cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.qv9s4mw9f
title: Data from: Modelling the potential impacts of climate change on the distribution of ichthyoplankton in the Yangtze Estuary, China

description: Aim: Species distribution models (SDMs) are an effective tool to explore
 the potential distribution of terrestrial, freshwater, and marine
 organisms; however, SDMs have been seldom used to model ichthyoplankton
 distributions and thus our understanding of how larval stages of fishes
 will respond to climate change is still limited. Here, we developed SDMs
 to explore potential impacts of climate change on habitat suitability of
 ichthyoplankton. Location: Yangtze Estuary, China Methods: Using long-term
 ichthyoplankton survey data and a large set of marine predictor variables,
 we developed ensemble SDMs for five abundant ichthyoplankton species in
 the Yangtze Estuary (Coilia mystus, Hypoatherina valenciennei,
 Larimichthys polyactis, Salanx ariakensis, and Chelidonichthys spinosus).
 Then, we projected their habitat suitability under present and future
 climate conditions. Results: The ensemble SDMs had good predictive
 performance and were successful in estimating the known distributions of
 the five species. Model projections highlighted two contrasting patterns
 of response to future climates: while C. mystus will likely expand its
 range, the ranges of the other four species will likely contract and shift
 northward. Main conclusions: According to our SDM projections, the five
 ichthyoplankton species that we tested in the Yangtze Estuary are likely
 to respond differently to future climate changes. These projected
 different responses seemingly reflect the differential functional
 attributes and life history strategies of these species. To the extent
 that climate change emerges as a critical driver of the future
 distribution of these species, our findings provide an important roadmap
 for designing future conservation strategies for ichthyoplankton in this
 region.
description: Ichthyoplankton samples were collected from 40 stations in the
 Yangtze Estuary between 1999 and 2013 (05/1999, 05/2001, 05/2004, 05/2007,
 05/2009, 05/2010, 05/2011, 05/2012, and 05/2013). Presence records of
 five abundant ichthyoplankton species in this region were used to develope
 species distribution models.
description: To increase sample size, samples between 1999 and 2013 (05/1999,
 05/2001, 05/2004, 05/2007, 05/2009, 05/2010, 05/2011, 05/2012, and
 05/2013) were pooled together.
DOI: 10.5061/dryad.qnk98sfbg
title: Responses of four dominant dryland plant species to climate change in the Junggar Basin, north-west China

description: Aim Dryland ecosystems are exceedingly sensitive to climate change.
 Desertification induced by both climate changes and human activities
 seriously threatens the dryland vegetation. However, the impact of climate
 change on distributions of dryland plant species has not been well
 documented. Here, we studied the potential distributions of four
 representative dryland plant species (Haloxylon ammodendron, Anabasis
 aphylla, Calligonum mongolicum, and Populus euphratica) under current and
 future climate scenarios in a temperate desert region, aiming to improve
 our understanding of the responses of dryland plant species to climate
 change and provide guidance for dryland conservation and afforestation.
 Location Junggar Basin, a large desert region in north-western China.
 Methods Occurrence data of the studied species were collected from an
 extensive field investigation of 2516 sampling sites in the Junggar Basin.
 Ensemble species distribution models using 10 algorithms were developed
 and used to predict the potential distribution of each studied species
 under current and future climate scenarios. Result H. ammodendron and A.
 aphylla were likely to lose most of their current suitable habitats under
 future climate scenarios, while C. mongolicum and P. euphratica were
 likely to expand their ranges or remain relatively stationary. Variable
 importance evaluation showed that the most important climate variables
 influencing species distributions differed across the studied species.
 These results may be explained by the different ecophysiological
 characteristics and adaptation strategies to the environment of the four
 studied species. Main conclusions We explored the responses of the
 representative dryland plant species to climate change in the Junggar
 Basin in north-western China. The different changes in suitability of
 different species imply that policymakers may need to reconsider the
 selection and combination of the afforestation species used in this area.
 This study can provide valuable reference for the management and
 conservation of dryland ecosystems under future climate change scenarios.
description: Extensive field investigations including 2516 sampling points
 were conducted in northern Xinjiang during the summer (May to September)
 of 2015 and 2016. In each sampling point, which is distributed every 1-2
 km along the major roads in this region, the latitude and longitude were
 recorded and the presence (marked as 1 in the dataset) and absence (marked
 as 0 in the dataset) of the studied species (i.e. <i>Haloxylon
 ammodendron</i>, <i>Anabasis aphylla</i>,
 <i>Calligonum mongolicum</i>, and <i>Populus
 euphratica</i>) were identified.
DOI: 10.5061/dryad.m905qftwx
title: Data from: Changes in age-structure over four decades were a key determinant of population growth rate in a long-lived mammal

description: 1. A changing environment directly influences birth and mortality rates,
 and thus population growth rates. However, population growth rates in the
 short-term are also influenced by population age-structure. Despite its
 importance, the contribution of age-structure to population growth rates
 has rarely been explored empirically in wildlife populations with
 long-term demographic data. 2. Here, we assessed how changes in
 age-structure influenced short-term population dynamics in a semi-captive
 population of Asian elephants (Elephas maximus). 3. We addressed this
 question using a demographic dataset of female Asian elephants from timber
 camps in Myanmar spanning 45 years (1970-2014). First, we explored
 temporal variation in age-structure. Then, using annual matrix population
 models, we used a retrospective approach to assess the contributions of
 age-structure and vital rates to short-term population growth rates with
 respect to the average environment. 4. Age-structure was highly variable
 over the study period, with large proportions of juveniles in the years
 1970 and 1985, and made a substantial contribution to annual population
 growth rate deviations. High adult birth rates between 1970-1980 would
 have resulted in large positive population growth rates, but these were
 prevented by a low proportion of reproductive-aged females. 5. We
 highlight that an understanding of both age-specific vital rates and
 age-structure is needed to assess short-term population dynamics.
 Furthermore, this example from a human-managed system suggests that the
 importance of age-structure may be accentuated in populations experiencing
 human disturbance where age-structure is unstable, such as those in
 captivity or for endangered species. Ultimately, changes to the
 environment drive population dynamics by influencing birth and mortality
 rates, but understanding demographic structure is crucial for assessing
 population growth.
DOI: 10.5061/dryad.qbzkh18cz
title: Mapping the EORTC QLQ-C30 and QLQ-H&N35 to the EQ-5D for head and neck cancer: can disease-specific utilities be obtained?

description: Introduction Innovations in head and neck cancer (HNC) treatment are often
 subject to economic evaluation prior to their reimbursement and subsequent
 access for patients. Mapping functions facilitate economic evaluation of
 new treatments when the required utility data is absent, but quality of
 life data is available. The objective of this study is to develop a
 mapping function translating the EORTC QLQ-C30 to EQ-5D-derived utilities
 for HNC through regression modeling, and to explore the added value of
 disease-specific EORTC QLQ-H&N35 scales to the model.  
 Methods Data was obtained on patients with primary HNC treated with
 curative intent derived from two hospitals. Model development was
 conducted in two phases: 1. Predictor selection based on theory- and
 data-driven methods, resulting in three sets of potential predictors from
 the quality of life questionnaires; 2. Selection of the best out of four
 methods: ordinary-least squares, mixed-effects linear, Cox and beta
 regression, using the first set of predictors from EORTC QLQ-C30 scales
 with most correspondence to EQ-5D dimensions. Using a stepwise approach,
 we assessed added values of predictors in the other two sets. Model fit
 was assessed using Akaike and Bayesian Information Criterion (AIC and BIC)
 and model performance was evaluated by MAE, RMSE and limits of agreement
 (LOA).   Results The beta regression model showed best model fit,
 with global health status, physical-, role- and emotional functioning and
 pain scales as predictors. Adding HNC-specific scales did not improve the
 model. Model performance was reasonable; R2=0.39, MAE=0.0949, RMSE=0.1209,
 95% LOA of -0.243 to 0.231 (bias -0.01), with an error correlation of
 0.32. The estimated shrinkage factor was 0.90.   Conclusions
 Selected scales from the EORTC QLQ-C30 can be used to estimate utilities
 for HNC using beta regression. Including EORTC QLQ-H&N35 scales
 does not improve the mapping function. The mapping model may serve as a
 tool to enable cost-effectiveness analyses of innovative HNC treatments,
 for example for reimbursement issues. Further research should assess the
 robustness and generalizability of the function by validating the model in
 an external cohort of HNC patients.
description: Data was obtained through the Dutch Head and Neck Audit
 (DHNA). 
description: Not applicable.
DOI: 10.5061/dryad.j6q573n84
title: Disentangling the mechanisms underpinning disturbance-mediated invasion data

description: Disturbances can play a major role in biological invasions: by destroying
 biomass, they alter habitat and resource abundances. Previous field
 studies suggest that disturbance-mediated invader success is a consequence
 of resource influxes, but the importance of other potential covarying
 causes, notably the opening up of habitats, have yet to be directly
 tested. Using experimental populations of the bacterium Pseudomonas
 fluorescens we determined the relative importance of disturbance-mediated
 habitat opening and resource influxes, plus any interaction between them,
 for invader success of two ecologically distinct morphotypes. Resource
 addition increased invasibility, while habitat opening had little impact
 or interacted with resource addition. Both invaders behaved similarly,
 despite occupying different ecological niches in the microcosms. Treatment
 also affected the composition of the resident population, which further
 affected invader success. Our results provide experimental support for the
 observation that resource input is a key mechanism through which
 disturbance increases invasibility.
DOI: 10.5061/dryad.d2547d7zb
title: Community weighted mean traits of multi-trophic communities in the Baltic Sea

description: The dataset contains the time-series of community weighted mean traits of
 four organism groups (phytoplankton, zooplankton, benthos, fish) in three
 different areas of the Baltic Sea and the associated R code to make the
 figures as in Pecuchet et al. Ecography
DOI: 10.5061/dryad.ht76hdr9z
title: Influence of polydimethylsiloxane substrate stiffness on corneal epithelial cells

description: Many cell types are known to modulate their behavior in response to
 changes in material stiffness, however little is known about how stiffness
 effects corneal epithelial cells. This study aims to investigate the
 response of a corneal epithelial cell line to polydimethylsiloxane (PDMS)
 substrates with a range of Young’s moduli from 10 kPa to 1500 kPa.
 Cellular morphology, proliferation, differentiation and mechanobiology
 were examined. Cells grown on PDMS adopted the typical cobblestone
 morphology exhibited by the corneal epithelium. Proliferative markers pERK
 and Ki67 were higher in cells cultured on stiffer substrates compared to
 those on softer substrates. Material stiffness was also found to influence
 the cell phenotype with cells on stiffer substrates having higher
 cytokeratin 3 gene expression, a mature epithelial marker, while cells on
 softer substrates expressed more cytokeratin 14, a basal epithelial
 marker. Cells grown on softer substrates also displayed higher levels of
 focal adhesions and intermediate filaments compared to cells on stiff
 substrates. This research will aid in designing novel biomaterials for the
 culture and transplantation corneal epithelial cells.
DOI: 10.5061/dryad.tx95x69sm
title: Ambiguity coding allows accurate inference of evolutionary parameters from alignments in an aggregated state-space

description: How can we best learn the history of a protein's evolution? Ideally,
 a model of sequence evolution should capture both the process that
 generates genetic variation and the functional constraints determining
 which changes are fixed. However, in practical terms the most suitable
 approach may simply be the one that combines the convenience of easily
 available input data with the ability to return useful parameter
 estimates. For example, we might be interested in a measure of the
 strength of selection (typically obtained using a codon model) or an
 ancestral structure (obtained using structural modelling based on inferred
 amino acid sequence and side chain configuration). But what if data in the
 relevant state-space are not readily available? We show that it is
 possible to obtain accurate estimates of the outputs of interest using an
 established method for handling missing data. Encoding observed characters
 in an alignment as ambiguous representations of characters in a larger
 state-space allows the application of models with the desired features to
 data that lack the resolution that is normally required. This strategy is
 viable because the evolutionary path taken through the observed space
 contains information about states that were likely visited in the
 "unseen" state-space. To illustrate this, we consider two
 examples with amino acid sequences as input. We show that ω, a parameter
 describing the relative strength of selection on non-synonymous and
 synonymous changes, can be estimated in an unbiased manner using an
 adapted version of a standard 61-state codon model. Using simulated and
 empirical data, we find that ancestral amino acid side chain configuration
 can be inferred by applying a 55-state empirical model to 20-state amino
 acid data. Where feasible, combining inputs from both ambiguity-coded and
 fully resolved data improves accuracy. Adding structural information to as
 few as 12.5% of the sequences in an amino acid alignment results in
 remarkable ancestral reconstruction performance compared to a benchmark
 that considers the full rotamer state information. These examples show
 that our methods permit the recovery of evolutionary information from
 sequences where it has previously been inaccessible.
DOI: 10.5061/dryad.jwstqjq4r
title: Functional organization of woody plant assemblages along precipitation and human disturbance gradients in a seasonally dry tropical forest

description: Chronic anthropogenic disturbances (CAD) and rainfall are important
 drivers of plant community assembly, but little is known about the role
 played by inter and intraspecific trait variation as communities respond
 to these pervasive forces. Here we examined the hypothesis that lower
 precipitation and higher CAD reduce both intra and interspecific trait
 variation in Caatinga dry forests. We sampled woody plants across 15 plots
 along precipitation and CAD gradients and measured resource-use traits.
 Effects of precipitation and CAD on RaoQ functional diversity were
 decomposed into species turnover and intraspecific variability. We used
 “T-statistics” to assess the trait sorting from the regional pool to local
 communities (i.e. external filtering), and within-community forces leading
 to low trait overlap (i.e. internal filtering) at individual- and
 species-level. Intraspecific variability explained at least one third of
 the total trait variation and 46% of variation in multitrait diversity
 across communities. Increasing disturbance reduced multitrait diversity,
 while precipitation affected some particular traits, such as wood density.
 Overall, precipitation determined species sorting across communities,
 while disturbance relaxed internal filters, leading to higher trait
 overlap within communities due to higher intraspecific variability. Our
 results suggest that the woody Caatinga flora contains a substantial
 amount of both inter and intraspecific trait variation. This variation is
 not randomly distributed within and across communities, but varies
 according to rainfall conditions and disturbance intensity. These findings
 reinforce the emerging idea that human-disturbances can reorganize plant
 communities at multiple scales and highlight trait variability as a key
 biological asset for the resilience of dry forests.
DOI: 10.5061/dryad.bg79cnp70
title: Data from: Diversity, dynamics and effects of long terminal repeat retrotransposons in the model grass Brachypodium distachyon

description: Transposable elements (TEs) are the main reason for the high plasticity of
 plant genomes, where they occur as communities of diverse evolutionary
 lineages. Because research has typically focused on single abundant
 families or summarized TEs at a coarse taxonomic level, our knowledge
 about how these lineages differ in their effects on genome evolution is
 still rudimentary. Here we investigate the community composition and
 dynamics of 32 long terminal repeat retrotransposon (LTR-RT) families in
 the 272 Mb genome of the Mediterranean grass Brachypodium distachyon. We
 find that much of the recent transpositional activity in the
 B. distachyon genome is due to centromeric Gypsy families and
 Copia elements belonging to the Angela lineage. With a half-life as low as
 66 ky, the latter are the most dynamic part of the genome and an important
 source of within-species polymorphisms. Second, GC-rich Gypsy elements of
 the Retand lineage are the most abundant TEs in the genome. Their presence
 explains more than 20 percent of the genome-wide variation in GC content
 and is associated with higher methylation levels. Our study shows how
 individual TE lineages change the genetic and epigenetic constitution of
 the host beyond simple changes in genome size.
DOI: 10.5061/dryad.3r2280gbx
title: Data from: Spatially sparse emitters localization with QVBEM algorithm

description: We study the estimation of the spatially sparse radio emitter locations
 from space, via the proposed Quad-tree variational Bayesian expectation
 maximization (QVBEM) algorithm. Firstly, we assume that the emitters are
 approximately lie on a uniform grid points in the region under
 surveillance. The VBEM algorithm is applied and the points exceeding the
 threshold level are considered as potential targets. Then, the grids are
 refined around the potential targets via the Quad-tree algorithm and the
 process is iterated. It allows us to find the location of sparse emitters
 with much less computational complexity due to the use of fewer grid
 points.
DOI: 10.5061/dryad.2jm63xsjn
title: Data from: Epicuticular compounds of Protopiophila litigata (Diptera: Piophilidae): identification and sexual selection across two years in the wild

description: The epicuticular compounds (ECs) of insects serve both to waterproof the
 cuticle and, in many taxa, as pheromones that are important for various
 social interactions including mate choice within populations. However, ECs
 have not been individually identified in many species and most studies of
 their role in mate choice have been performed in a laboratory setting.
 Here we newly identify and quantify the ECs of the antler fly,
 Protopiophila litigata Bonduriansky, and use a cross-sectional selection
 analysis to quantify their association with male mating success in the
 wild across two years (2013 and 2017). The ECs of antler flies include
 straight-chain and methylated alkanes, alkenes, and a family of branched
 wax esters. We find all ECs to be shared between males and females but
 also demonstrate sexual dimorphism in the abundance of several. Male EC
 relative abundances were significantly associated with mating success in
 both years, although the multivariate direction of selection differed
 significantly between the years. Surprisingly, only two of the 18
 compounds (or groups of compounds) we identified were similarly associated
 with mating success across the sampling years. In 2017, we further
 partitioned sexual selection into intra- and intersexual components,
 revealing selection on ECs to be significant via female choice but not
 male-male competition. Our study is one of few to investigate the
 potential role of ECs in mating success in the wild and adds to a growing
 body of evidence demonstrating significant temporal variability in
 selection in natural populations.
description: <strong>field-male-mating.csv</strong> GC:FID peak
 areas for 18 major epicuticular compounds (or co-eluting groups of
 compounds) collected in two years from wild male <em>Protopihila
 litigata</em> that were either mating or single. Peak numbers
 correspond to those in Fig. 1 and Table 1 of the associated
 manuscript.
 <strong>male-female-lab.csv</strong> Includes both
 GC:FID peak areas and absolute abundances -- calculated based on an alkane
 standard -- of 18 ECs collected from 20 male and 19
 female <em>Protopiophila litigata</em> reared in the
 laboratory.
DOI: 10.5061/dryad.f1vhhmgsg
title: Modular chromosome rearrangements reveal parallel and nonparallel adaptation in a marine fish

description: Genomic architecture and standing variation can play a key role in
 ecological adaptation, and contribute to the predictability of evolution.
 In Atlantic cod (Gadus morhua), four large chromosomal rearrangements have
 been associated with ecological gradients and migratory behaviour in
 regional analyses. However, the degree of parallelism , the extent of
 independent inheritance, and functional distinctiveness of these
 rearrangements remains poorly understood. Here, we use a 12K single
 nucleotide polymorphism (SNP) array to demonstrate extensive individual
 variation in rearrangement genotype within populations across the species
 range, suggesting that local adaptation to fine-scale ecological variation
 is enabled by rearrangements with independent inheritance. Our results
 demonstrate significant association of rearrangement with migration
 phenotype and environmental gradients across the species range. Individual
 rearrangements exhibit functional modularity, but also contain loci
 showing multiple environmental associations. Clustering in genetic
 distance trees and reduced differentiation within rearrangements across
 the species range are consistent with shared variation as a source of
 contemporary adaptive diversity in Atlantic cod. Conversely, we also find
 that haplotypes in the LG12 and LG1 rearranged region have diverged across
 the Atlantic, despite consistent environmental associations. Exchange of
 these structurally variable genomic regions, as well as local selective
 pressures have likely facilitated individual diversity within Atlantic cod
 stocks. Our results highlight the importance of genomic architecture and
 standing variation in enabling fine-scale adaptation in marine species.