cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.cn0q14t
title: Data from: The fluctuating resource hypothesis explains invasibility, but not exotic advantage following disturbance

description: Invasibility is a key indicator of community susceptibility to changes in
 structure and function. The fluctuating resource hypothesis (FRH)
 postulates that invasibility is an emergent community property, a
 manifestation of multiple processes that cannot be reliably predicted by
 individual community attributes like diversity or productivity. Yet,
 research has emphasized the role of these individual attributes, with the
 expectation that diversity should deter invasibility and productivity
 enhance it. In an effort to explore how these and other factors may
 influence invasibility, we evaluated the relationship between invasibility
 and species richness, productivity, resource availability, and resilience
 in experiments crossing disturbance with exotic seed addition in 1-m2
 plots replicated over large expanses of grasslands in Montana, USA and La
 Pampa, Argentina. Disturbance increased invasibility as predicted by FRH,
 but grasslands were more invasible in Montana than La Pampa whether
 disturbed or not, despite Montana’s higher species richness and lower
 productivity. Moreover, invasibility correlated positively with nitrogen
 availability and negatively with native plant cover. These patterns
 suggested that resource availability and the ability of the community to
 recover from disturbance (resilience) better predicted invasibility than
 either species richness or productivity, consistent with predictions from
 FRH. However, in ambient, unseeded plots in Montana, disturbance reduced
 native cover by &gt;50% while increasing exotic cover &gt;200%.
 This provenance bias could not be explained by FRH, which predicts that
 colonization processes act on species’ traits independent of origins. The
 high invasibility of Montana grasslands following disturbance was
 associated with a strong shift from perennial to annual species, as
 predicted by succession theory. However, this shift was driven primarily
 by exotic annuals, which were more strongly represented than perennials in
 local exotic versus native species pools. We attribute this provenance
 bias to extrinsic biogeographic factors such as disparate evolutionary
 histories and/or introduction filters selecting for traits that favor
 exotics following disturbance. Our results suggest that 1) invasibility is
 an emergent property best explained by a community’s efficiency in
 utilizing resources, as predicted by FRH; but 2) understanding
 provenance-biases in biological invasions requires moving beyond FRH to
 incorporate extrinsic biogeographic factors that may favor exotics in
 community assembly.
description: SEED ADDITION DATA FOR
 ARCHIVERecruitment data from
 seed addition plotsSOIL DATA FOR
 ARCHIVESoil nutrient
 dataRESILIENCE DATA BY
 PROVENANCE FOR ARCHIVECover and richness by
 provenance category in unseeded plotsRESILIENCE DATA BY LIFE
 HISTORY FOR ARCHIVECover by provenance and
 life history category in unseeded plots
DOI: 10.5061/dryad.8hm07
title: Data from: Biochar from "Kon Tiki" flame curtain and other kilns: effects of nutrient enrichment and kiln type on crop yield and soil chemistry

description: Biochar application to soils has been investigated as a means of improving
 soil fertility and mitigating climate change through soil carbon
 sequestration. In the present work, the invasive shrub "Eupatorium
 adenophorum" was utilized as a sustainable feedstock for making
 biochar under different pyrolysis conditions in Nepal. Biochar was
 produced using several different types of kilns; four sub types of flame
 curtain kilns (deep-cone metal kiln, steel shielded soil pit, conical soil
 pit and steel small cone), brick-made traditional kiln, traditional
 earth-mound kiln and top lift up draft (TLUD). The resultant biochars
 showed consistent pH (9.1 ± 0.3), cation exchange capacities (133 ± 37
 cmolc kg-1), organic carbon contents (73.9 ± 6.4 %) and surface areas (35
 to 215 m2/g) for all kiln types. A pot trial with maize was carried out to
 investigate the effect on maize biomass production of the biochars made
 with various kilns, applied at 1% and 4% dosages. Biochars were either
 pretreated with hot or cold mineral nutrient enrichment (mixing with a
 nutrient solution before or after cooling down, respectively), or added
 separately from the same nutrient dosages to the soil. Significantly
 higher CEC (P&lt; 0.05), lower Al/Ca ratios (P&lt; 0.05), and high
 OC% (P&lt;0.001) were observed for both dosages of biochar as compared
 to non-amended control soils. Importantly, the study showed that biochar
 made by flame curtain kilns resulted in the same agronomic effect as
 biochar made by the other kilns (P &gt; 0.05). At a dosage of 1%
 biochar, the hot nutrient-enriched biochar led to significant increases of
 153% in above ground biomass production compared to cold nutrient-enriched
 biochar and 209% compared to biochar added separately from the nutrients.
 Liquid nutrient enhancement of biochar thus improved fertilizer
 effectiveness compared to separate application of biochar and fertilizer.
description: soil
 datasets-paperI-kilntype_enrichmentdatasets-AGB
 roduction-kilntype-enrichmentData-figuresbiochar-characterization-different_kilntypes
DOI: 10.5061/dryad.89459
title: Data from: Variation in leaf anatomical traits from tropical to cold-temperate forests and linkage to ecosystem functions

description: 1. Leaf anatomical traits may reflect plant's adaption to
 environmental changes and influence ecosystem functions, as they regulate
 light absorption and gas exchange to some extent. Here, we hypothesized
 that leaf anatomical traits were closely related to gross primary
 productivity (GPP) because photosynthesis commonly occurs in the
 chloroplasts of palisade and spongy tissues in leaf. 2. Eight leaf
 anatomical traits were measured in 916 plant species inhabiting from
 tropical to cold-temperate forests in eastern China: adaxial epidermis
 thickness (AD), abaxial epidermis thickness (AB), leaf thickness (LT),
 palisade tissue thickness (PT), and spongy tissue thickness (ST),
 palisade-spongy tissue ratio (PT/ST), palisade tissue-leaf thickness ratio
 (PT/LT), and spongy tissue-leaf thickness ratio (ST/LT). 3. Leaf
 anatomical traits showed significant latitudinal patterns at species,
 plant functional groups (PFGs), and communities levels (P &lt; 0.05),
 and they differed between PFG and community. Temperature and precipitation
 were the main factors influencing AD, AB, PT/ST, and PT/LT, explaining
 33–72% of the total variation at large scale. Furthermore, AB, LT, PT/ST,
 and PT/LT were significantly correlated with the aridity index. 4. Our
 findings filled the data gap of plant anatomical traits at regional
 scales, and broadened current knowledge on the adaptation strategies of
 plant anatomical traits, which also provided new evidence for linkages of
 plant traits and functioning across natural communities.
description: FE-2016-01148-R1-Data of
 leaf anatomical traitsleaf anatomical
 traits
DOI: 10.15468/dl.pytaj8
title: Occurrence Download

description: A dataset containing 117 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is Mexico",
 "TaxonKey is Arizona elegans",
 "Year 1960-2026"
 ]
}

 The dataset includes 117 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000748-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.mr2mh
title: Data from: Lost in the other half: improving accuracy in geometric morphometric analyses of one side of bilaterally symmetric structures

description: Systematists and evolutionary biologists have widely adopted
 Procrustes-based geometric morphometrics for measuring size and shape in
 biology. Many structures, and in fact most animals, are bilaterally
 symmetric with an internal plane of symmetry (also called object
 symmetry). Often, when quantifying asymmetric variation is not an aim,
 only one or the other side is measured and analyzed. This approach has
 been used in hundreds of studies. Its implicit assumption is that the
 information on the other side is redundant and a single side will,
 therefore, produce results mirroring those one would have obtained from
 the analysis of the entire structure with all its left and right
 landmarks. However, the extent to which this assumption is met has, to my
 knowledge, never been explored. Using two example data sets, I will show
 that congruence may be high in analyses at a macroevolutionary level but
 much lower at a microevolutionary one, and inaccuracies might especially
 affect shape. I will discuss some of the other factors that may influence
 results and will suggest a simple expedient that can improve both the
 visualization and accuracy of shape analyses in one-side-only studies.
description: carabidscarabid data with raw landmark coordinates of the entire configurationhumanshuman data with raw landmark coordinates of the entire configuration
DOI: 10.5061/dryad.v540q
title: Data from: Evolution of elaborate parental care: phenotypic and genetic correlations between parent and offspring traits

description: The evolution of elaborate forms of parental care is an important topic in
 behavioral ecology, yet the factors shaping the evolution of complex
 suites of parental and offspring traits are poorly understood. Here, we
 use a multivariate quantitative genetic approach to study phenotypic and
 genetic correlations between parental and offspring traits in the burying
 beetle Nicrophorus vespilloides. To this end, we recorded 2 prenatal
 traits (clutch size and egg size), 2 postnatal parental behaviors (direct
 care directed toward larvae and indirect care directed toward resource
 maintenance), 1 offspring behavior (begging), and 2 measures of breeding
 success (larval dispersal mass and number of dispersing larvae). Females
 breeding on larger carcasses provided less direct care but produced larger
 larvae than females breeding on smaller carcasses. Furthermore, there were
 positive phenotypic correlations between clutch size, direct, and indirect
 care. Both egg size and direct care were positively correlated with
 dispersal mass, whereas clutch size was negatively correlated with
 dispersal mass. Clutch size and number of dispersed larvae showed genetic
 variance both in terms of differences between populations of origin and
 significant heritabilities. However, we found no evidence of genetic
 variance underlying other parental or offspring traits. Our results
 suggest that correlations between suites of parental traits are driven by
 variation in individual quality rather than trade-offs, that some parental
 traits promote offspring growth while others increase the number of
 offspring produced, and that parental and offspring traits might respond
 slowly to selection due to low levels of additive genetic variance.
description: Phenotypic and genetic
 correlations between parent and offspring traitsThe data describing
 phenotypic and genetic correlations between parent and offspring traits in
 the burying beetle Nicrophorus vespilloides. The data derive from a full
 sib, paternal half-sib breeding design.AndrewsKruukSmisethBE2016.xlsx
DOI: 10.7910/dvn/eo4ce8
title: The Role of the Fish Seed Compact Model in Enhancing Aquaculture Productivity and Household Food Security in Rural Bangladesh

description: This study evaluated the role of the Fish Seed Compact Model in enhancing aquaculture productivity and household food security among intervention and control farmers in rural Bangladesh. It documents the implementation of the model, which aims to strengthen the fish seed supply chain, improve farm-level practices, and support household food security. Data were collected through a comprehensive household- and farm-level survey covering aquaculture practices, input use, biosecurity and management behaviors, production and income, market participation, food security, dietary diversity, and gender-related decision-making. The dataset provides a rich foundation for analyzing linkages between seed access, adoption of best management practices, farm productivity, and household outcomes. The study is expected to generate evidence for scaling integrated seed system interventions to promote resilient and inclusive aquaculture development in Bangladesh.
description: KOBO Toolbox, 2.017.10
description: Type: Dataset; Sub-type(s): Survey Data
description: Household- and farm-level survey data provided in Excel format
DOI: 10.5061/dryad.kr3c9
title: Data from: Multilocus genotyping of Giardia duodenalis isolates from children in Oromia Special Zone, central Ethiopia

description: Background: Giardia duodenalis is the etiologic agent of giardiasis in
 humans and other mammals worldwide. The burden of disease is high among
 children in developing countries where sanitation is inadequate. However,
 the epidemiology and genetic diversity of this parasite is poorly
 understood in Ethiopia. This study aimed to determine the prevalence and
 genetic diversity of G. duodenalis in asymptomatic children in Oromia
 Special Zone, central Ethiopia. Results: A total of 286 fresh fecal
 specimens were collected from children and screened using microscopy and
 PCR. The prevalence of Giardia duodenalis was 10.8 % (31/286) and 16.8 %
 (48/286) as detected by microscopy and nested PCR, respectively. The
 infection rate by the study area, sex and age group difference was not
 significant (P &gt; 0.05). Genotyping results showed that 22.9 %
 (11/48) of the isolates belonged to assemblage A while 77.1 % (37/48)
 belonged to assemblage B. Although double peaks were observed at the
 chromatogram level, no mixed assemblage or sub-assemblage infections were
 demonstrated. Isolates of assemblage A mostly belonged to the
 sub-assemblage AII and showed similarity with previously described
 isolates. However, there was great genetic variability within assemblage B
 that showed heterogeneous nucleotide positions. Fifteen of them were new
 genotypes: 5 at the triose phosphate isomerase (tpi), 2 at the β-giardin
 (bg), and 8 at the glutamate dehydrogenase (gdh) genes. Conclusions:
 Giardia duodenalis mainly assemblage B infection was predominant among the
 asymptomatic children in the study area. The high polymorphism found in
 isolates of assemblage B warrants a more defining tool to discriminate
 assemblage B at the sub-assemblage level. The findings of the present
 study indicate that there is a need to carry out national screening
 programs aiming to detect asymptomatic infections to minimize the
 reservoir of the disease.
description: Phylogenetic
 treeFigure. 1 Phylogenetic
 tree of G. duodenalis based on nucleotide sequences of the tpi gene (a)
 and gdh gene (b). Trees were constructed using the neighbor-joining method
 based on genetic distance calculated by the Kimura 2-parameter model,
 implemented in MEGA version 5.2. Bootstrap values &gt; 50 % from 1,000
 replicates is shown on nodes. Reference sequences from the major G.
 duodenalis sub-assemblages are written by blue color in bold. Isolates
 showed known and novel sequences obtained from this study are marked by
 rectangles (blue) and triangles (red), respectively.
DOI: 10.5061/dryad.33fv8
title: Data from: The Red Death meets the abdominal bristle: polygenic mutation for susceptibility to a bacterial pathogen in Caenorhabditis elegans

description: Understanding the genetic basis of susceptibility to pathogens is an
 important goal of medicine and of evolutionary biology. A key first step
 toward understanding the genetics and evolution of any phenotypic trait is
 characterizing the role of mutation. However, the rate at which mutation
 introduces genetic variance for pathogen susceptibility in any organism is
 essentially unknown. Here we quantify the per-generation input of genetic
 variance by mutation (VM) for susceptibility of Caenorhabditis elegans to
 the pathogenic bacterium Pseudomonas aeruginosa (defined as the median
 time of death, LT50). VM for LT50 is slightly less than VM for a variety
 of life-history and morphological traits in this strain of C. elegans, but
 is well within the range of reported values in a variety of organisms.
 Mean LT50 did not change significantly over 250 generations of mutation
 accumulation. Comparison of VM to the standing genetic variance (VG)
 implies a strength of selection against new mutations of a few tenths of a
 percent. These results suggest that the substantial standing genetic
 variation for susceptibility of C. elegans to P. aeruginosa can be
 explained by polygenic mutation coupled with purifying selection.
description: Etienne et al.
 Data_Evolution_14.0446.R2This data file contains
 the raw data from the survivorship assays that are used in the LT50 assays
 for the mutation accumulation (MA) lines.
DOI: 10.5061/dryad.h7n25
title: Data from: Prelude to a panzootic: gene flow and immunogenetic variation in northern little brown myotis vulnerable to bat white-nose syndrome

description: The fungus that causes bat white-nose syndrome (WNS) recently leaped from
 eastern North America to the Pacific Coast. The pathogen’s spread is
 associated with the genetic population structure of a host (Myotis
 lucifugus). To understand the fine-scale neutral and immunogenetic
 variation among northern populations of M. lucifugus, we sampled 1142
 individuals across the species’ northern range. We used genotypes at 11
 microsatellite loci to reveal the genetic structure of, and directional
 gene flow among, populations to predict the likely future spread of the
 pathogen in the northwest and to estimate effective population size (Ne).
 We also pyrosequenced the DRB1-like exon 2 of the class II major
 histocompatibility complex (MHC) in 160 individuals to explore
 immunogenetic selection by WNS. We identified three major neutral genetic
 clusters: Eastern, Montane Cordillera (and adjacent sampling areas), and
 Haida Gwaii, with admixture at intermediate areas and significant
 substructure west of the prairies. Estimates of Ne were unexpectedly low
 (289–16 000). Haida Gwaii may provide temporary refuge from WNS, but the
 western mountain ranges are not barriers to its dispersal in M. lucifugus
 and are unlikely to slow its spread. Our major histocompatibility complex
 (MHC) data suggest potential selection by WNS on the MHC, but gene
 duplication limited the immunogenetic analyses.
description: Microsatellite genotypes
 for 11 loci (Myotis lucifugus)DavyEtAl.2017FACETS-Myotis_lucifugus_microsatellite_genotypes-11loci.xlsx
DOI: 10.5061/dryad.6q5g3
title: Data from: Fine-scale assessment of genetic diversity of trembling aspen in northwestern North America

description: Background In North America, the last ice age is the most recent event
 with severe consequences on boreal species’ ranges. Phylogeographic
 patterns of range expansion in trembling aspen (Populus tremuloides)
 suggested that Beringia is likely to be a refugium and the “ice-free
 corridor” in Alberta may represent a region where small populations
 persisted during the last glacial maximum (LGM). The purpose of this study
 was to ascertain whether the origins of trembling aspen in western North
 America are reflected in the patterns of neutral genetic diversity and
 population structure. A total of 28 sites were sampled covering the
 northwestern part of aspen’s distribution, from Saskatchewan to Alaska.
 Twelve microsatellite markers were used to describe patterns of genetic
 diversity. The genetic structure of trembling aspen populations was
 assessed by using multivariate analyses, Mantel correlograms,
 neighbor-joining trees and Bayesian analysis. Results Microsatellite
 markers revealed little to no neutral genetic structure of P. tremuloides
 populations in northwestern North America. Low differentiation among
 populations and small isolation by distance (IBD) were observed. The most
 probable number of clusters detected by STRUCTURE was K = 3 (∆K = 5.9).
 The individuals in the populations of the 3 clusters share a common gene
 pool and showed a high level of admixture. No evidence was found that
 either Beringia or the “ice-free corridor” were refugia. Highest allelic
 richness (AR) and lowest heterozygosity (Ho) were observed in Alberta
 foothills of the Rocky Mountains. Conclusions Contrary to our hypothesis,
 our results showed that microsatellite markers revealed little to no
 genetic structure in P. tremuloides populations. Consequently, no
 divergent populations were observed near supposed refugia. The lack of
 detectable refugia in Beringia and in the “ice-free corridor” was due to
 high levels of gene flow between trembling apsen populations. More
 favorable environmental conditions for sexual reproduction and successful
 trembling aspen seedling establishment may have contributed to increase
 allelic richness through recombination in populations from the Albertan
 foothills of the Rocky Mountains.
description: Aspen_SSR_Data_Latutrie_et _alThis excel dataset is composed of 3 pages, one with the geographical coordinates of the sampled sites, and two pages with the data in the STRUCTURE and GenAlex formats.Donnée_Phylo_chap1.xlsx
DOI: 10.5061/dryad.1573
title: Data from: Molecular genetic analysis of virus isolates from wild and cultivated plants demonstrates that East Africa is a hotspot for the evolution and diversification of Sweet potato feathery mottle virus

description: Sweet potato feathery mottle virus (SPFMV, genus Potyvirus) is globally
 the most common pathogen of cultivated sweetpotatoes (Ipomoea batatas;
 Convolvulaceae). Although &gt;100 SPFMV isolates have been
 sequence-characterized from cultivated sweetpotatos across the world,
 little is known about SPFMV isolates from wild hosts and the evolutionary
 forces shaping SPFMV population structures. In this study, forty-six SPFMV
 isolates from 14 wild species of genera Ipomoea, Hewittia, and Lepistemon
 (barcoded for the matK gene) and 13 isolates from cultivated sweetpotatoes
 were partially sequenced. Wild plants were infected with the EA, C, or O
 strain, or co-infected with the EA and C strains of SPFMV. In East Africa,
 SPFMV populations in wild species and sweetpotato were genetically
 undifferentiated, suggesting inter-host transmission of SPFMV. Globally,
 spatial diversification of the 178 isolates analyzed was observed, strain
 EA being largely geographically restricted to East Africa. Recombination
 was frequently detected in the 6K2-VPg-NIaPro region of the EA strain,
 demonstrating a recombination 'hotspot'. Recombination between
 strains EA and C was rare, despite their frequent co-infections in wild
 plants, suggesting purifying selection against strain EA/C recombinants.
 Positive selection was predicted on 17 amino acids distributed over the
 entire coat protein in the globally distributed strain C, as compared to
 only four amino acids in the coat protein N-terminus of the EA strain.
 This selection implies a more recent introduction of the C strain and a
 higher adaptation of the EA strain to the local ecosystem. Thus, East
 Africa appears as a hotspot for evolution and diversification of SPFMV.
description: UPLOADEDTOMOLECULARECOLOGYDRYADFORPUBLICUSE14-05-2010.zipThere are 23 files in the up-loaded zip folder. One is a README file giving descriptions of the other 22 data files. Please read the README file for detailed information before using the data provided in other files.