cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.fttdz08t7
title: β diversity among ant communities on fragmented habitat islands: the roles of species trait, phylogeny and abundance

description: Habitat loss and fragmentation reduce biodiversity and alter species
 composition in local communities. β diversity describes the variation in
 species composition between or among communities in fragmented landscapes
 and has two components: species turnover and nestedness. In this study, we
 assessed β diversity of ant assemblages on 24 island fragments in the
 Thousand Island Lake, China. We constructed a species-level phylogenetic
 tree and measured five morphological traits of all ant species captured.
 We then assessed taxonomic (both incidence-based and abundance-weighted),
 functional, and phylogenetic β diversity and partitioned β diversity into
 turnover and nestedness (as well as the contributions of particular
 species and particular islands). Finally, we examined the relationships
 between β diversity and a suite of geographical variables (i.e.,
 difference in island area, difference in isolation and inter-island
 distance) using Mantel tests. We found taxonomic and phylogenetic turnover
 components dominated overall β diversity whereas the functional turnover
 and nestedness components contributed equally to overall β diversity.
 Overall β diversity increased with increasing differences in isolation and
 inter-island distance, however, only abundance-weighted overall β
 diversity decreased with increasing differences in island size. Our
 results indicate that species that were abundant on large islands were
 also abundant on small islands. We conclude that dispersal limitation of
 ants likely shapes the pattern of β-diversity along isolation and
 inter-island distance gradients. Additionally, functional redundancy of
 species (i.e., different species share similar functional roles) could
 also explain β-diversity patterns among fragmented habitat islands. Our
 results highlight the necessity of incorporating both incidence-based and
 abundance-weighted community data when examining β diversity in fragmented
 landscapes. By partitioning β diversity into the contributions of
 particular species and particular fragments, our study implies that small
 patches can be valuable for maintaining biodiversity among ant
 communities.
description: Rarefied abundance-based community data, trait data, phylogenetic
 tree, and island variable data used to estimate the taxonomic (both
 incidence-based and abundance-weighted), functional and phylogenetic beta
 diversity of ants communities on 24 fragmeneted islands in the Thousand
 Island Lake, China.
DOI: 10.5061/dryad.b8gtht7d1
title: Data from: Coalescence times, life history traits and conservation concerns: an example from four coastal shark species from the Indo-Pacific

description: Dispersal abilities play a crucial role in shaping the extent of
 population genetic structure, with more mobile species being panmictic
 over large geographic ranges and less mobile ones organized in
 meta-populations exchanging migrants to different degrees. In turn,
 population structure directly influences the coalescence pattern of the
 sampled lineages, but the consequences on the estimated variation of the
 effective population size (Ne) over time obtained by means
 of unstructureddemographic models remain poorly understood.
 However, this knowledge is crucial for biologically interpreting the
 observed Ne trajectory and further devising conservation
 strategies in endangered species. Here we investigated
 the demographic history of four shark species (Carharhinus
 melanopterus, Carharhinus limbatus, Carharhinus
 amblyrhynchos, Galeocerdo cuvier) with different degrees of
 endangered status and life history traits related to dispersal distributed
 in the Indo-Pacific and sampled off New Caledonia. We compared several
 evolutionary scenarios representing
 both structured (meta-population)
 and unstructured models and then inferred
 the Ne variation through time. By performing extensive
 coalescent simulations, we provided a general framework relating the
 underlying population structure and the
 observed Ne dynamics. On this basis, we concluded that
 the recent decline observed in three out of the four considered species
 when assuming unstructured demographic models can be
 explained by the presence of population structure. Furthermore, we also
 demonstrated the limits of the inferences based on the sole site frequency
 spectrum and warn that statistics based on linkage disequilibrium will be
 needed to exclude recent demographic events affecting meta-populations.
DOI: 10.57841/casdc.0007108
title: 电化学自动化测试工作站记录数据
DOI: 10.5061/dryad.t1g1jwt2v
title: Transcriptome dataset to: Chemical genetics in Silene latifolia elucidate regulatory pathways involved in gynoecium development

description: This collection contains RNA-seq data obtained from young flower
 buds of Silene latifolia for each sample in the main manuscript
 in triplicate (male, female, two generations of hermaphrodites). The RNA
 was isolated from adult plants of U15 population and two subsequent
 generations, made by full-sib mating (U15=15 generations, U16=16
 generations, U17=17 generations). The petals and sepals were removed
 before RNA-isolation. To avoid the bias made by sampling of old flower
 buds, only the first flowers were always sampled. The deposited RNA-seq
 data were not processed. 
description: <strong>RNA
 isolation</strong> RNA was isolated in biological
 triplicates from <em>Silene latifolia </em>flowers of stage 11
 based on Zluvova <i>et. al</i>. (2007). Transcriptome
 sequencing libraries were prepared from total RNA with the Illumina TruSeq
 mRNA Library Prep Kit at the Genomics Core Facility (Genecore, EMBL,
 Heidelberg). The sequencing of the libraries was conducted at the Genecore
 on Illumina NextSeq500 instrument with 75-bp paired-end reads. The quality
 of sequencing reads was inspected in FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastq).  <strong>References</strong> Zluvova J, Georgiev S, Janousek B, Charlesworth D, Vyskot B, Negrutiu I. Early events in the evolution of the Silene latifolia Y chromosome: male specialization and recombination arrest. <i>Genetics</i>. 2007;177(1):375-386. doi:10.1534/genetics.107.071175
description: Please, find the "ReadMe" file. Note that there are no
 missing values.
DOI: 10.5061/dryad.jq2bvq890
title: Proximity to natural habitat and flower plantings increases insect populations and pollination services in South African apple orchards

description: Introducing areas of wildflower vegetation within crop fields has been
 shown to enhance pollinator activity and pollination services to crops,
 and findings in Europe showed an interaction effect between floral
 treatments and landscape context. Natural fynbos patches in the South
 African Cape Floristic Region (CFR) are potential reservoirs for
 beneficial insects that could enhance pollinator populations and crop
 pollination in commercial apple orchards. However, the effect of proximity
 to natural habitat and floral enhancement treatments on crop pollinators
 and yield are yet to be fully tested in southern temperate regions. To
 elucidate the impact of enhanced floral resources to apple flower visitors
 and crop yield, we established small experimental patches of flowers in
 non-productive areas of commercial apple (Malus domestica) orchards in the
 CFR. Experimental orchards were embedded in landscapes with varying
 proportions of natural habitat within 1 km. We used pollinator exclusion
 experiments to determine the benefits of insect pollination on apple
 yield, quality and economic value.  We found that the primary
 pollinators of apple flowers in the region is the endemic Cape honey bee,
 Apis mellifera capensis. Floral plantings enhanced overall pollinator
 abundance and honey bee flower visitation within the orchards, and
 positively affected apple size and economic value. Increased landscape
 complexity had a significantly positive effect on wild bees but not on
 honey bees.  Synthesis and applications. We demonstrate that
 presence of floral plantings within orchards enhances pollinator activity
 within apple orchards and apple quality. This sustainable management
 practice may represent a profitable choice for growers, which could
 increase pollination services while reducing reliance on renting hives.
 These practices can indirectly contribute to increased landscape-scale
 resilience and connectivity, while also benefiting pollinators within the
 remaining natural habitat.
DOI: 10.5061/dryad.2ngf1vhnw
title: Molecular data and analysis specifications for a study on Atriophallophorus parasites from New Zealand

description: This dataset accompanies the manuscript "Phylogeography and Cryptic
 Species Structure of a Locally Adapted Parasite in New Zealand". In
 our study we have shown that multiple species of the trematode parasite
 from the Atriophallophorus genus co-exist within the same lakes. When
 focusing on the most common of these species, Atriophallophorus
 winterbourni, we found that the Southern Alps and Pleistocene glaciation
 are a likely explanation for its phylogeographic patterns. This dataset
 consists of three parts: (I) An Excel file containing SNP data, all sample
 information and the output of phylogeographic analysis with MASCOT1, (II)
 all sequence alignments, including NADH5, 28S, ITS2 and COI, as they are
 used for the manuscript and (III) input files for the various analyses as
 they were prepared for the analysis. 1MASCOT: marginal approximation of
 the structured coalescent as implemented in BEAST2
description: DNA was extracted from a single patasite metacercaria from
 <em>Potamopyrgus antipodarum </em>snails from different lakes
 on New Zealand's South Island. The genetic structure of these
 parasites was characterised using both mitochondrial NADH5 sequence data
 and multilocus SNP data.
description: BEAST2: http://www.beast2.org/ MrBayes: http://nbisweden.github.io/MrBayes/index.html
DOI: 10.5061/dryad.f1vhhmgxj
title: Data from: Can fractal dimensions objectivize gastropod shell morphometrics? A case study from Lake Lugu (SW China)

description: Morphometrics are fundamental for statistical analyses of fossils,
 particularly because soft parts or DNA are rarely preserved and thus hard
 parts such as shells are commonly the only source of information.
 Geometric morphometrics i.e. landmark analysis has been successfully
 established but exhibits a couple of shortcomings. On the one hand
 landmarking is rather subjective and on the other hand the application at
 the level of micro-sculpture is difficult. With the aid of high-resolution
 3D scanning technology and analyses of fractal dimensions, we test whether
 shortcomings of linear and geometric morphometrics can be overcome. As a
 model group, we selected a clade of modern viviparid gastropods from Lake
 Lugu, the shells of which show a high degree of sculptural variation.
 Linear and landmark analyses were applied to the same shells, in order to
 root the fractal dimensions. The genetic diversity of the gastropod clade
 was basically assessed. The genetic results suggest that the gastropod
 clade represents a single species. The results of all morphometric methods
 applied are in line with the genetic results, which is that no clustering
 of morpho-types occurs. Apart from this overall agreement, landmark and
 fractal dimension analyses do not correspond with each other but represent
 data sets with different information. Generally, the fractal dimension
 values quantify the roughness of the shell surface, the resolution of the
 3D-scans determining the level. In our approach, we captured the
 micro-sculpture but not the first-order sculptural elements, which
 explains that fractal dimension and landmark data are not in phase. We can
 show that analyzing fractal dimensions of gastropod shells opens a window
 to more detailed information that can be considered in evolutionary and
 ecological contexts. We propose that using 3D-scans with a low resolution
 may successfully substitute landmark analyses because it overcomes the
 subjective landmarking. Analyses of 3D-scans with higher resolution than
 used in this study will provide surface roughness information at the
 mineralogical level. We suggest that fractal dimension analyses of a
 combination of differently resolved 3D-models will significantly improve
 the quality of shell morphometrics.
description: See Wiese et al., 2022
DOI: 10.5061/dryad.mw6m905x6
title: Parental care in Darwin's finches

description: Selection should act on parental care and favour parental investment
 decisions that optimise the number of offspring produced. Such predictions
 have been robustly tested in predation risk contexts, but little is known
 about parental care investment trade-offs under conditions of parasitism.
 The avian vampire fly, Philornis downsi (Diptera: Muscidae), is a
 myasis-causing ectoparasite accidentally introduced to the Galápagos
 Islands, and one of the major causes of failure in Darwin’s finch nests.
 With an 11-year dataset spanning 21 years, we examine the relationship
 between parental care behaviours and the number of fly larvae and pupae in
 Darwin’s finch nests. We do so across three host species (Camarhynchus
 parvulus, C. pauper, Geospiza fuliginosa) and one hybrid Camarhynchus
 group. Nests with longer female brooding duration had fewer parasites, and
 this effect intensified with higher male food delivery to chicks. Neither
 male age nor number of nest provisioning visits alone were directly
 associated with parasite burden. While the causal mechanisms remain
 unknown, we provide the first empirical study showing that female in-nest
 attendance duration is negatively related to ectoparasite burden. We
 predict selection for coordinated host male and female behaviour to reduce
 gaps in nest attendance, especially under conditions of novel and
 introduced ectoparasites.
description: Focal observations of nesting behaviour were made at
 Darwin's finch nests. After the nesting outcome, the number of
 <em>Philornis downsi</em> larvae per nest were
 counted.
description: The raw data are presented per nest per row; column headings
 describe the column contents. Sheet 2 describes the column labels. Data on
 nesting behaviour at Darwin's finch nests were collected from one
 hour focal observations of individually monitored nests on Santa Cruz and
 Floreana Islands, Galapagos Archipelago, between 2000 and 2020.
DOI: 10.5061/dryad.dfn2z352c
title: Cell type labels for all clustering and normalization combinations compared for CODEX multiplexed imaging

description: We performed CODEX (co-detection by indexing) multiplexed imaging
 on four sections of the human colon (ascending, transverse, descending,
 and sigmoid) using a panel of 47 oligonucleotide-barcoded antibodies.
 Subsequently images underwent standard CODEX image processing (tile
 stitching, drift compensation, cycle concatenation, background
 subtraction, deconvolution, and determination of best focal plane), and
 single cell segmentation. Output of this process was a dataframe of nearly
 130,000 cells with fluorescence values quantified from each marker. We
 used this dataframe as input to 1 of the 5 normalization techniques of
 which we compared z, double-log(z), min/max, and arcsinh normalizations to
 the original unmodified dataset. We used these normalized dataframes as
 inputs for 4 unsupervised clustering algorithms: k-means, leiden, X-shift
 euclidian, and X-shift angular. From the clustering outputs, we then
 labeled the clusters that resulted for cells observed in the data
 producing 20 unique cell type labels. We also labeled cell types by
 hiearchical hand-gating data within cellengine (cellengine.com). We also
 created another gold standard for comparison by overclustering unormalized
 data with X-shift angular clustering. Finally, we created one last label
 as the major cell type call from each cell from all 21 cell type labels in
 the dataset.  Consequently the dataset has individual cells
 segmented out in each row. Then there are columns for the X, Y position in
 pixels in the overall montage image of the dataset. There are also columns
 to indicate which region the data came from (4 total). The rest are labels
 generated by all the clustering and normalization techniques used in the
 manuscript and what were compared to each other. These also were the data
 that were used for neighborhood analysis for the last figure of the
 manuscript. These are provided at all four levels of cell type level
 granularity (from 7 cell types to 35 cell types). 
description: This dataset could be used to observed relationships in cell type
 calls for CODEX Multiplexed Imaging data with different normalization and
 clustering technique combinations. It could also be used to test machine
 learning algorithms for cell type label transfer accuracy
 methods.
DOI: 10.5061/dryad.pvmcvdnm9
title: Grassland bird population declines at three Breeding Bird Survey spatial scales in contrast to a large native prairie

description: Grassland biomes in North America are threatened by agricultural
 intensification with implications for grassland associated bird
 populations via habitat loss, alteration, pesticide use and declining
 landscape heterogeneity. Despite decades of conservation concern, steep
 declines of North American grassland bird populations continue. Key to
 optimizing conservation effort is understanding how land-use practices,
 such as agriculture, across the annual cycle affects population status.
 Determining the relative influence of impacts on grassland bird declines
 is difficult given that the most robust estimates of population trends,
 the North American Breeding Bird Survey (BBS), are from surveys throughout
 agriculturally dominated regions. Our goal was to explore whether
 agriculture during the breeding season is a major driver of grassland bird
 declines. We derived trends for 16 grassland bird species spanning 23
 years (1994-2016) at a large (459 km2), native prairie site, Suffield
 National Wildlife Area (SNWA) in Alberta, Canada.  We compared
 those trends to the BBS across three spatial scales, a regional monitoring
 scheme with higher than average native grass cover (GBM), BCR 11 - Canada
 (Canada) and all of BCR 11 (BCR 11). Trends measured as annual percent
 change and credible interval varied greatly among species and survey
 strata. Across all species, declines were greatest for Canada (-1.3%, CI:
 -2.8, 0.0) and BCR 11 (-1.9%, CI: -3.2, -0.6).  This contrasts
 with positive mean trends for GBM routes (1.0%, CI: -0.4, 2.3) and the
 SNWA data (1.7%, CI: 0.3, 3.3). Six of 16 species at SNWA were increasing
 with one decreasing. Five species increased at GBM and four declined.
 Canada had 10 species declines and three increases and BCR 11 had 10
 declines and no increases. None of six grassland obligate species declined
 at SNWA, two declined at GBM, and all six declined over the two larger BBS
 strata. Our results showing fewer negative population trends at a large
 native grassland site compared to BBS at three spatial scales across the
 North American prairies support the prediction that agricultural
 intensification on breeding grounds is a major driver of declining
 populations and protection of remaining native grasslands should remain a
 key component of grassland bird conservation efforts.
DOI: 10.5061/dryad.djh9w0w14
title: Tradeoffs with utility-scale solar development and ungulates on western rangelands

description: Utility scale solar energy (USSE) has become an efficient and
 cost-effective form of renewable energy, with an expanding footprint into
 rangelands that provide important habitat for many ungulate populations.
 Using GPS data collected before and after construction, we documented the
 potential impacts of USSE on pronghorn, including direct habitat loss,
 indirect habitat loss, and barrier effects to both resident and migratory
 population segments. Our case study highlights the challenges that USSE
 poses to ungulate conservation, including 1) impermeable security fencing
 that removes habitat and reduces connectivity, and 2) the lack of
 guidelines for minimizing solar impacts to ungulates. We encourage
 agencies and industry to work towards a unified siting process and develop
 ungulate-specific best management practices to minimize habitat loss and
 retain landscape connectivity. Ungulate biodiversity and ecosystem
 services (e.g., long-distance migrations) in arid rangelands are important
 considerations when balancing the global benefits of renewable energy with
 local wildlife impacts.
description: Data were collected from pronghorn equipped with GPS-collars that
 collected locations every 2 hours.
description: Shapefiles are associated with Figures 1, 2, and 3 from the
 manuscript. Figure 1 includes pre- and post-construction GPS points and
 utilization distributions. Figure 2 includes line files of migratory
 pronghorn from study area. And Figure 3 includes line files of migratory
 pronghorn from nearby population. See ReadMe file for details.
DOI: 10.5061/dryad.k0p2ngf8q
title: Contrasting effects of two phenotypes of an alpine cushion plant on understory species drive community assembly

description: In alpine systems, cushion plants act as foundation species by
 ameliorating local environmental conditions. Empirical studies indicate
 that contrasting phenotypes of alpine cushion species have different
 effects on understory plant species, either facilitative or competitive.
 Furthermore, dependent species within each community type might also
 exhibit different responses to each cushion phenotype, which can be
 clustered into several “response groups”. Additionally, these
 species-groups specific responses to alpine cushion species phenotypes
 could alter community assembly. However, very few studies have assessed
 responses of dependent communities at species-group levels, in particular
 for both above- and below-ground communities. Here, we selected a loose
 and a tight phenotype of the alpine cushion species Thylacospermum
 caespitosum in two sites in northwest China, and use the relative
 intensity of interactions index to quantify cushion plant effects on
 subordinate communities of plants and soil fungi and bacteria. We assessed
 variations in responses of both above- and below-ground organisms to
 cushion plant effects at species-group level. Species-group level analyses
 showed that the effects of the phenotype varied among groups of each of
 the three community types, and different species-groups were composed of
 unique taxa. Additionally, we found that loose cushions enhanced
 stochastic processes in community assembly, for plants and soil fungi but
 not for soil bacteria. These variations of phenotypic effects on different
 species-group induced contrasting taxonomic composition between groups and
 altered community assembly thereby. Our study highlights the occurrence of
 contrasting effects of two phenotypes of a foundation cushion plant on
 understory plants, soil fungi and bacteria community composition, but not
 necessarily on their richness. We also showed that assessing responses of
 understory species at the species-group level allows a more realistic and
 mechanistic understanding of biotic interactions both for above- and
 below-ground communities.
description: Please see the README document ("README.txt") and the
 accompanying published article: Ziyang Liu, Richard Michalet, et al.
 Contrasting effects of two phenotypes of an alpine cushion plant on
 understory species drive community assembly, Science of The Total
 Environment, Volume 859, Part 2, 2023, 160154, https://doi.org/10.1016/j.scitotenv.2022.160154.