cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.mm6f4
title: Data from: Biodiversity conservation in agriculture requires a multi-scale approach

description: Biodiversity loss—one of the most prominent forms of modern environmental
 change—has been heavily driven by terrestrial habitat loss and, in
 particular, the spread and intensification of agriculture. Expanding
 agricultural land-use has led to the search for strong conservation
 strategies, with some suggesting that biodiversity conservation in
 agriculture is best maximized by reducing local management intensity, such
 as fertilizer and pesticide application. Others highlight the importance
 of landscape-level approaches that incorporate natural or semi-natural
 areas in landscapes surrounding farms. Here, we show that both of these
 practices are valuable to the conservation of biodiversity, and that
 either local or landscape factors can be most crucial to conservation
 planning depending on which types of organisms one wishes to save. We
 performed a quantitative review of 266 observations taken from 31 studies
 that compared the impacts of localized (within farm) management strategies
 and landscape complexity (around farms) on the richness and abundance of
 plant, invertebrate and vertebrate species in agro-ecosystems. While both
 factors significantly impacted species richness, the richness of sessile
 plants increased with less-intensive local management, but did not
 significantly respond to landscape complexity. By contrast, the richness
 of mobile vertebrates increased with landscape complexity, but did not
 significantly increase with less-intensive local management. Invertebrate
 richness and abundance responded to both factors. Our analyses point to
 clear differences in how various groups of organisms respond to differing
 scales of management, and suggest that preservation of multiple taxonomic
 groups will require multiple scales of conservation.
description: Dataset
 S1Results of the
 literature search and the effect sizes calculated from the studies that
 fit the selection requirements.
DOI: 10.5061/dryad.s7282
title: Data from: Accelerating plant DNA barcode reference library construction using herbarium specimens: improved experimental techniques

description: A well-covered reference library is crucial for successful identification
 of species by DNA barcoding. The biggest difficulty in building such a
 reference library is the lack of materials of organisms. Herbarium
 collections are potentially an enormous resource of materials. In this
 study, we demonstrate that it is likely to build such reference libraries
 using the reconstructed (self-primed PCR amplified) DNA from the herbarium
 specimens. We used 179 rosaceous specimens to test the effects of DNA
 reconstruction, 420 randomly sampled specimens to estimate the usable
 percentage and another 223 specimens of true cherries (Cerasus, Rosaceae)
 to test the coverage of usable specimens to the species. The barcode rbcLb
 (the central four-sevenths of rbcL gene) and matK was each amplified in
 two halves and sequenced on Roche GS 454 FLX+. DNA from the herbarium
 specimens was typically shorter than 300 bp. DNA reconstruction enabled
 amplification fragments of 400–500 bp without bringing or inducing any
 sequence errors. About one-third of specimens in the national herbarium of
 China (PE) were proven usable after DNA reconstruction. The specimens in
 PE cover all Chinese true cherry species and 91.5% of vascular species
 listed in Flora of China. It is very possible to build well-covered
 reference libraries for DNA barcoding of vascular species in China. As
 exemplified in this study, DNA reconstruction and DNA-labelled
 next-generation sequencing can accelerate the construction of local
 reference libraries. By putting the local reference libraries together, a
 global library for DNA barcoding becomes closer to reality.
description: matK
 sequencesmatK-all-aligned-final-V8.fasrbcL sequencesrbcL-all-aligned-final-V5.fasRosaceae rbcL error detection sequencesRosaceae_rbcL_error_detection_v2.nex
DOI: 10.5061/dryad.6d1qm1j
title: Data from: Individual-level trait variation and negative density dependence affects growth in tropical tree seedlings

description: 1. Individual-level interactions with neighbours and their surrounding
 environments are key factors influencing performance that ultimately shape
 and maintain diversity in tropical plant communities. Theory predicts that
 the strength of these interactions depends on the similarity among
 neighbours, the turnover in composition caused by individuals that enter
 as new recruits and individuals that die, and fitting to local conditions.
 Despite considerable phenotypic variation among individuals and high
 community dynamics, these three factors have rarely been considered
 together for understanding growth variation, especially for seedling
 communities in the tropics. 2. We address this outstanding challenge by
 quantifying the influence of trait dissimilarity among neighbours,
 temporal turnover in neighbours, and individual trait variation on
 seedling growth, based on an unprecedented dataset containing
 individual-level demographic and functional trait data for tropical tree
 seedlings. 3. The results showed that trait dissimilarity associated with
 resource acquisition does not influence growth. However, conspecific
 negative density dependent effects on growth were evident through the
 initial density of conspecifics and increased in conspecifics during the
 study period. Also, individuals with relatively larger investments in leaf
 biomass allocation attained higher growth rates. 4. Synthesis: Together,
 these findings indicate that tropical seedling communities are structured
 by local abiotic factors that ultimately result in individual variation in
 resource acquisition traits and by biotic interactions driven by negative
 density dependence. These biotic interactions are highly dynamic and
 depend on conspecifics turnover, even at short temporal scales. Thus, to
 gain further insights into the forces structuring seedling communities,
 future studies should account for temporal variability in immediate
 neighbours and individual-level phenotypic variation that influence
 individual interactions.
description: tt.for.dryad
DOI: 10.5281/zenodo.18381724
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Carl August Ehrenberg, http://www.wikidata.org/entity/Q121703. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q121703
DOI: 10.5281/zenodo.8080454
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Carl August Ehrenberg, http://www.wikidata.org/entity/Q121703. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q121703
DOI: 10.5061/dryad.k380f
title: Data from: Maternal environment affects the genetic basis of seed dormancy in Arabidopsis thaliana

description: The genetic basis of seed dormancy, a key life-history trait important for
 adaptive evolution in plant populations, has yet been studied only using
 seeds produced under controlled conditions in greenhouse environments.
 However, dormancy is strongly affected by maternal environmental
 conditions, and interactions between seed genotype and maternal
 environment have been reported. Consequently, the genetic basis of
 dormancy of seeds produced under natural field conditions remains unclear.
 We examined the effect of maternal environment on the genetic architecture
 of seed dormancy using a recombinant inbred line (RIL) population derived
 from a cross between two locally adapted populations of Arabidopsis
 thaliana from Italy and Sweden. We mapped quantitative trait loci (QTL)
 for dormancy of seeds produced in the greenhouse and at the native field
 sites of the parental genotypes. The Italian genotype produced seeds with
 stronger dormancy at fruit maturation than did the Swedish genotype in all
 three environments, and the maternal field environments induced higher
 dormancy levels compared to the greenhouse environment in both genotypes.
 Across the three maternal environments, a total of nine dormancy QTL were
 detected, three of which were only detected among seeds matured in the
 field, and six of which showed significant QTL × maternal environment
 interactions. One QTL had a large effect on dormancy across all three
 environments and colocalized with the candidate gene DOG1. Our results
 demonstrate the importance of studying the genetic basis of putatively
 adaptive traits under relevant conditions.
description: Genotype and phenotype
 data for dormancy QTL analysisData file for use in
 R/qtl containing RIL genotype data and RIL mean dormancy
 phenotypes.RILgeno_phenotypes.csvR/qtl script for dormancy QTL analysisR/qtl analysis annotated scriptSeeddormancy_QTLanalysis.R
DOI: 10.5061/dryad.vc62h
title: Data from: Hybridization of an invasive shrub affects tolerance and resistance to defoliation by a biological control agent

description: Evolution has contributed to the successful invasion of exotic plant
 species in their introduced ranges, but how evolution affects particular
 control strategies is still under evaluation. For instance, classical
 biological control, a common strategy involving the utilization of highly
 specific natural enemies to control exotic pests, may be negatively
 affected by host hybridization because of shifts in plant traits, such as
 root allocation or chemical constituents. We investigated introgression
 between two parent species of the invasive shrub tamarisk (Tamarix spp.)
 in the western U.S., and how differences in plant traits affect
 interactions with a biological control agent. Introgression varied
 strongly with latitude of origin and was highly correlated with plant
 performance. Elevated levels of T. ramosissima introgression resulted in
 both higher investment in roots and tolerance to defoliation and less
 resistance to insect attack. Because tamarisk hybridization occurs
 predictably on the western U.S. landscape, managers may be able to exploit
 this information to maximize control efforts. Genetic differentiation in
 plant traits in this system underpin the importance of plant hybridization
 and may explain why some biological control releases are more successful
 than others.
description: Raw_data_AFLPs_Williams_et_alAFLP data for all tamarisk plants in the studyRaw_data_Performance_and_Tolerance_Williams_et_alPlant performance and tolerance data for outdoor experimentRaw_data_Resistance_Williams_et_alReistance and larval performance data for bioassay experiment with plant pellets
DOI: 10.5061/dryad.h781v
title: Data from: The microbially-mediated soil organic carbon loss under degenerative succession in an alpine meadow

description: Land-cover change has long been recognized as having marked effect on the
 amount of soil organic carbon (SOC). However, the microbially-mediated
 processes and mechanisms on SOC are still unclear. In this study, the soil
 samples in a degenerative succession from alpine meadow to alpine steppe
 meadow in the Qinghai-Tibetan Plateau were analyzed using high-throughput
 technologies, including Illumina sequencing and GeoChip functional gene
 arrays. The soil microbial community structure and diversity were
 significantly (P &lt; 0.05) different between alpine meadow and alpine
 steppe meadow, the microbial ɑ-diversity in alpine steppe meadow was
 significantly (P &lt; 0.01) higher than in alpine meadow. Molecular
 ecological network analysis indicated that the microbial community
 structure in alpine steppe meadow was more complex and tighter than in the
 alpine meadow. The relative abundance of soil microbial labile carbon
 degradation genes (e.g., pectin and hemicellulose) was significantly
 higher in alpine steppe meadow than in alpine meadow, but the relative
 abundance of soil recalcitrant carbon degradation genes (e.g. chitin and
 lignin) showed the opposite tendency. The Biolog Ecoplate experiment
 showed that microbially-mediated soil carbon utilization was more active
 in alpine steppe meadow than in alpine meadow. Consequently, more soil
 labile carbon might be decomposed in alpine steppe meadow than in alpine
 meadow. Therefore, the degenerative succession of alpine meadow because of
 climate change or anthropogenic activities would most likely decreased SOC
 and nutrients medicated by changing soil microbial community structure and
 their functional potentials for carbon decomposition.
description: Microbial community and
 network of meadow alpine soil by Illumina sequencingThe Qinghai-Tibet
 Plateau is the highest and the largest low-latitude plateau in the world,
 and also it is an extremely sensitive region to the impact of global
 warming and environmental changes. The alpine meadow, widely distributed
 on the Tibetan Plateau, occupies over 40% of the Qinghai-Tibetan Plateau
 area and plays a critical role in regional sustainable development,
 biodiversity and water resource conservation. The alpine meadow also was a
 large soil organic-carbon pool.In recently decades, succession and
 degradation were gradually occurring between different alpine meadow
 types, such as alpine meadow might appear in the alpine steppe meadow
 region according to years of field investigation which could be the
 consequences of the climate warming and anthropogenic activities. The aims
 of our study were to determine the effect of degenerated succession from
 alpine meadow (AM) to alpine steppe meadow (ASM) on soil organic carbon
 and soil microbial community structure.The archived files included one OTU
 table generated from the 16S rRNA gene sequencing data, as well as the
 input and output files for the network analyses.Dryad data
 deposit.7z
DOI: 10.5281/zenodo.18318772
title: Magellan GTDR anomalies

description: # Created by Gerard Gallardo i Peres# ---------------------------------------------------------#### ----------------------------------------------------------# Author:   Gerard Gallardo i Peres /  Imperial College London, isardSAT## Reviewers:  Dr. Philippa J. Mason   /  Prof. Richard C. Ghail###################################################################################                            #######                            #######          #####################################            ##########           ###############          #####################################           ##########           ###############          #####################################          ##########           ###############          #################################                        #######                            #######                           ###################################################################################################

This dataset contains maps of the potential anomalies and low quality pixels of the GTDR volume mg_3002 and the GTDR volume mg_3003. Each of these maps shows the anomalies and associated variables in Mercator and Sinusoidal projection, generated and projected from/as described in:

https://pds-geosciences.wustl.edu/mgn/mgn-v-gxdr-v1/mg_3002/document/gxdr.txt

The map files are all in GeoTIFF format and are projected using the 1985 COSPAR Venus reference ellipsoid (https://epsg.io/104901). They are embedded with the complete georeferencing metadata (coordinate reference system, geotransform, and spatial extent) to facilitate their direct use in GIS software. The _anomaly maps show the location of the potential anomalies, with pixel values equal to -99999. The _lq_pixels maps show the location of the potential anomalies and their surrounding 'low quality' neighbours, with pixel values equal to -99999. These are overlain on top of the corresponding GTDR topography, given as values of elevation above the reference radius value of the product R = 6039999 m. Pixel values equal to 0 correspond to data gaps from the original GTDR products or to pixels outside the projection area. 

*Note: we recommend using the Mercator 3003 version of the files as the standard/reference one.
DOI: 10.5281/zenodo.14808956
title: Magellan GTDR anomalies

description: # Created by Gerard Gallardo i Peres# ---------------------------------------------------------#### ----------------------------------------------------------# Author:   Gerard Gallardo i Peres /  Imperial College London, isardSAT## Reviewers:  Dr. Philippa J. Mason   /  Prof. Richard C. Ghail###################################################################################                            #######                            #######          #####################################            ##########           ###############          #####################################           ##########           ###############          #####################################          ##########           ###############          #################################                        #######                            #######                           ###################################################################################################

This dataset contains maps of the potential anomalies and low quality pixels of the GTDR volume mg_3002 and the GTDR volume mg_3003. Each of these maps shows the anomalies and associated variables in Mercator and Sinusoidal projection, generated and projected from/as described in:

https://pds-geosciences.wustl.edu/mgn/mgn-v-gxdr-v1/mg_3002/document/gxdr.txt

The map files are all in GeoTIFF format and are projected using the 1985 COSPAR Venus reference ellipsoid (https://epsg.io/104901). They are embedded with the complete georeferencing metadata (coordinate reference system, geotransform, and spatial extent) to facilitate their direct use in GIS software. The _anomaly maps show the location of the potential anomalies, with pixel values equal to -99999. The _lq_pixels maps show the location of the potential anomalies and their surrounding 'low quality' neighbours, with pixel values equal to -99999. These are overlain on top of the corresponding GTDR topography, given as values of elevation above the reference radius value of the product R = 6039999 m. Pixel values equal to 0 correspond to data gaps from the original GTDR products or to pixels outside the projection area. 

*Note: we recommend using the Mercator 3003 version of the files as the standard/reference one.
DOI: 10.5061/dryad.t2g67
title: Data from: The tale of the shrinking weapon: seasonal changes in nutrition affect weapon size and sexual dimorphism, but not contemporary evolution

description: Sexually selected traits are often highly variable in size within
 populations due to their close link with the physical condition of
 individuals. Nutrition has a large impact on physical condition, and thus,
 any seasonal changes in nutritional quality are predicted to alter the
 average size of sexually selected traits as well as the degree of sexual
 dimorphism in populations. However, although traits affected by mate
 choice are well studied, we have a surprising lack of knowledge of how
 natural variation in nutrition affects the expression of sexually selected
 weapons and sexual dimorphism. Further, few studies explicitly test for
 differences in the heritability and mean-scaled evolvability of sexually
 selected traits across conditions. We studied Narnia femorata (Hemiptera:
 Coreidae), an insect where males use their hind legs as weapons and the
 femurs are enlarged, to understand the extent to which weapon expression,
 sexual dimorphism and evolvability change across the actual range of
 nutrition available in the wild. We found that insects raised on a poor
 diet (cactus without fruit) are nearly monomorphic, whereas those raised
 on a high-quality diet (cactus with ripe fruit) are distinctly sexually
 dimorphic via the expression of large hind leg weapons in males. Contrary
 to our expectations, we found little evidence of a potential for
 evolutionary change for any trait measured. Thus, although we show weapons
 are highly condition dependent, and changes in weapon expression and
 dimorphism could alter evolutionary dynamics, our populations are unlikely
 to experience further evolutionary changes under current conditions.
description: Dryad submission Miller
 McDonald MooreProvides sire and dam
 ID's as well as diet treatment and morphological trait
 measurements
DOI: 10.5061/dryad.nn3j4
title: Data from: Statistical inference of allopolyploid species networks in the presence of incomplete lineage sorting

description: Polyploidy is an important speciation mechanism, particularly in land
 plants. Allopolyploid species are formed after hybridization between
 otherwise intersterile parental species. Recent theoretical progress has
 led to successful implementation of species tree models that take
 population genetic parameters into account. However, these models have not
 included allopolyploid hybridization and the special problems imposed when
 species trees of allopolyploids are inferred. Here, two new models for the
 statistical inference of the evolutionary history of allopolyploids are
 evaluated using simulations and demonstrated on two empirical data sets.
 It is assumed that there has been a single hybridization event between two
 diploid species resulting in a genomic allotetraploid. The evolutionary
 history can be represented as a species network or as a multi-labeled
 species tree, in which some pairs of tips are labeled with the same
 species. In one of the models (AlloppMUL), the multi-labeled species tree
 is inferred directly. This is the simplest model and the most widely
 applicable, since fewer assumptions are made. The second model (AlloppNET)
 incorporates the hybridization event explicitly which means that fewer
 parameters need to be estimated. Both models are implemented in the BEAST
 framework. Simulations show that both models are useful and that AlloppNET
 is more accurate if the assumptions it is based on are valid. The models
 are demonstrated on previously analyzed data from the genus Pachycladon
 (Brassicaceae) and from the genus Silene (Caryophyllaceae).
description: Data, R code,
 manualSee
 README.txtSuppFiles.zip