Indigenous
 chicken from East AfricaEastAfricaOnly.txt
DOI: 10.5061/dryad.6t6t1
title: Data from: Variation in female mate preference in response to eavesdropping "interloper" males

description: Eavesdropping by conspecific males that are competing for mates has been
 demonstrated across a variety of taxa. However, few studies have
 investigated how eavesdropping may actually impact female mating
 decisions. Specifically, females may change their mating preferences based
 on whether the eavesdropping male varies in its phenotype (e.g.,
 expression of condition-indicating secondary sexual characters or
 courtship vigor) relative to the male that initiated courtship. We
 examined variation in female preferences in the context of eavesdropping
 in the brush-legged wolf spider, Schizocosa ocreata. Female S. ocreata
 typically prefer males with large tufts and males that court at higher
 rates. In live mating trials, however, females preferentially mated with
 the males that courted first. It has yet to be investigated whether female
 preferences change when males of varying phenotypes are encountered
 sequentially, as might be expected in an eavesdropping context. We used
 video playback experiments to introduce females to a virtual courting male
 (initial male), followed by a second virtual courting male thirty seconds
 later (interloper male). We separately manipulated 2 aspects of male
 courtship (tuft size and courtship vigor) to measure female responses to
 an interloper male of lower, higher, or equal phenotypic expression. For
 both traits, females had an overall preference for the initial males.
 However, when the interloper male had large tufts or had high courtship
 vigor, female S. ocreata shifted the relative number of their receptivity
 displays. These results suggest that eavesdropping could be beneficial for
 interloper males, but the benefits may vary depending on the male’s
 phenotype.
description: Interloper - courtship
 vigor - R analysis - MS visit analysis - Stoffer et al Beh
 EcoData used for Objective
 2Interloper trials - tuft
 size - MS analysis Aug 2015 - Stoffer et al Beh EcoPortion of data used for
 Objective 1 - tuft sizeInterloper trials - tuft
 size - MS analysis - Stoffer et al Beh EcoPortion of data used in
 Objective 1 - tuft size
DOI: 10.5061/dryad.ck276
title: Data from: Eurasian house mouse (Mus musculus L.) differentiation at microsatellite loci identifies the Iranian plateau as a phylogeographic hotspot

description: Background The phylogeography of the house mouse (Mus musculus L.), an
 emblematic species for genetic and biomedical studies, is only partly
 understood, essentially because of a sampling bias towards its most
 peripheral populations in Europe, Asia and the Americas. Moreover, the
 present-day phylogeographic hypotheses stem mostly from the study of
 mitochondrial lineages. In this article, we complement the mtDNA studies
 with a comprehensive survey of nuclear markers (19 microsatellite loci)
 typed in 963 individuals from 47 population samples, with an emphasis on
 the putative Middle-Eastern centre of dispersal of the species. Results
 Based on correspondence analysis, distance and allele-sharing trees, we
 find a good coherence between geographical origin and genetic make-up of
 the populations. We thus confirm the clear distinction of the three best
 described peripheral subspecies, M. m. musculus, M. m. domesticus and M.
 m. castaneus. A large diversity was found in the Iranian populations,
 which have had an unclear taxonomic status to date. In addition to samples
 with clear affiliation to M. m. musculus and M. m. domesticus, we find two
 genetic groups in Central and South East Iran, which are as distinct from
 each other as they are from the south-east Asian M. m. castaneus. These
 groups were previously also found to harbor distinct mitochondrial
 haplotypes. Conclusion We propose that the Iranian plateau is home to two
 more taxonomic units displaying complex primary and secondary
 relationships with their long recognized neighbours. This central region
 emerges as the area with the highest known diversity of mouse lineages
 within a restricted geographical area, designating it as the focal place
 to study the mechanisms of speciation and diversification of this species.
description: Microsatellite_data_Genetix_formatMicrosatellite data in genetix format used in the paper: Eurasian house mouse (Mus musculus L.) differentiation at microsatellite loci identifies the Iranian plateau as a phylogeographic hotspot
DOI: 10.5061/dryad.tf536
title: Data from: Increased transgenerational epigenetic variation, but not predictable epigenetic variants, after environmental exposure in two apomictic dandelion lineages

description: DNA methylation is one of the mechanisms underlying epigenetic
 modifications. DNA methylations can be environmentally induced and such
 induced modifications can at times be transmitted to successive
 generations. However, it remains speculative how common such
 environmentally induced transgenerational DNA methylation changes are and
 if they persist for more than one offspring generation. We exposed
 multiple accessions of two different apomictic dandelion lineages of the
 Taraxacum officinale group (Taraxacum alatum and T. hemicyclum) to drought
 and salicylic acid (SA) treatment. Using methylation-sensitive amplified
 fragment length polymorphism markers (MS-AFLPs) we screened anonymous
 methylation changes at CCGG restriction sites throughout the genome after
 stress treatments and assessed the heritability of induced changes for two
 subsequent unexposed offspring generations. Irrespective of the initial
 stress treatment, a clear buildup of heritable DNA methylation variation
 was observed across three generations, indicating a considerable
 background rate of heritable epimutations. Less evidence was detected for
 environmental effects. Drought stress showed some evidence for
 accession-specific methylation changes, but only in the exposed generation
 and not in their offspring. By contrast, SA treatment caused an increased
 rate of methylation change in offspring of treated plants. These changes
 were seemingly undirected resulting in increased transgenerational
 epigenetic variation between offspring individuals, but not in predictable
 epigenetic variants. While the functional consequences of these
 MS-AFLP-detected DNA methylation changes remain to be demonstrated, our
 study shows that (1) stress-induced transgenerational DNA methylation
 modification in dandelions is genotype and context-specific; and (2)
 inherited environmental DNA methylation effects are mostly undirected and
 not targeted to specific loci.
description: Preite_etal_2018_EcolEvol_HpaII_Rawdata_and_ConsensusData from: Preite et al. 2018 (DOI: 10.1002/ece3.3871) Increased transgenerational epigenetic variation, but not predictable epigenetic variants, after environmental exposure in two apomictic dandelion lineages. Excel file shows HpaII raw data (methylation sensitive -AFLPs), consensus and deviation from consensus across generations.
DOI: 10.15468/dl.fg375m
title: Occurrence Download

description: A dataset containing 46883 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Nereididae, Sabellidae, Syllidae, Serpulidae, Capitellidae, Spionidae, Cirratulidae, Balanidae, Caprellidae, Carcinidae, Cheluridae, Cymothoidae, Varunidae, Euphausiidae, Ischyroceridae, Corophiidae, Limnoriidae, Aoridae, Talitridae, Palaemonidae, Sphaeromatidae, Paranthuridae, Hyalidae, Penaeidae, Mastigiidae, Pseudodiaptomidae, Panopeidae, Mysidae, Stenothoidae, Vesiculariidae, Electridae, Bugulidae, Celleporidae, Cryptosulidae, Bitectiporidae, Cribrilinidae, Nolellidae, Schizoporellidae, Sinoflustridae, Candidae, Watersiporidae, Sciaenidae, Ascidiidae, Styelidae, Cionidae, Clavelinidae, Cyprinidae, Moronidae, Didemnidae, Sparidae, Perophoridae, Engraulidae, Gobiidae, Latidae, Mugilidae, Pyuridae, Molgulidae, Muraenidae, Cichlidae, Poeciliidae, Polyclinidae, Blenniidae, Scorpaenidae, Soleidae, Uranoscopidae, Bougainvilliidae, Blackfordiidae, Cassiopeidae, Cladonematidae, Hydractiniidae, Cordylophoridae, Diadumenidae, Tubulariidae, Aiptasiidae, Campanulariidae, Pennariidae, Dendrophylliidae, Bolinopsidae, Mytilidae, Calyptraeidae, Teredinidae, Dotidae, Eubranchidae, Tethydidae, Ellobiidae, Ostreidae, Tateidae, Muricidae, Veneridae, Polyceridae, Semelidae, Trinchesiidae, Kareniaceae, Peridiniaceae, Amphoriscidae, Bonnemaisoniaceae, Caulacanthaceae, Caulerpaceae, Codiaceae, Dasyaceae, Gracilariaceae, Halymeniaceae, Cystocloniaceae, Solieriaceae, Rhodomelaceae, Sargassaceae, Ulvaceae, Alariaceae, Scombridae, Serranidae)",
 "Geometry POLYGON ((33.925781 30.297018, 30.849609 30.221102, 36.738281 17.978733, 42.539063 11.867351, 46.054688 9.362353000000001, 53.613281 12.297068, 64.6875 21.616579, 66.269531 25.403585, 65.302734 29.993002, 50.976563 32.398516, 33.925781 30.297018))"
 ]
}

 The dataset includes 46883 records from 264 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000740-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.744fb
title: Data from: A meta-analysis reveals a positive correlation between genetic diversity metrics and environmental status in the long-lived seagrass Posidonia oceanica

description: The seagrass Posidonia oceanica is a key engineering species structuring
 coastal marine systems throughout much of the Mediterranean basin. Its
 decline is of concern, leading to the search for short- and long-term
 indicators of seagrass health. Using ArcGIS maps from a recent,
 high-resolution (1–4 km) modelling study of 18 disturbance factors
 affecting coastal marine systems across the Mediterranean (Micheli et al.
 2013, http://globalmarine.nceas.ucsb.edu/mediterranean/), we tested for
 correlations with genetic diversity metrics (allelic diversity,
 genotypic/clonal diversity and heterozygosity) in a meta-analysis of 56
 meadows. Contrary to initial predictions, weak but significantly positive
 correlations were found for commercial shipping, organic pollution
 (pesticides) and cumulative impact. This counterintuitive finding suggests
 greater resistance and resilience of individuals with higher genetic and
 genotypic diversity under disturbance (at least for a time) and/or
 increased sexual reproduction under an intermediate disturbance model. We
 interpret the absence of low and medium levels of genetic variation at
 impacted locations as probable local extinctions of individuals that
 already exceeded their resistance capacity. Alternatively, high diversity
 at high-impact sites is likely a temporal artefact, reflecting the
 mismatch with pre-environmental impact conditions, especially because
 flowering and sexual recruitment are seldom observed. While genetic
 diversity metrics are a valuable tool for restoration and mitigation,
 caution must be exercised in the interpretation of correlative patterns as
 found in this study, because the exceptional longevity of individuals
 creates a temporal mismatch that may falsely suggest good meadow health
 status, while gradual deterioration of allelic diversity might go
 unnoticed.
description: QuestionnaireResults of questionnaire on meadow statusData_accessibility_questionnaire.xlsxGenotype data set with threat categoriesSummary of genetic diversity and disturbances for each meadow.Data_accessibility_genotype data set with threat categories.xlsxIndividual heterozygosityIndividual heterozygosity and residuals of relevant threats.Data_accessibility_heterovsthreat_Residuals.txt
DOI: 10.5061/dryad.r8t33
title: Data from: Aggregation and a strong Allee effect in a cooperative outbreak insect

description: Most species that are negatively impacted when their densities are low
 aggregate to minimize this effect. Aggregation has the potential to change
 how Allee effects are expressed at the population level. We studied the
 interplay between aggregation and Allee effects in the mountain pine
 beetle (Dendroctonus ponderosae Hopkins), an irruptive bark beetle that
 aggregates to overcome tree defenses. By cooperating to surpass a critical
 number of attacks per tree, the mountain pine beetle is able to breach
 host defenses,oviposit and reproduce. Mountain pine beetles and
 Hymenopteran parasitoids share some biological features, the most notable
 of which is obligatory host death as a consequence of parasitoid attack
 and development. We developed spatiotemporal models of mountain pine
 beetle dynamics that were based on the Nicholson-Bailey framework but
 which featured beetle aggregation and a tree-level attack threshold. By
 fitting our models to data from a local mountain pine beetle outbreak, we
 demonstrate that due to aggregation, attack thresholds at the tree level
 can be overcome by a surprisingly low ratio of beetles per susceptible
 tree at the stand level. This results confirms the importance of
 considering aggregation in models of organisms that are subject to strong
 Allee effects.
description: Spatial data
 layersMPBDispersalAggData.zip