cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.923npv
title: Occurrence Download

description: A dataset containing 64 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Baccharis ulicina Hook. & Arn.",
 "Year is less than or equal to 2000",
 "Year is greater than or equal to 1970",
 {
 "or" : [
 {
 "not" : {
 "EstablishmentMeans" : [
 "is one of (MANAGED, INTRODUCED)"
 ]
 }
 },
 "EstablishmentMeans is null"
 ]
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 1000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 64 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007292-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.1jwstqjsp
title: Data from: Targeted Helping and Cooperation in Zoo-living Chimpanzees and Bonobos

description: Directly comparing the behaviour of our two closest living relatives,
 chimpanzees and bonobos, during prosocial tasks is essential to deepen our
 understanding about the evolution of human prosociality. We examined
 whether helpers of six dyads of chimpanzees and bonobos transferred tools
 to a conspecific. In experiment ‘Helping’, transferring a tool did not
 benefit the helper while in experiment ‘Cooperation’ the helper only
 obtained a reward by transferring the correct tool. Chimpanzees did not
 share tools with conspecifics in either experiment, except for a
 mother-daughter pair, where the mother shared a tool twice in experiment
 ‘Helping’. In contrast, all female-female bonobo dyads sometimes
 transferred a tool even without benefit. When helpers received an
 incentive, we found consistent transfers in all female-female bonobo dyads
 but none in male-female dyads. Even though reaching by the bonobo
 receivers increased the likelihood that a transfer occurred, we found no
 significant species difference in whether receivers reached to obtain
 tools. Thus, receivers’ behaviour might not explain the lack of transfers
 from chimpanzee helpers. This study supports the notion that bonobos might
 have a greater ability to understand social problems and the collaborative
 nature of such tasks.
description: Data_Helping
 & Cooperation_S.Nolte & J.Call Contains two data sheets
 (bonobos and chimpanzees separately) that were used for the
 analyses Data_Helping &
 Cooperation_Nolte & Call.xlsx
DOI: 10.5061/dryad.w9ghx3fn1
title: Historical review of terminology applied to cambial variants in Nyctaginaceae

description: Premise of research. The alternative patterns of secondary growth
 (vascular cambial variants) in stems of Nyctaginaceae are outstanding and
 has been widely investigated since late 19th century. However, there are
 controversial interpretations in the literature regarding the existence of
 one or two types of cambial variants (successive cambia vs. interxylary
 phloem). Thus, this study aims to explore the morphological diversity of
 stems in Nyctaginaceae, to unravel the real nature of the cambial variant
 present in most species of the family. Methodology. Altogether we analyzed
 60 species, focusing on 18 from 12 genera, which were used for the
 developmental studies. Anatomical and ontogenetic features were
 characterized from images produced by standardized plant techniques for
 macro and microscope analyses. Pivotal results. Our analyses reveal that
 most species of Nyctaginaceae present stems with polycyclic eustele, which
 later develop a single cambium that produces secondary xylem and secondary
 phloem at unequal rates along the stem circumference. This unusual
 activity results in the absence of a regular cylinder and in the formation
 of secondary phloem strands (surrounded by conjunctive tissue) which are
 embedded within the secondary xylem. In cross-section, adult stems can be
 characterized by having different arrangements (i.e., phloem islands,
 patches, concentric bands), which results from difference in rates of
 phloem and conjunctive tissue forming the strands. The cambial variant in
 these stems are described as interxylary phloem, as similarly observed in
 other eudicot lineages. Conclusions. Our examination of the stem
 development of Nyctaginaceae confirms the presence of interxylary phloem,
 which has been overlooked in the family since most studies reiterates the
 descriptions of successive cambia as the common pattern of cambial variant
 within the family. These findings emphasize the importance of
 developmental studies to further our understand of stem macromorphologies
 and highlight the complexity and diversity of stem architectures in
 Nyctaginaceae.
DOI: 10.5061/dryad.6m905qfz1
title: Snout shape and masticatory apparatus of the rodent-like mesotheriid ungulates (Typotheria, Notoungulata): Exploring evolutionary trends in dietary strategies through ancestral reconstructions

description: Mesotheriidae includes small to medium-sized herbivores that belong to the
 so-called South American native ungulates. Mesotheriids radiated from the
 early Oligocene to the early–middle Pleistocene and were traditionally
 grouped into two subfamilies: Trachytheriinae and Mesotheriinae. Beyond
 the conspicuous fossil record of the group, little is known about its
 palaeobiology and, particularly, the dietary habits. So far, different
 studies suggest grazing habits, similar to extant ungulates, but recent
 contributions are challenging this vision to some degree. In this
 contribution, we explore dietary preferences in mesotheriids, focusing on
 food intake and oral processing strategies. We performed a shape analysis
 of the snout and reconstructed ancestral shapes to assess evolutionary
 trends within the clade. Also, we considered other morphological variables
 linked to the masticatory apparatus (zygomatic plate, incisive foramina,
 cheek teeth morphology) to perform a functional characterization. Our
 results allowed us to recognize three snout configurations: Trachytherus,
 "Intermediate", and Mesotherium morphotypes that can be
 associated with different food intake capabilities and, considering also
 other morphological proxies, to consume different food items. Taking into
 account the information about palaeoenvironmental conditions, the
 evolution of the snout anatomy and associated features were interpreted in
 the context of a consumption gradient from coarse and tough foods (root,
 tuber, tough leaves) to grasses per se. We propose that during the
 ecomorphological evolution of mesotheriids, a first phase during the late
 Oligocene-Miocene took place, in which specialization to- and
 diversification within an ecomorphospace linked to the consumption of
 hard-to-break food items occurred. A second phase incipiently started
 during the late Miocene, and well-defined during Pliocene-Pleistocene,
 characterized by an ecomorphological displacement towards grazing habits.
 Inferred habits in Mesotheriidae could give light to the palaeoecological
 evolution and niche partition within South American herbivorous mammalian
 communities.
DOI: 10.5061/dryad.h18931zj6
title: Data from: Genomic signatures of artificial selection during early domestication of a wood crop

description: To determine how a century of artificial selection has changed the genome
 of E. grandis, we generated SNP genotypes for 1080 individuals from three
 advanced South African breeding programmes using the EUChip60K chip, and
 investigated population structure and genome-wide differentiation patterns
 relative to wild progenitors.
description: Genomic DNA was isolated from leaf or xylem tissue of 1080
 individual field grown <em>E. grandis</em> trees. Single
 nucleotide polymorphism (SNP) genotpying was performed for each sample
 using the EUChip60K SNP chip (Silva-Junior <em>et al.</em>,
 2015). Genotypic classes were redefined as described by
 Silva-Junior<em> et al.</em> (2015) using GenomeStudio
 (Illumina) and SNPs with unique mapping positions to the v.2 reference
 <em>E. grandis </em>genome sequence was retained.
description: The genotypes are presented in a single comma separated
 dataframe with samples in rows (n = 1080), SNP ID in columns (m = 57,567),
 and alleles separated by an underscore ( "_").  Missing data are
 indicated as "NA".
DOI: 10.5061/dryad.sbcc2fr4k
title: Plant sedimentary ancient DNA data from Far East Russia

description: Woody plants are expanding into the Arctic in response to the warming
 climate. The impact on arctic plants is not well understood due to the
 limited knowledge about plant assembly rules. Past plant diversity over
 long time series is rare. Here, we applied sedimentary ancient DNA
 metabarcoding targeting the P6 loop of the chloroplast trnL gene to a
 sediment record from Lake Ilirney (central Chukotka, Far Eastern Russia)
 covering the last 28 thousand years. Our results show that forb-rich
 steppe-tundra and dwarf-shrub tundra dominated during the cold climate
 before 14 ka, while deciduous erect-shrub tundra was abundant during the
 warm period since 14 ka. Larix invasion during the late Holocene
 substantially lagged behind the likely warmest period between 10 and 6 ka,
 where the vegetation coverage was densest. We reveal highest richness
 during 28–23 ka and a second richness peak during 13–10 ka, with both
 periods being accompanied by low shrub abundance. During the cold period
 before 14 ka, rich communities were phylogenetically clustered,
 suggesting low genetic divergence in the communities despite the great
 number of species. This probably originates from environmental filtering
 along with niche differentiation due to limited resources under harsh
 environmental conditions. In contrast, during the warmer period after 14
 ka, rich communities were phylogenetically overdispersed. This results
 from a high number of species which were found to harbor high genetic
 divergence, likely originating from an erratic recruitment process in the
 course of warming. Some of our evidence may be of relevance for inferring
 future arctic plant assembly rules and diversity changes. By analogy to
 the past, we expect a lagged response of tree invasion. Plant richness may
 overshoot in the short term; in the long-term, however, the ongoing
 expansion of deciduous shrubs will eventually result in a phylogenetically
 more diverse community.
description: The dataset is prepared for the manuscript "Plant
 sedimentary ancient DNA record from Far East Russia covering the last 28
 ka reveal different assembly rules in cold and warm climates". It
 contains the processing of the raw sequencing data using bioinfomatics
 tools. Below is the detailed data organisation: 
   1_raw_data: The raw sequencing
 files<br> R1 = Forward:
 190531_NB501850_A_L1-4_ALRK-5_R1.fastq<br> R2 = Reverse:
 190531_NB501850_A_L1-4_ALRK-5_R2.fastq
   2_scripts: The metabarcoding pipeline
 for analyzing the raw sequencing data using OBITools<br>
 Data_analyses_using_OBITools.txt  
 3_tagfile: de-multiplex tagged pooled samples<br>
 tagfile_SEQRUN.txt  
 4_database: the Arctic and Boreal vascular plant and bryophyte
 database and reference library<br> database =
 arctborbryo_gh.fasta<br> library = ecochange.zip
   5_dataset: output of the metabarcoding
 pipeline and final dataset. The final dataset is filtered as detailed in
 Supplementary_material Appendix 3.<br>
 assigned_SEQRUN_unique_clean_arctborbryo_anno.txt<br>
 final_dataset.xlsx
DOI: 10.5061/dryad.mgqnk98xm
title: Landscape genomics of a widely distributed snake (Dolichophis caspius, Gmelin, 1789) across Eastern Europe and Western Asia

description: Across the distribution of the Caspian whipsnake (Dolichophis caspius),
 populations have become increasingly disconnected due to habitat
 alterations. To understand population dynamics and the adaptive potential
 of this widespread but locally endangered snake, we investigated
 population structure, admixture and effective migration patterns. We took
 a landscape-genomic approach to identify selected genotypes associated
 with environmental variables relevant to D. caspius. With double-digest
 restriction-site associated DNA (ddRAD) sequencing of 53 samples resulting
 in 17,518 single nucleotide polymorphisms (SNPs), we identified eight
 clusters within D. caspius reflecting complex evolutionary patterns of the
 species. Estimated Effective Migration Surfaces (EEMS) revealed
 higher-than-average gene flow in most of the Balkan Peninsula and
 lower-than-average gene flow along the middle section of the Danube River.
 Landscape genomic analysis identified 751 selected genotypes correlated
 with seven climatic variables. Isothermality correlated with the highest
 number of selected genotypes (478) located in 41 genes, followed by annual
 range (127) and annual mean temperature (87). We conclude that
 environmental variables, especially the day-to-night temperature
 oscillation in comparison to the summer-to-winter oscillation, may have an
 important role in the distribution and adaptation of D. caspius.
description: One hundred twenty-four DNA samples extracted from carcass
 tissue, shed skin and blood and buccal swabs originating from eight
 European and Asian countries were collected for this study and deposited
 at the Collection of Genetic Resources of the Hungarian Natural History
 Museum in Budapest. Spatial data (longitude and latitude in decimal
 degrees) were recorded using a GPS device for each sampled individual
 (Figure 1, Table 1). We extracted DNA from buccal swabs using the
 <i>blackPREP Swab DNA Kit</i> according to kit protocols
 (Analytik Jena AG, Jena, Germany). For shed skin and carcass (liver and
 muscle) samples, the DNEasy Blood and Tissue Kit (Qiagen, Hilden, Germany)
 was applied following manufacturer’s instructions but adding 30 μl of
 Proteinase K (20 mg/μl) to increase lysis efficacy. Prior to the
 extraction, skin samples were soaked in water for 24 hours at room
 temperature and manually sliced into fragments of ~5mm to facilitate
 enzymatic lysis. Samples’ DNA quality (measured by absorbance) was
 determined using a NanoDrop 2000 spectrophotometer (Thermo Scientific,
 Waltham, USA). The 96 best extractions were selected based on a
 concentration threshold of 10 ng/μL and 260/280 ratio values &gt; 1.85
 and used for ddRAD sequencing.
DOI: 10.5061/dryad.9s4mw6mdq
title: Teaching and learning in ecology: a horizon scan of emerging challenges and solutions

description: We currently face significant, anthropogenic, global environmental
 challenges and therole of ecologists in mitigating these challenges is
 arguably more important than ever. Consequently there is an urgent need to
 recruit and train future generations of ecologists, both those whose main
 area is ecology, but also those involved in the geological, biological and
 environmental sciences. Here we present the results of a horizon scanning
 exercise that identified current and future challenges facing the teaching
 of ecology, through surveys of teachers, students and employers of
 ecologists. Key challenges identified were grouped in terms of the
 perspectives of three groups: students, for example the increasing
 disconnect between people and nature; teachers, for example the challenges
 associated with teaching the quantitative skills that are inherent to the
 study of ecology; and society, for example poor societal perceptions of
 the field of ecology. In addition to the challenges identified, we propose
 a number of solutions developed at a workshop by a team of ecology
 teaching experts, with supporting evidence of their potential to address
 many of the problems raised. These proposed solutions include developing
 living labs, teaching students to be ecological entrepreneurs and
 influencers, embedding skills-based learning and coding in the curriculum,
 an increased role for learned societies in teaching and learning, and
 using new technology to enhance fieldwork studies including virtual
 reality, artificial intelligence and realtime spoken language translation.
 Our findings are focused towards UK higher education, but they should be
 informative for students and teachers of a wide range of educational
 levels, policy makers and professional ecologists worldwide.
description: Two-part Delphi survey publicised on social media, followed by a
 workshop to explore and discuss the results.
DOI: 10.5061/dryad.5mkkwh744
title: Data from: Diabetes, brain infarcts, cognition and small vessels in the Canadian alliance for healthy hearts and minds study

description: Background:  Diabetes is a risk factor for cerebrovascular
 disease and cognitive impairment. The anatomical basis for this is
 uncertain. Methods: The Canadian Alliance for Healthy Hearts and Minds
 (CAHHM) collected brain and carotid magnetic resonance imaging (MRI) and
 two cognitive tests (DSST and MoCA) in a cross-sectional sample of men and
 women. Brain MRIs identified brain infarcts (BI), lacunar BI, high white
 matter hyperintensity (WMH), vascular brain injury (VBI - BI or high WMH)
 and small vessel VBI (lacunar BI or high WMH). Carotid MRIs estimated
 carotid wall volume, a measure of subclinical atherosclerosis. Cognitive
 scores were standardized to each site’s mean score, and cognitive
 impairment was identified by one or both test scores ≤ 1 standard
 deviation below the site’s mean score on that test.  
   Results: The 7733 participants included 495 (6.4%) with
 diabetes, of whom 388 were taking diabetes drugs. After age and sex
 adjustment, diabetes was independently associated with BI (OR 1.53, 95%CI
 1.05, 2.24), VBI (OR 1.64, 95%CI 1.26, 2.13), small vessel VBI (OR 1.67,
 95%CI 1.28, 2.19) and cognitive impairment (OR 1.47, 95%CI 1.20, 1.80).
 The association between diabetes and small vessel VBI persisted after
 adjustment for cerebrovascular disease risk factors and non-lacunar
 infarcts (OR 1.52, 95%CI 1.15, 2.01), and the association with cognitive
 impairment persisted after adjustment for small vessel VBI (OR 1.27, 95%CI
 1.03, 1.56).   Conclusion: Small vessel disease characterizes
 much of the relationship between diabetes and VBI. However, additional
 factors are required to disentangle the relationship between diabetes and
 cognitive impairment.
DOI: 10.6078/d1ct4g
title: Data from: The influence of spatially heterogeneous anthropogenic change on bill size evolution in a coastal songbird

description: Natural history collections provide an unparalleled resource for
 documenting population responses to past anthropogenic change. However, in
 many cases, traits measured on specimens may vary temporally in response
 to a number of different anthropogenic pressures or demographic processes.
 While teasing apart these different drivers is challenging, approaches
 that integrate analyses of spatial and temporal series of specimens can
 provide a robust framework for examining whether traits exhibit common
 responses to ecological variation in space and time. We applied this
 approach to analyze bill morphology variation in California Savannah
 Sparrows (Passerculus sandwichensis). We found that bill surface area
 increased in birds from higher salinity tidal marshes that are hotter and
 drier. Only the coastal subspecies, alaudinus,exhibited a
 significant increase in bill size through time. As with patterns of
 spatial
 variation, alaudinus populations occupying
 higher salinity tidal marshes that have become warmer and drier over the
 past century exhibited the greatest increases in bill surface area. We
 also found a significant negative correlation between bill surface area
 and total evaporative water loss (TEWL) and estimated that observed
 increases in bill size could result in a reduction of up to 16.2% in daily
 water losses. Together, these patterns of spatial and temporal variation
 in bill size were consistent with the hypothesis that larger bills are
 favored in freshwater-limited environments as a mechanism of dissipating
 heat, reducing reliance on evaporative cooling, and increasing water
 conservation. With museum collections increasingly being leveraged to
 understand past responses to global change, this work highlights the
 importance of considering the influence of many different axes of
 anthropogenic change and of integrating spatial and temporal series
 analyses to better understand the influence of specific human impacts on
 population change over time.
DOI: 10.5061/dryad.v15dv41ts
title: Parasite exposure and host susceptibility jointly drive the emergence of epidemics

description: Parasite transmission is thought to depend on both parasite exposure and
 host susceptibility to infection; however, the relative contribution of
 these two factors to epidemics remains unclear. We used interactions
 between an aquatic host and its fungal parasite to evaluate how parasite
 exposure and host susceptibility interact to drive epidemics. In six
 lakes, we tracked the following factors from pre-epidemic to epidemic
 emergence: 1) parasite exposure (measured observationally as fungal spores
 attacking wild-caught hosts), 2) host susceptibility (measured
 experimentally as the number of fungal spores required to produce terminal
 infection), 3) host susceptibility traits (barrier resistance and internal
 clearance, both quantified with experimental assays), and 4) parasite
 prevalence (measured observationally from wild-caught hosts). Tracking
 these factors over six months and in almost 7,000 wild-caught hosts
 provided key information on the drivers of epidemics. We found that
 epidemics depended critically on the interaction of exposure and
 susceptibility; epidemics only emerged when a host population’s level of
 exposure exceeded its individuals’ capacity for recovery. Additionally, we
 found that host internal clearance traits (the hemocyte response) were
 critical in regulating epidemics. Our study provides an empirical
 demonstration of how parasite exposure and host susceptibility interact to
 inhibit or drive disease in natural systems and demonstrates that
 epidemics can be delayed by asynchronicity in the two processes. Finally,
 our results highlight how individual host traits can scale up to influence
 broad epidemiological patterns.
description: All methods related to the present data can be found in the
 methods and appendix of Stewart Merrill et al. 2020 Ecology. 
description: <strong>Parasite_data.xlsx </strong>contains the raw
 exposure data, including each individual
 <em>Daphnia</em>'s infection stage and the number of
 spores they were exposed to.
 <strong>Immune_data.xlsx</strong> contains the raw
 susceptibility data for wildcaught <em>Daphnia</em> exposed
 experimentally to <em>Metschnikowia</em> in the lab.
 <strong>Parasite_data_summarized.xlsx</strong>
 summarizes infection stages (to provide prevalences), while also providing
 average exposure (spore counts) and susceptibility (susceptibility
 thresholds) for each lake by time combination. See
 metadata tabs in each data file for information on usage. Metadata
 describes each column header, provides supplementary information, and
 lists any exclusions that may be necessary for analyses.