cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4nh84
title: Data from: Assessing spatio-temporal priorities for species’ recovery in broad-scale dynamic landscapes

description: 1. As threats to biodiversity from environmental change increase,
 assessing priorities for mitigation action becomes increasingly important.
 However, there have been few attempts to schedule actions across broad
 spatial extents that explicitly account for dynamic ecological processes
 and threats. 2. We combined a dynamic occupancy model with a decision
 analysis framework to spatially allocate multiple recovery actions to
 maximize species’ probability of occupancy under threats posed by climate
 and land-use change. We used the koala Phascolarctos cinereus across the
 Australian state of New South Wales (810 000 km2) to illustrate this
 approach. We considered four actions implemented on a 10 × 10 km2 grid:
 reduce domestic dog attacks through dog control, reduce vehicle collisions
 through fencing highways, protect habitat through land acquisitions and
 restore Eucalyptus forest. We used the occupancy model to predict
 ecological responses to recovery actions and simulated annealing to
 identify spatio-temporal priorities for each action. We contrasted the
 results against priorities generated using a traditional static
 distribution model. 3. To maximize the probability of koala occupancy in
 50 years’ time, with an annual budget of up to AU$20 million, investment
 priorities were located in the eastern part of koala's range,
 focusing on dog control with some investment in habitat protection and
 restoration. With higher budgets, investment priorities shifted towards
 habitat protection and restoration in the western part of the range.
 However, priorities based on the static distribution model, which had a
 lower predictive accuracy than the dynamic model, were different.
 Regardless of budget, priorities derived from the static model were
 predominantly located in the western part of koala's range, focusing
 on highway fencing with some investment in dog control. 4. Synthesis and
 applications. Our approach for integrating spatio-temporal dynamics into
 conservation prioritization across broad spatial extents provides a
 significant advance on existing approaches based on static distribution
 models. The finding that the inferior static model produced different
 priorities to the dynamic model cautions against the use of static models
 for conservation planning in dynamic landscapes. Additionally, the
 substantial changes in priorities with budget indicate that conservation
 planning under dynamic landscape and climate change must carefully
 consider priority actions and locations relative to the conservation
 resources available.
description: Historical and projected
 climate and land-use for New South Wales, AustraliaHistoricalFutureData.zipEstimated land value for NSW, AustraliaLandValue.csv
DOI: 10.5061/dryad.5241h
title: Data from: Mapping and validation of a major QTL affecting resistance to pancreas disease (salmonid alphavirus) in Atlantic salmon (Salmo salar)

description: Pancreas disease (PD), caused by a salmonid alphavirus (SAV), has a large
 negative economic and animal welfare impact on Atlantic salmon
 aquaculture. Evidence for genetic variation in host resistance to this
 disease has been reported, suggesting that selective breeding may
 potentially form an important component of disease control. The aim of
 this study was to explore the genetic architecture of resistance to PD,
 using survival data collected from two unrelated populations of Atlantic
 salmon; one challenged with SAV as fry in freshwater (POP 1) and one
 challenged with SAV as post-smolts in sea water (POP 2). Analyses of the
 binary survival data revealed a moderate-to-high heritability for host
 resistance to PD in both populations (fry POP 1 h2~0.5; post-smolt POP
 2 h2~0.4). Subsets of both populations were genotyped for single
 nucleotide polymorphism markers, and six putative resistance quantitative
 trait loci (QTL) were identified. One of these QTL was mapped to the same
 location on chromosome 3 in both populations, reaching chromosome-wide
 significance in both the sire- and dam-based analyses in POP 1, and
 genome-wide significance in a combined analysis in POP 2. This
 independently verified QTL explains a significant proportion of host
 genetic variation in resistance to PD in both populations, suggesting a
 common underlying mechanism for genetic resistance across lifecycle
 stages. Markers associated with this QTL are being incorporated into
 selective breeding programs to improve PD resistance.
description: Pancreas disease
 variance estimation and QTL mapping filesGenotype, phenotype and
 pedigree files for POP1 (fry) and POP2 (post-smolt)Pancreas_disease_data.zip
DOI: 10.5061/dryad.r12jk
title: Data from: The population genomic signature of environmental selection in the widespread insect-pollinated tree species Frangula alnus at different geographical scales

description: The evaluation of the molecular signatures of selection in species lacking
 an available closely related reference genome remains challenging, yet it
 may provide valuable fundamental insights into the capacity of populations
 to respond to environmental cues. We screened 25 native populations of the
 tree species Frangula alnus subsp. alnus (Rhamnaceae), covering three
 different geographical scales, for 183 annotated single-nucleotide
 polymorphisms (SNPs). Standard population genomic outlier screens were
 combined with individual-based and multivariate landscape genomic
 approaches to examine the strength of selection relative to neutral
 processes in shaping genomic variation, and to identify the main
 environmental agents driving selection. Our results demonstrate a more
 distinct signature of selection with increasing geographical distance, as
 indicated by the proportion of SNPs (i) showing exceptional patterns of
 genetic diversity and differentiation (outliers) and (ii) associated with
 climate. Both temperature and precipitation have an important role as
 selective agents in shaping adaptive genomic differentiation in F. alnus
 subsp. alnus, although their relative importance differed among spatial
 scales. At the ‘intermediate’ and ‘regional’ scales, where limited genetic
 clustering and high population diversity were observed, some indications
 of natural selection may suggest a major role for gene flow in
 safeguarding adaptability. High genetic diversity at loci under selection
 in particular, indicated considerable adaptive potential, which may
 nevertheless be compromised by the combined effects of climate change and
 habitat fragmentation.
description: SNP sequences and
 GENALEX fileSequences of the 250
 SNPs (together with their functional annotations) are available in tab 1
 of the file. In tab 2, the original GENALEX file on the 183 successfully
 genotyped SNPs is provided.DRYAD.xlsx
DOI: 10.5517/ccdc.csd.cc2pyf03
title: CCDC 2500925: Experimental Crystal Structure Determination

description: Related Article: Zhuang Wang|2025|CSD Communication|||
description: Related Article: Zhuang Wang, Zhaoyu Zhang, Xinyu Xie, Yan Hao, Shaomin Fu, Bo Liu|2026|Org.Lett.|||doi:10.1021/acs.orglett.5c04968
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccqj9j1
title: CCDC 671073: Experimental Crystal Structure Determination

description: Related Article: Rahul Banerjee, Anh Phan, Bo Wang, Carolyn Knobler, Hiroyasu Furukawa, Michael O'Keeffe, Omar M. Yaghi|2008|Science|319|939|doi:10.1126/science.1152516
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5061/dryad.65pm3
title: Data from: Reduced genetic diversity and increased dispersal in Guigna (Leopardus guigna) in Chilean fragmented landscapes

description: Landscape fragmentation is often a major cause of species extinction as it
 can affect a wide variety of ecological processes. The impact of
 fragmentation varies among species depending on many factors, including
 their life-history traits and dispersal abilities. Felids are one of the
 groups most threatened by fragmented landscapes because of their large
 home ranges, territorial behavior, and low population densities. Here, we
 model the impacts of habitat fragmentation on patterns of genetic
 diversity in the guigna (Leopardus guigna), a small felid that is closely
 associated with the heavily human-impacted temperate rainforests of
 southern South America. We assessed genetic variation in 1798 base pairs
 of mitochondrial DNA sequences, 15 microsatellite loci, and 2 sex
 chromosome genes and estimated genetic diversity, kinship, inbreeding, and
 dispersal in 38 individuals from landscapes with differing degrees of
 fragmentation on Chiloé Island in southern Chile. Increased fragmentation
 was associated with reduced genetic diversity, but not with increased
 kinship or inbreeding. However, in fragmented landscapes, there was a
 weaker negative correlation between pairwise kinship and geographic
 distance, suggesting increased dispersal distances. These results
 highlight the importance of biological corridors to maximize connectivity
 in fragmented landscapes and contribute to our understanding of the
 broader genetic consequences of habitat fragmentation, especially for
 forest-specialist carnivores.
description: Mitochondrial DNA
 sequencesFile may be viewed using
 ProSeq software at http://dps.plants.ox.ac.uk/sequencing/proseq.htm
 [Filatov DA (2009) Processing and population genetic analysis of
 multigenic datasets with ProSeq3 software. Bioinformatics 25:
 3189-3190].chiloe.psf
DOI: 10.5061/dryad.kj4mh
title: Data from: "Transcriptomic resources for the critically endangered stellate sturgeon Acipenser stellatus" in Genomic Resources Notes accepted 1 April 2015 – 31 May 2015

description: This article documents the public availability of transcriptomic resources
 of the non-model and critically endangered starlet sturgeon Acipenser
 stellatus.
description: make_repeated_assemblyPython script to perform iterative assemblies using MIRA 3.2 assemblerCDNA1-2_11_2010_1_final_assemblyContig sequences of the assembled transcripts (FASTA + QUAL files) in gz compressed tar archivestellatus_annot_GAF_20121111_1852Contigs annotations obtained via Blast2GO (GAF) in zip archivestellatus_kegg_txt_20121109_1825KEGG pathways annotated via Blast2GO (TAB delimited file) in zip archivestellatus_varPutative SNP and INDEL data (VCF) in zip archive
DOI: 10.5061/dryad.fd3m4
title: Data from: Can we identify genes with increased phylogenetic reliability?

description: Topological heterogeneity among gene trees is widely observed in
 phylogenomic analyses and some of this variation is likely caused by
 systematic error in gene tree estimation. Systematic error can be
 mitigated by improving models of sequence evolution to account for all
 evolutionary processes relevant to each gene or identifying those genes
 whose evolution best conforms to existing models. However, the best method
 for identifying such genes is not well established. Here, we ask if
 filtering genes according to their clock-likeness or posterior predictive
 effect size (PPES, an inference-based measure of model violation) improves
 phylogenetic reliability and congruence. We compared these approaches to
 each other, and to the common practice of filtering based on rate of
 evolution, using two different metrics. First, we compared gene-tree
 topologies to accepted reference topologies. Second, we examined
 topological similarity among gene trees in filtered sets. Our results
 suggest that filtering genes based on clock-likeness and PPES can yield a
 collection of genes with more reliable phylogenetic signal. For the two
 exemplar data sets we explored, from yeast and amniotes, clock-likeness
 and PPES outperformed rate-based filtering in both congruence and
 reliability.
description: Doyle_etal_SystBiol_SuppInforepMissPatternsA python script to find the pattern of missing data in an empirical data set and replicate it in simulated datasets.
DOI: 10.5061/dryad.48643
title: Data from: Three-dimensional surface parameters and multi-fractal spectrum of corroded steel

description: To study multi-fractal behavior of corroded steel surface, a range of
 fractal surfaces of corroded surfaces of Q235 steel were constructed by
 using the Weierstrass-Mandelbrot method under a high total accuracy. The
 multi-fractal spectrum of fractal surface of corroded steel was calculated
 to study the multi-fractal characteristics of the W-M corroded surface.
 Based on the shape feature of the multi-fractal spectrum of corroded steel
 surface, the least squares method was applied to the quadratic fitting of
 the multi-fractal spectrum of corroded surface. The fitting function was
 quantitatively analyzed to simplify the calculation of multi-fractal
 characteristics of corroded surface. The results showed that the
 multi-fractal spectrum of corroded surface was fitted well with the method
 using quadratic curve fitting, and the evolution rules and trends were
 forecasted accurately. The findings can be applied to research on the
 mechanisms of corroded surface formation of steel and provide a new
 approach for the establishment of corrosion damage constitutive models of
 steel.
description: S_4
 TableS_4_Table.xlsxS_7_Table
DOI: 10.5061/dryad.8416
title: Data from: DNA barcoding of the ichthyofauna of Taal Lake, Philippines

description: This study represents the first molecular survey of the ichthyofauna of
 Taal Lake and the first DNA barcoding attempt in Philippine fishes. Taal
 Lake, the third largest lake in the Philippines, is considered a very
 important fisheries resource and is home to the world’s only freshwater
 sardine, Sardinella tawilis. However, over-exploitation and introduction
 of exotic fishes have caused a massive decline in the diversity of native
 species as well as overall productivity of the lake. In this study, 118
 individuals of 23 native, endemic, and introduced fishes of Taal Lake were
 barcoded using the partial DNA sequence of the mitochondrial cytochrome
 oxidase I (COI) gene. These species belong to 21 genera, 17 families and 9
 orders. Divergence of sequences within and between species was determined
 using Kimura 2-parameter (K2P) distance model and a neighbor-joining tree
 was generated with 1000 bootstrap replications using the K2P model. All
 COI sequences for each of the 23 species were clearly discriminated among
 genera. The average within species, within genus, within family, and
 within order percent genetic divergence was 0.60%, 11.07%, 17.67%, and
 24.08%, respectively. Our results provide further evidence that COI DNA
 barcodes are effective for rapid and accurate identification of fishes and
 for identifying certain species that need further taxonomic investigation.
description: Image
 filesImages of the fishes
 collected from Taal Lake, Philippines.Image
 Data.rarTrace
 FilesTrace files of the COI
 sequences of all the fishes collected from Taal Lake,
 PhilippinesSpecimenDataVoucher info, Taxonomy, Specimen Details and Collection Data of the fishes collected in Taal Lake, PhilippinesImageDataStandard lengths, BOLD process ID of the fishes collected in Taal Lake, Philippinesconsensus sequencesConsensus sequences of the COI barcodes of the fishes collected in Taal Lake, Philippines
DOI: 10.5061/dryad.kd00n
title: Data from: Population genomics of the euryhaline teleost Poecilia latipinna

description: Global climate change and increases in sea levels will affect coastal
 marine communities. The conservation of these ecologically important areas
 will be a challenge because of their wide geographic distribution,
 ecological diversity and species richness. To address this problem, we
 need to better understand how the genetic variation of the species in
 these communities is distributed within local populations, among
 populations and between distant regions. In this study we apply genotyping
 by sequencing (GBS) and examine 955 SNPs to determine Sailfin molly
 (Poecilia latipinna) genetic diversity among three geographically close
 mangrove salt marsh flats in the Florida Keys compared to populations in
 southern and northern Florida. The questions we are asking are whether
 there is sufficient genetic variation among isolated estuarine fish within
 populations and whether there are significant divergences among
 populations. Additionally, we want to know if GBS approaches agree with
 previous studies using more traditional molecular approaches. We are able
 to identify large genetic diversity within each saltmarsh community (π ≈
 36%). Additionally, among the Florida Key populations and the mainland or
 between southern and northern Florida regions, there are significant
 differences in allele frequencies seen in population structure and
 evolutionary relationships among individuals. Surprisingly, even though
 the cumulative FST value using all 955 SNPs within the three Florida Key
 populations is small, there are 29 loci with significant FST values, and
 11 of these were outliers suggestive of adaptive divergence. These data
 suggest that among the salt marsh flats surveyed here, there is
 significant genetic diversity within each population and small but
 significant differences among populations. Much of the genetic variation
 within and among populations found here with GBS is very similar to
 previous studies using allozymes and microsatellites. However, the
 meaningful difference between GBS and these previous measures of genetic
 diversity is the number of loci examined, which allows more precise
 delineations of population structure as well as facilitates identifying
 loci with excessive FST values that could indicate adaptive divergence.
description: Sailfin_Molly_total_HapmapInitial unfiltered SNP (18,255 SNP) for 144 individual Sailfin Mollies (Poecilia latipinna) were collected from five populations in the spring of 2014. Of the 144 individual sequenced, 122 (thirty per site) were had sufficient sequences and depth of reads for analyses (see filter data set)SF_955_hapmapFilter SNP (955 SNP) for 122 collected from five populations in the spring of 2014. These 955 SNP in 122 individual were used for all analyze because they had sufficient sequences and depth of reads.955_Tags64bp sequences for each 955 SNP.NCBI BioProject PRJNA280774Raw sequence reads for all 144 individuals are available at NCBI BioProject Accession: PRJNA280774 ID: 280774.
DOI: 10.5061/dryad.8424
title: Data from: Tunicates and not cephalochordates are the closest living relatives of vertebrates

description: Tunicates or urochordates (appendicularians, salps and sea squirts),
 cephalochordates (lancelets) and vertebrates (including lamprey and
 hagfish) constitute the three extant groups of chordate animals.
 Traditionally, cephalochordates are considered as the closest living
 relatives of vertebrates, with tunicates representing the earliest
 chordate lineage. This view is mainly justified by overall morphological
 similarities and an apparently increased complexity in cephalochordates
 and vertebrates relative to tunicates. Despite their critical importance
 for understanding the origins of vertebrates, phylogenetic studies of
 chordate relationships have provided equivocal results. Taking advantage
 of the genome sequencing of the appendicularian Oikopleura dioica, we
 assembled a phylogenomic data set of 146 nuclear genes (33,800
 unambiguously aligned amino acids) from 14 deuterostomes and 24 other
 slowly evolving species as an outgroup. Here we show that phylogenetic
 analyses of this data set provide compelling evidence that tunicates, and
 not cephalochordates, represent the closest living relatives of
 vertebrates. Chordate monophyly remains uncertain because
 cephalochordates, albeit with a non-significant statistical support,
 surprisingly grouped with echinoderms, a hypothesis that needs to be
 tested with additional data. This new phylogenetic scheme prompts a
 reappraisal of both morphological and palaeontological data and has
 important implications for the interpretation of developmental and genomic
 studies in which tunicates and cephalochordates are used as model animals.
description: Delsuc_Nature2006Amino acid concatenation of 146 genes for 38 metazoans.
DOI: 10.5061/dryad.ch1bb
title: Data from: Frost hollows of the boreal forest: a spatiotemporal perspective

description: 1. Frost hollows (FH) are small, confined lichen-dominated ecosystems
 surrounded by lichen woodlands. FH are impacted by repetitive frosts
 occurring during the growing season. We evaluated the dynamics of FH
 across the boreal forest in eastern Canada and assessed the influence of
 latitude as the main geoclimatic factor controlling their development. 2.
 The distribution and abundance of FH along 39 longitudinal transects were
 based on aerial photographs and field validation. Black spruce (Picea
 mariana) in FH and adjacent woodlands were sampled for age determination,
 year of tree establishment, height growth rate of spruce, and intensity
 and frequency of frost rings. 3. Most FH are located in the southern part
 of the boreal forest, in depressions bordered by dry, open, lichen
 woodlands. The inception and development of FH are not dependent on
 latitude but rather on the presence of lichen woodlands. Frost-induced
 thúfurs and frost rings were more frequent and abundant in the
 southernmost FH, whereas the northernmost FH were devoid of thúfurs. Black
 spruce established synchronously in FH across the boreal forest, an
 indication of a climatic control associated with cloudier, humid
 conditions reducing radiative frost activity. Most FH spruce established
 after 1933 and peaked in the 1980s. Fewer frost events were recorded in
 the 1980s than in the 1990s. In the latter decade, frost events became
 more frequent, intense and synchronous across the boreal forest. 4.
 Synthesis. The distribution of frost hollows (FH) is related to the
 presence of dry lichen woodlands that exacerbate frost activity during the
 growing season. Synchronous frost-ring frequency across the biome also
 suggests that shared climatic conditions, in particular freezing
 temperature, humidity and cloudiness, are at the origin of the dynamics of
 FH. A longer growing season creates propitious conditions for a higher
 frequency of frost events and more intense soil cryoturbation. FH are
 climate-sensitive ecosystems which can be used as proxies of the impact of
 global change on the boreal biome.
description: Frost
 hollows_identificationSite
 1-1_establishmentSite
 1-1_rings_diagSite
 1-2_establishmentSite
 1-2_rings_diagSite
 1-3_establishmentSite
 1-3_rings_diagSite
 16-1_establishmentSite
 16-1_rings_diagSite
 16-2_establishmentSite
 16-2_rings_diagSite
 25-1_establishmentSite
 25-1_rings_diagSite
 25-2_establishmentSite
 25-2_rings_diagSite
 27-1_establishmentSite
 27-1_rings_diagSite
 27-2_establishmentSite
 27-2_rings_diagSite
 30-1_establishmentSite
 30-1_rings_diagSite
 30-2_establishmentSite
 30-2_rings_diagSite
 31-1_establishmentSite
 31-1_rings_diagSite
 36-1_establishmentSite
 36-1_rings_diagSite
 36-2_establishmentSite
 36-2_rings_diag