cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.88w4ws
title: Occurrence Download

description: A dataset containing 58 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Gastrodia elata",
 "Year 1975-2026"
 ]
}

 The dataset includes 58 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003124-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.12jm63z10
title: Comparative physiology of canopy tree leaves in evergreen and deciduous forests in lowland Thailand

description: Three major forest types in lowland Thailand and its adjacent parts in
 Southeast Asia are mixed deciduous forest (MDF), dry dipterocarp forest
 (DDF) and dry evergreen forest (DEF). We report the leaf physiology of
 canopy trees in these forests. The leaf mass-based photosynthetic rates
 (Amax), stomatal conductance (Gmax) and photosynthetic nitrogen use
 efficiency were significantly different between the deciduous forests (MDF
 and DDF) and the evergreen forest (DEF). The canopy trees of MDF with
 thick, eutrophic soils had the highest intrinsic water use efficiency
 (Amax/Gmax) among the forest types. Forest-to-forest variations in leaf
 mass area were related to different nutrient use strategies (less vs. more
 conservative) associated with different soil nutrients rather than with
 leaf phenology/longevity. In the interspecific variations within each
 forest, Amax in MDF and DEF was limited by foliar phosphate, whereas that
 in DDF was limited by foliar nitrogen. The close association between leaf
 physiology and soil properties suggests that climate change and increasing
 human impacts will disrupt this association, leading to forest degradation
 and dysfunction.
description: We examined leaf gas exchange in the canoy leaves of the mixed deciduous forest (MDF), dry dipterocarp
 forest (DDF) and dry evergreen forest (DEF) in Thailand, using LI-6400.
 After the mesurements in the fields, we collected leaf disks from the
 leaves and then examined leaf mass per area, nutrients (nitrogen,
 phosphate, calcium, magnesium,
 potassium) and delta 13C in our
 labopratory.
DOI: 10.15468/dl.qszdpv
title: Occurrence Download

description: A dataset containing 3896341 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Asia",
 "Country is China",
 "DatasetKey is EOD – eBird Observation Dataset",
 "Year 2012-2026"
 ]
}

 The dataset includes 3896341 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003120-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.cfxpnvx7s
title: Demographic consequences of heterogeneity in conspecific density dependence among mast fruiting tropical trees

description: The role of conspecific density dependence (CDD) in the maintenance of
 species richness is a central focus of tropical forest ecology. However,
 tests of CDD often ignore the integrated effects of CDD over multiple
 life-stages and their long-term impacts on population demography. We
 combined a 10-year time series of seed production, seedling recruitment
 and sapling and tree demography of three dominant Southeast Asian tree
 species that adopt a mast fruiting phenology. We used these data to
 construct individual-based models that examine the effects of CDD on
 population growth rates (λ) across life-history stages. Recruitment was
 driven by positive CDD for all species, supporting the predator satiation
 hypothesis, while negative CDD affected seedling and sapling growth of two
 species, significantly reducing λ. This negative CDD on juvenile growth
 overshadowed the positive CDD of recruitment, suggesting the cumulative
 effects of CDD during seedling and sapling development has greater
 importance than the positive CDD during infrequent masting events.
 Overall, CDD varied between positive and negative across life-history
 stages for all species, suggesting that assessments of CDD on transitions
 between just two stages (e.g. seeds-seedlings or juveniles-mature trees)
 likely misrepresents the importance of CDD on population growth and
 stability.
description: We placed nine plots of 2 × 2 m
 around each mature tree, located along three transects radiating from the
 stem at 0°, 120° and 240° N to prevent directional biases in seed fall
 from factors such as wind and slope. Along each transect, plots were
 centred at 2 m (directly under the crown), 6 m (crown edge) and 18 m
 (outside the crown) from the stem. There was a total of 81 plots (3
 species × 3 mature trees per species × 9 plots per tree = 81 plots). These
 plots allowed us to assess the role of conspecific density dependence on
 seed, seedling and sapling dynamics.In addition to the detailed seedling
 data, we used the two censuses from the Forest Global Earth Observatory
 plot (ForestGEO; 50-ha area of primary forest), located in the Danum
 Valley Conservation Area (approximately 20 km from the seedling census
 plots), to estimate growth and survival of trees. These data were
 collected following standard protocols, which includes mapping,
 identifying and measuring the diameter at breast height of all stems
 greater than 10 mm. The first census began in 2010 and finished in 2016,
 and the second census began in 2018 and finished in 2019.
description: Part of this data comes from the ForestGEO plot network and use
 of this data comes with restrictions. It should be accessed from the
 ForestGEO portal directly. The use of the seed and seedling should
 consider including Michael O'Brien on any publications as it
 represents over a decade of continuous data collection.
DOI: 10.5061/dryad.q2bvq83n9
title: A relatively higher mutation rate in African humans is the dominant mechanism causing Neanderthals to appear closer to non-Africans, not introgression

description: It is widely thought that humans carry genetic legacies due to
 inter-breeding with Neanderthals, but all methods used to infer legacies
 ignore recurrent mutations and assume a constant mutation rate. These
 assumptions cause automatic rejection of a second hypothesis, where a
 higher mutation rate in Africans caused increased divergence from
 Neanderthals. Any fair test should strive to treat both hypotheses
 equally. Here I use mutation spectra, the relative frequencies of
 different mutating three-base combinations, to compare contrasting
 expectations from the two hypotheses. I find that putative introgressed
 bases are strongly enriched for recurrent mutations and lie in regions
 with unusually high mutation rates, distorted mutation spectra and
 unusually large African minus non-African heterozygosity differences.
 Moreover, putative introgressed bases should be absent from Africa and
 rare outside, yet almost the entire signal of introgression is carried by
 sites where putative Neanderthal alleles are fixed in non-Africans and at
 high frequency in Africans. Together, these observations support a model
 where signals of introgression are driven mostly or even entirely by
 mutation rate differences between human populations. This new model helps
 to explain why introgression is inferred ubiquitously, including in
 scenarios involving great apes where inter-breeding is biologically
 implausible. 
description: These data comprise compressed processed master files for
 individual chromosomes containing aligned sequence data for humans (1000
 genomes phase 3, either the low coverage GR37 or high coverage GR38),
 Neanderthals (the three high coverage genomes), the Denisovan and the
 chimpanzee. These files were compiled using custom C++ scripts (Archaic
 Masters) / vcftools (Master files). Full details of the file format are
 given in the ReadMe file. All raw source files are available in public
 data repositories. 
description: These masterfiles are designed to be processed using the C++
 scripts given in Electonic Supplementary Materials in the paper.
 Bioinformaticians (which I am not!) may well be able to analyse the public
 domain data rapidly and directly, but I choose to use these derivative
 files to speed up analyses. To conduct all analyses presented in the
 paper, you will need to download individual GR38 fasta files for each
 human chromosome (https://hgdownload.soe.ucsc.edu/goldenPath/hg38/chromosomes/) and edit the C++ scripts to make sure that the paths are all valid for the local computer. I am more than happy to help advise as far as I am able with any problems encountered.
DOI: 10.57707/fmi-b2share.0jzcm-1ve62
title: PV production data with ancillary PV and meteorological data including solar radiation measurements from FMI's open-air solar laboratories in Helsinki, Kuopio and Sodankylä (Finland) starting from August 2015 and ending Dec 2021

description: The data is described in Karhu et al. (2025) (to be submitted to Geoscience Data Journal). 

The data files (*.csv) are PV system specific i.e. each data file contains all meteorological ancillary-PV and PV production data from one of the four different systems specifically. Each data file has a header explaining the variables (separated with ';'). The variables are somewhat different from site to site.

FMI_Helsinki_PV.csv
FMI_Kuopio_PV.csv
FMI_Sodankyla_20deg_PV.csv
FMI_Sodankyla_90deg_PV.csv

In addition to the data files there is a compressed tar archive containing hourly taken photographic images of the modules of the FMI's open-air solar laboratory in Sodankylä:

Sodankyla_module_images_2018-2021.tar.gz
DOI: 10.57707/fmi-b2share.bg6ws-1gk41
title: PV production data with ancillary PV and meteorological data including solar radiation measurements from FMI's open-air solar laboratories in Helsinki, Kuopio and Sodankylä (Finland) starting from August 2015 and ending Dec 2021

description: The data is described in Karhu et al. (2025) (to be submitted to Geoscience Data Journal). 

The data files (*.csv) are PV system specific i.e. each data file contains all meteorological ancillary-PV and PV production data from one of the four different systems specifically. Each data file has a header explaining the variables (separated with ';'). The variables are somewhat different from site to site.

FMI_Helsinki_PV.csv
FMI_Kuopio_PV.csv
FMI_Sodankyla_20deg_PV.csv
FMI_Sodankyla_90deg_PV.csv

In addition to the data files there is a compressed tar archive containing hourly taken photographic images of the modules of the FMI's open-air solar laboratory in Sodankylä:

Sodankyla_module_images_2018-2021.tar.gz
DOI: 10.5061/dryad.w6m905qrv
title: Characterization data for the EtNAM population and Ethiopian durum wheat landraces diversity panel

description: In smallholder, low-input farming systems diffused in the Global South,
 farmers select and propagate crop varieties based on their traditional
 knowledge and experience. A quantitative integration of their knowledge
 into breeding pipelines may support the sustainable intensification of
 local farming. This data entry combines genomics with socioeconomics to
 tap into traditional knowledge in smallholder farming systems, focusing on
 durum wheat (Triticum durum Desf.). Data refer to a large nested
 association mapping (EtNAM) population that we developed by recombining
 elite international breeding line with Ethiopian traditional varieties
 maintained by local farmers. This entry carries also molecular and
 phenotypic data produced on a diversity panel (DP) of Ethiopian landraces
 previously characterized in four year-location combinations and published
 in Mengistu et al 2016 (https://doi.org/10.1111/pbi.12538). 
 EtNAM lines and DP genotypes were evaluated for agronomic performances and
 farmers’ appreciation in multiple locations, reveailing that gender and
 location can influence farmers’ preference and that women and men farmers
 can consistently identify the best durum wheat genotypes. We used this
 data to train a genomic selection (GS) model with farmer scores to show
 that their prediction accuracy over grain yield was higher than that of
 the benchmark GS model trained on grain yield. The data was also used in a
 genome wide association mapping (GWAS) and quantitative trait locus (QTL)
 mapping to identify genetic determinants of agronomic traits and farmer
 scores.  Our data shows that farmers’ traditional knowledge can
 be integrated in a quantitative framework to increase genetic gain in
 pre-breeding programs, supporting genomics-driven breeding for local
 adaptation. The Rdata files contain phenotypic and molecular
 characterization data for 1,200 recombinant inbred lines (RILs) deriving
 from the EtNAM and phenotypic and molecular characterization data for 400
 durum wheat genotypes in the Ethiopian DP.
description: Phenotypic data includes agronomic traits and participatory
 variety selection data collected in muiltiple locations in Ethiopia.
 Molecular charatcterization data is based on the wheat SNP array provided
 by TraitGenetics. Data has been processed for basic QC. See README for
 details 
description: Data included in this entry shoud be analyzed with the open
 source program R (https://cran.r-project.org/)
DOI: 10.5061/dryad.xd2547dk3
title: Invasive brown widow spiders disperse aerially under a broad range of environmental conditions

description: Spiders commonly disperse on silk lines as juveniles by
 means of rappelling or ballooning. These modes of dispersal, especially
 long-distance dispersal via ballooning, can greatly increase the distance
 an individual can move, and at the population level, the speed of
 range expansion and likelihood of gene
 flow. Nevertheless, few studies have examined how spiders
 disperse under field conditions, and which environmental and
 meteorological conditions may affect their decision to disperse.
 We tested dispersal by spiderlings of the invasive brown
 widow (Latrodectus geometricus) under field conditions
 in the Negev Desert of Israel.
 We documented pre-dispersal (climbing and tiptoeing) and
 dispersal (short-distance dispersal by rappelling and long-distance
 dispersal by ballooning) behaviours during the day (n = 147
 spiders) and night (n = 171 spiders), while recording
 wind speed, temperature, and humidity. We found that
 spiders ballooned significantly more during the day (14.3%) compared with
 1.8% of spiders ballooning at night. At night, spiders were more likely to
 disperse in conditions of higher wind speeds, lower temperature, and
 higher humidity, whereas during the day, environmental factors were less
 predictive of dispersal behaviour. In addition, we found significant
 differences in the proportion of spiderlings showing pre-dispersal and
 dispersal behaviour depending on family line. In conjunction with
 human-mediated dispersal, ballooning and rappelling may be an important
 mechanism of range expansion in the brown widow
 spider. Understanding the environmental and genetic factors
 affecting dispersal may lead to better management of invasive species.
description: These environmental data were collected using an Alnor anemometer
 (AVM-440, TSI) in the environs of the Jacob Blaustein Center for Desert
 Research, Midreshet Ben-Gurion, Israel. The spiderling behavioural data
 were collected by observing and classifying spider behaviour.
DOI: 10.5061/dryad.ghx3ffbrh
title: Global distribution and evolutionary transitions of floral symmetry in angiosperms

description: Floral symmetry plays a crucial role in plant-pollinator interactions and
 has remarkable impacts on angiosperm evolution. However, the
 spatiotemporal patterns in floral symmetry and drivers of these patterns
 remain poorly known. Here, using global distributions and floral symmetry
 data of 280,140 angiosperm species, we presented the global geographic and
 evolutionary patterns of floral symmetry composition and demonstrated the
 climatic drivers of these patterns. We found that the frequency of
 actinomorphic (radial) species increased with latitude, while that of
 zygomorphic (bilateral) species decreased. Solar radiation, present-day
 temperature and Quaternary temperature change explained the geographic
 variation in floral symmetry. Evolutionary transitions from actinomorphy
 to zygomorphy dominated floral symmetry evolution, although the rate of
 this transition decreased through the Cenozoic associated with decreasing
 paleo-temperature. Our study provides novel insights into the ecology and
 evolution of angiosperm floral symmetry and suggests that climate change
 may influence species distributions via its effect on floral symmetry.
DOI: 10.5061/dryad.sn02v6x6m
title: Rapid diversification of the Australian Amitermes group during late Cenozoic climate change

description: Late Cenozoic climate change led to the progressive aridification of
 Australia over the past 15 million years. This gradual biome turnover
 fundamentally changed Australia’s ecosystems, opening new niches and
 prompting diversification of plants and animals. One example are termites
 of the Australian Amitermes Group (AAG), consisting of the Australian
 Amitermes and affiliated genera. Although the most speciose and diverse
 higher termite group in Australia, little is known about its evolutionary
 history. We used ancestral range reconstruction and diversification
 analyses to illuminate (1) phylogenetic relationships of the AAG, (2)
 biogeographical processes leading to the current continent-wide
 distribution, and (3) timing and pattern of diversification in the context
 of late Cenozoic climate change. By estimating the largest time-calibrated
 phylogeny for this group to date, we demonstrate monophyly of the AAG and
 confirm that their ancestor arrived in Australia ~11-10 million years ago
 from Southeast Asia. Ancestral range reconstruction indicates that
 Australia’s monsoon region was the launching point for a continental
 radiation shaped by dispersal and within-biome speciation rather than
 vicariance. We found that multiple arid-zone species diversified from
 mesic and tropical ancestors in the Plio-Pleistocene, but also observed
 diversification in the opposite direction. Finally, we show that
 diversification steadily increased from ~8-9 Ma during the “Hill Gap” and
 accelerated from ~4 Ma in concert with major ecological change during the
 Pliocene. Consistent with rapid diversification, species accumulation then
 slowed down into the present, likely caused by progressive niche
 saturation. This study provides a stepping stone for predicting future
 responses of Australia's termite fauna in the face of human-mediated
 climate change.
description: <strong>Data includes Nexus alignment files and
 reconstructed phylogenetic trees.</strong>
 <strong>heimburgeretal2022_original_beast_tree.nex</strong> --&gt; time-dated pyhlogeny reconstructed with BEAST 2.6.1 including all 135 mitochondrial genome sequences <strong>heimburgeretal2022_original_iqtree.nwk</strong> --&gt; maximum-likelihood phylogeny reconstructed with IQ-TREE ver. 2.0.6 including all 135 mitochondrial genome sequences <strong>heimburgeretal2022_posterior_trees.nex</strong> --&gt; 100 randomly sampled, pruned trees from the posterior distribution of the Bayesian analysis <strong>heimburgeretal2022_pruned_beast_tree.nex</strong> --&gt; pruned time-dated phylogeny including non-Australian <em>Amitermes</em> and AAG taxa (for more details see Materials and Methods) <strong>heimburgeretal2022_with_3rd_codon_position.nex</strong> --&gt; Nexus alignment including 135 termite taxa and 3rd codon positions <strong>heimburgeretal2022_without_3rd_codon_position.nex</strong> --&gt; Nexus alignment including 135 termite taxa without 3rd codon positions (for more details see Materials and Methods)
DOI: 10.5061/dryad.zgmsbccdq
title: Hybrid evolution repeats itself across environmental contexts in Texas sunflowers (Helianthus)

description: To what extent is evolution repeatable? Little is known about whether the
 evolution of hybrids is more (or less) repeatable than non-hybrids. We
 used field experimental evolution in annual sunflowers (Helianthus) in
 Texas to ask the extent to which hybrid evolution is repeatable across
 environments compared to non-hybrid controls. We created hybrids between
 Helianthus annuus (L.) and H. debilis (Nutt.) and grew plots of both
 hybrids and non-hybrid controls through eight generations at three sites
 in Texas. We collected seeds from each generation and grew each generation
 × treatment × home site combination at two final common gardens. We
 estimated the strength and direction of evolution in terms of fitness and
 24 traits, tested for repeated versus non-repeated evolution, and assessed
 overall phenotypic evolution across lineages and in relation to a locally
 adapted phenotype. Hybrids consistently evolved higher fitness over time
 while controls did not, though trait evolution varied in strength across
 home sites. Repeated evolution was more evident in hybrids versus
 non-hybrid controls, and hybrid evolution was often in the direction of
 the locally adapted phenotype. Our findings have implications for both the
 nature of repeatability in evolution and the contribution of hybridization
 to evolution across environmental contexts.
description: Data were collected from common gardens in 2017 and 2019. Data
 were collected on paper, transcribed to Microsoft Excel, then processed
 using R.
DOI: 10.5061/dryad.xksn02vj7
title: The effect of flight efficiency on gap‐crossing ability in Amazonian forest birds

description: We used this dataset to examine the role of flight efficiency on
 gap-crossing ability in Amazonian forest birds. We used data from the
 Biological Dynamics of Forest Fragments Projects on recaptures of banded
 birds in an Amazonian forest bisected by a road. For a total of 45
 species, we estimated flight efficiency using the hand-wing index (a proxy
 for the wing’s aspect ratio) and used it as a predictor of the probability
 of road crossing in phylogenetic binomial regression models. We found that
 flight efficiency was a strong predictor of road-crossing probability:
 species with high hand-wing indices crossed the road more frequently than
 those with low hand-wing indices. In contrast, other characteristics such
 as body mass, diet, flocking behavior, and foraging stratum did not show
 significant associations with road crossing probability. Our results
 suggest that proxies of flight efficiency such as the hand-wing index can
 be powerful tools for predicting the vulnerability of bird species to
 forest fragmentation.
description: See Claramunt et al. 2022 https://doi.org/10.1111/btp.13109
description: See Claramunt et al. 2022 https://doi.org/10.1111/btp.13109