cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.37g4663
title: Data from: The use of metabarcoding for meiofauna ecological patterns assessment

description: Marine meiofauna comprises up to 22 phyla. Its morphological
 identification requires time and taxonomists' expertise, and
 molecular tools can make this task faster. We aim to disentangle
 meiofaunal diversity patterns at Araçá Bay by applying a model selection
 approach and estimating the effectiveness of metabarcoding (18S rDNA) and
 morphological methods for estimating the response of meiofauna diversity
 in small-scale interactions with environmental variables. A rarefaction
 curve indicated that ten samples were sufficient for estimating the total
 number of meiofauna OTUs in a tidal flat. In both approaches, richness was
 predicted by mean sand percentage, sediment sorting, and bacteria
 concentration. Nematode genera composition differed significantly between
 approaches, the result of taxonomic mismatch in the genetic database. The
 similarity between the model selected for diversity descriptors, the
 richness of nematode genera and meiofauna composition emphasized the
 utility of predictive models for metabarcoding estimates to detect
 small-scale interactions of these organisms.
description: Metabarcoding Sequences
 from Araçá Bay - MeiofaunaEach file contains the
 meiofauna sequences obtained by metabarcoding from 13 samples points, in a
 tidal flat, Araçá BaySequences
 Metabarcoding.zipScript and data R
 analysisThe file contains the
 data tables, and the R software scripts used in the statistical
 analysis.Scritp_dataR_metabarcodingToolMeiofauna.zipScripts UsearchThe file contain the Usearch software scripts for genetic sequences analysis.Scripts_sequences_Usearch.docx
DOI: 10.5061/dryad.s4302j0
title: Data from: Strain energy analysis of floor heave in longwall gateroads

description: Floor heave in longwall gateroads is a severe issue that affects the
 mining safety and efficiency. Researchers, however, have limited
 understanding on the floor heave mechanism because the deformation of the
 post-failure rocks in the floor is seldom considered previously. In this
 study, we developed a theoretical model using the strain energy theory to
 investigate the post-failure deformation of rocks. This model was
 validated before being implemented into a numerical modelling package,
 FLAC3D, for floor heave analysis. Based on a case study of a longwall
 entry employing stiff-yield pillar configuration, we observe that the
 massive floor heave occurs at the entry rib that takes less loads (yield
 pillar) and eventually propagates toward the other rib bearing significant
 amount of loads (stiff pillar). This observation sheds lights on the floor
 heave mechanism in longwall gateroads and has major implications on the
 control technologies for a safe and efficient longwall mining.
description: Data
DOI: 10.5061/dryad.525vm
title: Data from: An assessment of wheat yield sensitivity and breeding gains in hot environments

description: Genetic improvements in heat tolerance of wheat provide a potential
 adaptation response to long-term warming trends, and may also boost yields
 in wheat-growing areas already subject to heat stress. Yet there have been
 few assessments of recent progress in breeding wheat for hot environments.
 Here, data from 25 years of wheat trials in 76 countries from the
 International Maize and Wheat Improvement Center (CIMMYT) are used to
 empirically model the response of wheat to environmental variation and
 assess the genetic gains over time in different environments and for
 different breeding strategies. Wheat yields exhibited the most sensitivity
 to warming during the grain-filling stage, typically the hottest part of
 the season. Sites with high vapour pressure deficit (VPD) exhibited a less
 negative response to temperatures during this period, probably associated
 with increased transpirational cooling. Genetic improvements were assessed
 by using the empirical model to correct observed yield growth for changes
 in environmental conditions and management over time. These
 ‘climate-corrected’ yield trends showed that most of the genetic gains in
 the high-yield-potential Elite Spring Wheat Yield Trial (ESWYT) were made
 at cooler temperatures, close to the physiological optimum, with no
 evidence for genetic gains at the hottest temperatures. In contrast, the
 Semi-Arid Wheat Yield Trial (SAWYT), a lower-yielding nursery targeted at
 maintaining yields under stressed conditions, showed the strongest genetic
 gains at the hottest temperatures. These results imply that targeted
 breeding efforts help us to ensure progress in building heat tolerance,
 and that intensified (and possibly new) approaches are needed to improve
 the yield potential of wheat in hot environments in order to maintain
 global food security in a warmer climate.
description: regression.dat_nurseries_ADW2.RdatThis R data frame contains 1353 rows corresponding to the international trials in the CIMMYT database used in this study. The column names should be self-descriptive, and contain all the predictors used for this regression analysis.
DOI: 10.5061/dryad.15p8t
title: Data from: Patterns of genetic diversity reveal multiple introductions and recurrent founder effects during range expansion in invasive populations of Geranium carolinianum (Geraniaceae)

description: Genetic diversity, and thus the adaptive potential of invasive
 populations, is largely based on three factors: patterns of genetic
 diversity in the species' native range, the number and location of
 introductions, and the number of founding individuals per introduction.
 Specifically, reductions in genetic diversity ("founder
 effects") should be stronger for species with low within-population
 diversity in their native range and few introductions of few individuals
 to the invasive range. We test these predictions with Geranium
 carolinianum, a winter annual herb native to North America and invasive in
 China. We measure the extent of founder effects using allozymes and
 microsatellites, and ask whether this is consistent with its colonization
 history and patterns of diversity in the native range. In the native
 range, genetic diversity is higher and structure is lower than expected
 based on life-history traits. In China, our results provide evidence for
 multiple introductions near Nanjing, Jiangsu province, with subsequent
 range expansion to the west and south. Patterns of genetic diversity
 across China reveal weak founder effects that are driven largely by low-
 diversity populations at the expansion front, away from the introduction
 location. This suggests that reduced diversity in China has resulted from
 successive founder events during range expansion, and that the loss of
 genetic diversity in the Nanjing area was mitigated by multiple
 introductions from diverse source populations. This has implications for
 the future of G. carolinianum in China, as continued gene flow among
 populations should eventually increase genetic diversity within the more
 recently founded populations.
description: G. carolinianum allozyme
 and microsatellite dataAllozyme and
 microsatellite genotypes of G. carolinianum sampled from the US and
 ChinaG.carolinianum_allozymes
 microsatellites.xlsx
DOI: 10.5061/dryad.6fb43
title: Data from: Diminishing-returns epistasis among random beneficial mutations in a multicellular fungus

description: Adaptive evolution ultimately is fuelled by mutations generating novel
 genetic variation. Non-additivity of fitness effects of mutations (called
 epistasis) may affect the dynamics and repeatability of adaptation.
 However, understanding the importance and implications of epistasis is
 hampered by the observation of substantial variation in patterns of
 epistasis across empirical studies. Interestingly, some recent studies
 report increasingly smaller benefits of beneficial mutations once
 genotypes become better adapted (called diminishing-returns epistasis) in
 unicellular microbes and single genes. Here, we use Fisher's
 geometric model (FGM) to generate analytical predictions about the
 relationship between the effect size of mutations and the extent of
 epistasis. We then test these predictions using the multicellular fungus
 Aspergillus nidulans by generating a collection of 108 strains in either a
 poor or a rich nutrient environment that each carry a beneficial mutation
 and constructing pairwise combinations using sexual crosses. Our results
 support the predictions from FGM and indicate negative epistasis among
 beneficial mutations in both environments, which scale with mutational
 effect size. Hence, our findings show the importance of
 diminishing-returns epistasis among beneficial mutations also for a
 multicellular organism, and suggest that this pattern reflects a generic
 constraint operating at diverse levels of biological organization.
description: Epistasis data CM and MM
 for dryad
DOI: 10.5061/dryad.mp82q
title: Data from: How much do phenotypic plasticity and local genetic variation contribute to phenotypic divergences along environmental gradients in widespread invasive plants? A meta-analysis

description: For introduced species that have spread across a wide distributional
 range, phenotypic plasticity (PLA) has often been proposed as an important
 contributor to invasion success, because it increases the survival rate
 during initial colonization. In contrast, local genetic variation (LOC)
 has also been proposed to be important, because it could allow invaders to
 evolve high performance in a new habitat. While evolutionary ecologists
 have long been interested in understanding genetic mechanisms that allow
 rapid colonization and spread of species, until recently experimental
 tests of these concepts have been limited. As a step towards
 generalization in our understanding of the importance of PLA and LOC, we
 review the current state of the literature on this topic using
 meta-analysis. Here, we focused on three fundamental questions: 1) which
 strategy, PLA or LOC, better explains the phenotypic divergences during
 invader range expansion across different environmental gradients? 2) Which
 species characteristics correlate with the occurrence of these different
 phenomena? And 3) does the detection of PLA versus LOC depend on the trait
 studied? Using meta-analysis we found that plasticity explained a higher
 proportion of phenotypic variation regardless of the environmental
 gradients studied or plant growth forms. PLA predominated in clonal,
 self-compatible and perennial species, while LOC predominated in annual
 species. The patterns were trait-dependent: LOC was significantly more
 important than PLA in phenology, while opposite patterns were found in
 fecundity and biomass allocation. The frequent simultaneous detection of
 PLA and genotypic variation in PLA among invasive populations suggested
 that PLA might benefit from LOC to some extent. Our results also indicate
 that the contribution of plasticity to the competitive advantages of
 invasive plants may be more informative than the level of plasticity
 itself.
description: Data
 fileAll the F-, SS- and
 R-statistics for the calculation for the effect size for this meta
 analysis. Please refer to the equations for calculating the effect sizes
 in OIKOS02372 and the corresponding supporting
 information.
DOI: 10.18739/a20863750
title: Archaeological Excavations, Survey, and Environmental Sampling at Kotið, Grænagerði, Þrælagerði, Keflavík, and Helluland, North Iceland, 2022-2024

description: This dataset describes the investigation of Kotið, one of the oldest and earliest small sites in North Iceland, through coring and archaeological excavation. The objective was to determine the nature of human activity at the site and whether site inhabitants lived independent of wealthy farmsteads and pursued alternative subsistence strategies. The discovery of small, permanent habitations during the early settlement period is transforming understanding of the process of initial landscape colonization, requiring archaeologists to rethink their assumptions about the nature of social organization, subsistence, and settlement patterns during the Settlement of Iceland, ca. AD 870-1000. Archaeological study of this early settlement-period site began with systematic coring to establish the preservation, extent, and character of the cultural deposits. Open-air excavation followed with test trenching to expose the buildings identified during initial testing and to determine their form, size, and age. Collection and comprehensive analysis of artifacts, plant and animal remains, and soil samples complement study of the structure and provide insight into daily activities, subsistence, and length of habitation. Survey and test excavations were also carried out at the nearby sites of Þrælagerði, Grænagerði, Helluland, and Keflavík in order to contextualize the results from Kotið.
DOI: 10.5061/dryad.22834
title: Data from: The population origins and expansion of feral cats in Australia

description: The historical literature suggests that in Australia, the domestic cat
 (Felis catus) had a European origin [~200 years before present (ybp)], but
 it is unclear if cats arrived from across the Asian land bridge
 contemporaneously with the dingo (4000 ybp), or perhaps immigrated ~40000
 ybp in association with Aboriginal settlement from Asia. The origin of
 cats in Australia is important because the continent has a complex and
 ancient faunal assemblage that is dominated by endemic rodents and
 marsupials and lacks the large placental carnivores found on other large
 continents. Cats are now ubiquitous across the entire Australian continent
 and have been implicit in the range contraction or extinction of its small
 to medium sized (&lt;3.5kg) mammals. We analyzed the population
 structure of 830 cats using 15 short tandem repeat (STR) genomic markers.
 Their origin appears to come exclusively from European founders. Feral
 cats in continental Australia exhibit high genetic diversity in comparison
 with the low diversity found in populations of feral cats living on
 islands. The genetic structure is consistent with a rapid westerly
 expansion from eastern Australia and a limited expansion in coastal
 Western Australia. Australian cats show modest if any population structure
 and a close genetic alignment with European feral cats as compared to cats
 from Asia, the Christmas and Cocos (Keeling) Islands (Indian Ocean), and
 European wildcats (F. silvestris silvestris).
description: FeralCat_microsatellite_dataA complete set of microsatellite genotypes, location and input files for MSVAR analysisIBD_cat_dataData for IBD analysis
DOI: 10.5061/dryad.dm8m5
title: Data from: Survival analysis and classification methods for forest fire size

description: Factors affecting wildland-fire size distribution include weather, fuels,
 and fire suppression activities. We present a novel application of
 survival analysis to quantify the effects of these factors on a sample of
 sizes of lightning-caused fires from Alberta, Canada. Two events were
 observed for each fire: the size at initial assessment (by the first fire
 fighters to arrive at the scene) and the size at "being held" (a
 state when no further increase in size is expected). We developed a
 statistical classifier to try to predict cases where there will be a
 growth in fire size (i.e., the size at "being held" exceeds the
 size at initial assessment). Logistic regression was preferred over two
 alternative classifiers, with covariates consistent with similar past
 analyses. We conducted survival analysis on the group of fires exhibiting
 a size increase. A screening process selected three covariates: an index
 of fire weather at the day the fire started, the fuel type burning at
 initial assessment, and a factor for the type and capabilities of the
 method of initial attack. The Cox proportional hazards model performed
 better than three accelerated failure time alternatives. Both fire weather
 and fuel type were highly significant, with effects consistent with known
 fire behaviour. The effects of initial attack method were not
 statistically significant, but did suggest a reverse causality that could
 arise if fire management agencies were to dispatch resources based on
 a-priori assessment of fire growth potentials. We discuss how a more
 sophisticated analysis of larger data sets could produce unbiased
 estimates of fire suppression effect under such circumstances.
description: Alberta_Wildfire_Final-1996-2002This file contains attributes of different wildland fires that occured in Alberta, Canada between 1996 and 2002.Script_RThis file contains the R script used for this analysis.
DOI: 10.5061/dryad.rp4d6
title: Data from: Brain size and the risk of getting shot

description: Hunting kills hundreds of millions of animals annually, potentially
 constituting an important selection pressure on hunted species. We
 hypothesized that hunted individuals differing from survivors by having
 better ability to distinguish between dangerous humans and other human
 beings would be at a selective advantage. We tested whether shot
 individual birds had smaller brains than survivors, under the assumption
 that individuals with larger brains had superior escape ability. We used a
 large database on birds from Denmark to test whether getting shot was
 predicted by brain mass, while controlling statistically for the
 potentially confounding effects of age, sex, body mass and body condition.
 Analyses based on all species, or only species that were hunted, while
 controlling for differences in sampling effort in random effects models,
 showed consistently that shot individuals had smaller brains than
 survivors.
description: ESM Table
 S1
DOI: 10.5061/dryad.s44gk
title: Data from: Ultrasonic vocalizations emitted by flying squirrels

description: Anecdotal reports of ultrasound use by flying squirrels have existed for
 decades, yet there has been little detailed analysis of their
 vocalizations. Here we demonstrate that two species of flying squirrel
 emit ultrasonic vocalizations. We recorded vocalizations from northern
 (Glaucomys sabrinus) and southern (G. volans) flying squirrels calling in
 both the laboratory and at a field site in central Ontario, Canada. We
 demonstrate that flying squirrels produce ultrasonic emissions through
 recorded bursts of broadband noise and time-frequency structured frequency
 modulated (FM) vocalizations, some of which were purely ultrasonic.
 Squirrels emitted three types of ultrasonic calls in laboratory recordings
 and one type in the field. The variety of signals that were recorded
 suggest that flying squirrels may use ultrasonic vocalizations to transfer
 information. Thus, vocalizations may be an important, although still
 poorly understood, aspect of flying squirrel social biology.
description: Characteristic flying
 squirrel vocalizationsA set of 4 different
 high frequency vocalizations made by southern flying squirrels, stored in
 a zip archive as wav files. Type 1 vocalizations are broadband bursts;
 Type 2 vocalizations are frequency modulated, varying from about 27 to
 about 19 kHz, and contain higher frequency harmonics; Type 3 vocalizations
 are pure ultrasound exceeding 50 kHz; and Type 4 vocalizations are
 frequency modulated between about 51 kHz and 28 kHz. Types 1-3 were
 recorded from captive squirrels in a sound lab at McMaster University, and
 Type 4 was recorded in the field at Trent University's Oliver
 Research Centre near Bobcaygeon, Ontario.Calls.zip
DOI: 10.5061/dryad.r28qk
title: Data from: Social evolution in structured populations

description: Understanding the evolution of social behaviours such as altruism and
 spite is a long-standing problem that has generated thousands of articles
 and heated debates. Previous theoretical studies showed that whether
 altruism and spite evolve may be contingent on seemingly artificial model
 features, such as which rule is chosen to update the population (e.g.,
 Birth-Death or Death-Birth), and whether the benefits and costs of
 sociality affect fecundity or survival. Here we unify these features in a
 single comprehensive framework. We derive a general condition for social
 behaviour to be favoured over non-social behaviour, which is applicable in
 a large class of models for structured populations of fixed size. We
 recover previous results as special cases, and we are able to evaluate the
 relative effects of benefits and costs of social interactions on fecundity
 and survival. Our results highlight the crucial importance of identifying
 the relative scale at which competition occurs.
description: Debarre-etal_2014_scripts
DOI: 10.5061/dryad.6qg398d1
title: Data from: Wide variation in spatial genetic structure between natural populations of the European beech (Fagus sylvatica) and its implications for SGS comparability

description: Identification and quantification of spatial genetic structure (SGS)
 within populations remains a central element of understanding population
 structure at the local scale. Understanding such structure can inform on
 aspects of the species' biology, such as establishment patterns and
 gene dispersal distance, in addition to sampling design for genetic
 resource management and conservation. However, recent work has identified
 that variation in factors such as sampling methodology, population
 characteristics, and marker system can all lead to significant variation
 in SGS estimates. Consequently, the extent to which estimates of SGS can
 be relied upon to inform on the biology of a species or differentiate
 between experimental treatments is open to doubt. Following on from a
 recent report of unusually extensive SGS when assessed using amplified
 fragment length polymorphisms (AFLP) in the tree Fagus sylvatica, we
 explored whether this marker system led to similarly high estimates of SGS
 extent in other apparently similar populations of this species. In the
 three populations assessed, SGS extent was even stronger than this
 previously reported maximum, extending up to 360 m, an increase of up to
 800% in comparison with the generally accepted maximum of 30 - 40 m based
 on the literature. Within this species, wide variation in SGS estimates
 exists, whether quantified as SGS intensity, extent, or the Sp parameter.
 Consequently, we argue that greater standardisation should be applied in
 sample design and SGS estimation and highlight five steps that can be
 taken to maximize the comparability between SGS estimates.
description: JUMP AFLP Data_
 DryadAFLP data derived from
 natural populations of the European beech, Fagus sylvatica in the Pyrenees
 and Montseny Mountains in northeast Spain
DOI: 10.5281/zenodo.18381730
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Alvan Wentworth Chapman, http://www.wikidata.org/entity/Q448279. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q448279