cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3b3v4
title: Data from: Mapping tropical dry forest succession using multiple criteria spectral mixture analysis

description: Tropical dry forests (TDFs) in the Americas are considered the first
 frontier of economic development with less than 1% of their total original
 coverage under protection. Accordingly, accurate estimates of their
 spatial extent, fragmentation, and degree of regeneration are critical in
 evaluating the success of current conservation policies. This study
 focused on a well-protected secondary TDF in Santa Rosa National Park
 (SRNP) Environmental Monitoring Super Site, Guanacaste, Costa Rica. We
 used spectral signature analysis of TDF ecosystem succession (early,
 intermediate, and late successional stages), and its intrinsic
 variability, to propose a new multiple criteria spectral mixture analysis
 (MCSMA) method on the shortwave infrared (SWIR) of HyMap image. Unlike
 most existing iterative mixture analysis (IMA) techniques, MCSMA tries to
 extract and make use of representative endmembers with spectral and
 spatial information. MCSMA then considers three criteria that influence
 the comparative importance of different endmember combinations (endmember
 models): root mean square error (RMSE); spatial distance (SD); and
 fraction consistency (FC), to create an evaluation framework to select a
 best-fit model. The spectral analysis demonstrated that TDFs have a high
 spectral variability as a result of biomass variability. By adopting two
 search strategies, the unmixing results showed that our new MCSMA approach
 had a better performance in root mean square error (early: 0.160/0.159;
 intermediate: 0.322/0.321; and late: 0.239/0.235); mean absolute error
 (early: 0.132/0.128; intermediate: 0.254/0.251; and late: 0.191/0.188);
 and systematic error (early: 0.045/0.055; intermediate: −0.211/−0.214; and
 late: 0.161/0.160), compared to the multiple endmember spectral mixture
 analysis (MESMA). This study highlights the importance of SWIR in
 differentiating successional stages in TDFs. The proposed MCSMA provides a
 more flexible and generalized means for the best-fit model determination
 than common IMA methods.
description: Data files and figures
 for the paperData_files.zip
DOI: 10.7284/166513
title: SSV (Sound Speed Velocimeter) data collected during research cruise AR85-02 using a Valeport Thru-Hull SVS instrument system onboard the platform RV Neil Armstrong

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.17632/hyst4kxz82
title: Alternate-day Fasting Enhanced Weight Loss and Metabolic Benefits Over Pair-Fed Calorie Restriction in Obese mice

description: Raw data for the whole study.
DOI: 10.7284/166508
title: Water Temperature data collected during research cruise AR85-02 using a SeaBird SBE-48 instrument system onboard the platform RV Neil Armstrong

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.17632/hyst4kxz82.1
title: Alternate-day Fasting Enhanced Weight Loss and Metabolic Benefits Over Pair-Fed Calorie Restriction in Obese mice

description: Raw data for the whole study.
DOI: 10.5061/dryad.511h1
title: Data from: Methods in field chronobiology

description: Chronobiological research has seen a continuous development of novel
 approaches and techniques to measure rhythmicity at different levels of
 biological organization from locomotor activity (e.g. migratory
 restlessness) to physiology (e.g. temperature and hormone rhythms, and
 relatively recently also in genes, proteins and metabolites). However, the
 methodological advancements in this field have been mostly and sometimes
 exclusively used only in indoor laboratory settings. In parallel, there
 has been an unprecedented and rapid improvement in our ability to track
 animals and their behaviour in the wild. However, while the spatial
 analysis of tracking data is widespread, its temporal aspect is largely
 unexplored. Here, we review the tools that are available or have potential
 to record rhythms in the wild animals with emphasis on currently
 overlooked approaches and monitoring systems. We then demonstrate, in
 three question-driven case studies, how the integration of traditional and
 newer approaches can help answer novel chronobiological questions in
 free-living animals. Finally, we highlight unresolved issues in field
 chronobiology that may benefit from technological development in the
 future. As most of the studies in the field are descriptive, the future
 challenge lies in applying the diverse technologies to experimental
 set-ups in the wild. This article is part of the themed issue ‘Wild
 clocks: integrating chronobiology and ecology to understand timekeeping in
 free-living animals’.
description: Annotated GPS tracking
 dataAnnotated GPS-tracking
 data used to create Figure 2 (Example of daily foraging rhythms in three
 Montagu’s Harriers). One file is included per bird. The zip files includes
 a word file describing the different columns.
DOI: 10.7284/166514
title: Transmissometer data collected during research cruise AR85-02 using a SeaBird C-Star instrument system onboard the platform RV Neil Armstrong

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.17632/ckv4jnp2rr
title: Dynamic Nested Sampling: ORI and CAP

description: This folder contains all results, validation tests, and sensitivity analyses for the paper "Inferring Meteoroid Properties with Dynamic Nested Sampling: A Case Study of Orionid and Capricornid Shower Meteors", plus the conda environment used to reproduce the simulations (cluster strongly recommended).

- Results : contains the main CAMO+EMCCD and EMCCD-only solutions. 
- Validation : contains 8 test cases (4 CAMO+EMCCD and 4 EMCCD-only). 
- Sensitivity_Analysis : contains runs testing sensitivity to luminous efficiency assumptions and grain density variations.
DOI: 10.5061/dryad.qq11c
title: Data from: Ecosystem biomonitoring with eDNA: metabarcoding across the tree of life in a tropical marine environment

description: Effective marine management requires comprehensive data on the status of
 marine biodiversity. However, efficient methods that can document
 biodiversity in our oceans are currently lacking. Environmental DNA (eDNA)
 sourced from seawater offers a new avenue for investigating the biota in
 marine ecosystems. Here, we investigated the potential of eDNA to inform
 on the breadth of biodiversity present in a tropical marine environment.
 Directly sequencing eDNA from seawater using a shotgun approach resulted
 in only 0.34% of 22.3 million reads assigning to eukaryotes, highlighting
 the inefficiency of this method for assessing eukaryotic diversity. In
 contrast, using ‘tree of life’ (ToL) metabarcoding and 20-fold fewer
 sequencing reads, we could detect 287 families across the major divisions
 of eukaryotes. Our data also show that the best performing ‘universal’ PCR
 assay recovered only 44% of the eukaryotes identified across all assays,
 highlighting the need for multiple metabarcoding assays to catalogue
 biodiversity. Lastly, focusing on the fish genus Lethrinus, we recovered
 intra- and inter-specific haplotypes from seawater samples, illustrating
 that eDNA can be used to explore diversity beyond taxon identifications.
 Given the sensitivity and low cost of eDNA metabarcoding we advocate this
 approach be rapidly integrated into biomonitoring programs.
description: 18S
 V1-V318S V4COIFish
 16SCrust
 16SCeph
 16SMam
 16SSym
 23StrnLProkaryote
 16S
DOI: 10.7284/166501
title: TSG (Thermosalinograph) data collected during research cruise AR85-02 using a SeaBird SBE-45 instrument system onboard the platform RV Neil Armstrong

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.17632/ckv4jnp2rr.2
title: Dynamic Nested Sampling: ORI and CAP

description: This folder contains all results, validation tests, and sensitivity analyses for the paper "Inferring Meteoroid Properties with Dynamic Nested Sampling: A Case Study of Orionid and Capricornid Shower Meteors", plus the conda environment used to reproduce the simulations (cluster strongly recommended).

- Results : contains the main CAMO+EMCCD and EMCCD-only solutions. 
- Validation : contains 8 test cases (4 CAMO+EMCCD and 4 EMCCD-only). 
- Sensitivity_Analysis : contains runs testing sensitivity to luminous efficiency assumptions and grain density variations.
DOI: 10.5061/dryad.qb799
title: Data from: Evolution of extreme ontogenetic allometric diversity and heterochrony in pythons, a clade of giant and dwarf snakes

description: Ontogenetic allometry, how species change with size through their lives,
 and heterochony, a decoupling between shape, size and age, are major
 contributors to biological diversity. However, macro-evolutionary
 allometric and heterochronic trends remain poorly understood because
 previous studies have focused on small groups of closely related species.
 Here we focus on testing hypotheses about the evolution of allometry and
 how allometry and heterochrony drive morphological diversification at the
 level of an entire species-rich and diverse clade. Pythons are a useful
 system due to their remarkably diverse and well-adapted phenotypes and
 extreme size disparity. We collected detailed phenotype data on 40 of the
 44 species of python from 1,191 specimens. We used a suite of analyses to
 test for shifts in trajectories that modify morphological diversity.
 Heterochrony is the main driver of initial divergence within python
 clades, and shifts in the slopes of allometric trajectories make
 exploration of novel phenotypes possible later in divergence history. We
 found that allometric coefficients are highly evolvable and there is an
 association between ontogenetic allometry and ecology, suggesting that
 allometry is both labile and adaptive rather than a constraint on possible
 phenotypes.
description: BPtree.MCCFossil calibrated Maximum Clade Credibility (MCC) tree for pythons, boas and other henophidians, based on the alignment by Reynolds et al. 2014.Python_Body_MeasurementsRaw body measurements for the python specimens used in the studyPython_DataData on ecology, age and sex for the python specimens used in the studyPythonRawLandmarksLandmark and semi-landmark coordinates for the python specimens used in the study
DOI: 10.7284/127024
title: INS (Inertial Navigation System) data collected during research cruise FL1601 using a CodaOctopus F-185 instrument system onboard the platform RP FLIP

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.5061/dryad.d461s
title: Data from: Inferring dispersal across a fragmented landscape using reconstructed families in the Glanville fritillary butterfly

description: Dispersal is important for determining both a species ecological
 processes, such as population viability, and its evolutionary processes,
 like gene flow and local adaptation. Yet obtaining accurate estimates in
 the wild through direct observation can be challenging or even impossible,
 particularly over large spatial and temporal scales. Genotyping many
 individuals from wild populations can provide detailed inferences about
 dispersal. We therefore utilized genomewide marker data to estimate
 dispersal in the classic metapopulation of the Glanville fritillary
 butterfly (Melitaea cinxia L.), in the Åland Islands in SW Finland. This
 is an ideal system to test the effectiveness of this approach due to the
 wealth of information already available covering dispersal across small
 spatial and temporal scales, but lack of information at larger spatial and
 temporal scales. We sampled three larvae per larval family group from
 3,732 groups over a six-year period and genotyped for 272 SNPs across the
 genome. We used this empirical dataset to reconstruct cases where
 full-sibs were detected in different local populations to infer female
 effective dispersal distance, i.e. dispersal events directly contributing
 to gene flow. On average this was one kilometer, closely matching previous
 dispersal estimates made using direct observation. To evaluate our power
 to detect full-sib families we performed forward simulations using an
 individual-based model constructed and parameterized for the Glanville
 fritillary metapopulation. Using these simulations 100% of predicted
 full-sibs were correct and over 98% of all true full-sib pairs were
 detected. We therefore demonstrate that even in a highly dynamic system
 with a relatively small number of markers, we can accurately reconstruct
 full-sib families and for the first time make inferences on female
 effective dispersal. This highlights the utility of this approach in
 systems where it has previously been impossible to obtain accurate
 estimates of dispersal over both ecological and evolutionary scales.
description: Archive of data
 associated with "Inferring dispersal across a fragmented landscape
 using reconstructed families in the Glanville fritillary
 butterfly"This archive contains
 the following data files: master-input.csv, master-output.csv,
 colony-input-master, colony-output-master-trimmed. See README file for
 full description of files.supplementary-data-COLONY2.tar.gz
DOI: 10.7284/127025
title: INS (Inertial Navigation System) data collected during research cruise FL1601 using a CodaOctopus F-185 instrument system onboard the platform RP FLIP

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/166786
title: pCO2 (Partial Pressure of Carbon Dioxide) data collected during research cruise HLY2502 using a GeneralOceanics GO 8060 pCO2 instrument system onboard the platform USCGC Healy

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.5061/dryad.9d6b2
title: Data from: Evidence that Myotis lucifugus ‘subspecies’ are five non-sister species, despite gene flow

description: While genetic exchange between non-sister species was traditionally
 considered to be rare in mammals, analyses of molecular data in multiple
 systems suggest that it may be common. Interspecific gene flow, if
 present, is problematic for phylogenetic inference, particularly for
 analyses near the species level. Here, we explore how to detect and
 account for gene flow during phylogeny estimation using data from a clade
 of North American Myotis bats where previous results have led researchers
 to suspect that gene flow among lineages is present. Initial estimates of
 phylogenetic networks and species trees indicate that subspecies described
 within M. lucifugus are paraphyletic. In order to explore the extent to
 which gene flow is likely to interfere with phylogeny estimation, we use
 posterior predictive simulation and a novel ABC approach based on gene
 tree distances. The former indicates that the species tree model is a poor
 fit to the data, and the latter provides evidence that a species tree with
 gene flow is a better fit. Taken together, we present evidence that the
 currently recognized M. lucifugus subspecies are paraphyletic, exchange
 alleles with other Myotis species in regions of secondary contact, and
 should be considered independent evolutionary lineages despite their
 morphological similarity.
description: Data.MyotisFasta files of ultraconserved elements loci for 11 lineages of North American MyotisSupplementary MaterialDryad_SuppMaterial.pdf
DOI: 10.7284/100736
title: Meteorological Station data collected during research cruise NH0904 using a SIO MET-System instrument system onboard the platform RV New Horizon

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.5061/dryad.pj75b
title: Data from: A new species of Telipogon (Orchidaceae) from Mexico and its phylogenetic position among Mesoamerican species

description: Telipogon is a Neotropical genus with approximately 200 species, the
 majority are epiphytes and distributed in South America; Mexico is the
 northernmost most area of distribution with only two recorded species.
 Here we describe a third species, T. corticatus Amezcua-Trigos and Sosa,
 collected in cloud forests of eastern Mexico, in Veracruz. It is a species
 solely growing in mossy patches in the exfoliating bark of trees of the
 Juglandaceae species, Oreomunnea mexicana. Reddish-brown flowers, large
 sepals close to each other in the open flower, two thirds of the length of
 the lip, petals elliptic, large auricles of column with long hairs and
 wide apex, a sagittate lip separated from the column with a base with a
 marked sinus, and a curved anther are diagnostic characters for this
 species. Phylogenetic position of T. corticatus along with Mesoamerican
 species was identified based in ITS and in the plastid matK, atpB-rbcL DNA
 markers considering representative taxa in subtribe Oncidiinae that
 Telipogon belongs. Telipogon corticatus along with the Mesoamerican T.
 helleri and T. cobanenis were retrieved as closely related, and associated
 to clades consisting of Central American species.
description: atpBrbcL-AlinData matrix of the plastid atpBrbcLITS-AlinITS data MATRIXmatK-AlinData matrix of matKCp_concat.nexus.conBayes tree concatenated matrixITSAlinMat.nexus.conITS Bayes tree filenucleocloro.nex.conBayes tree concatenated matrixRAxML_bootstrap.Cp_concat_redML tree plastid matrixRAxML_bipartitions.ITSAlinMatML ITS treeRAxML_bootstrap.Cp+NclConcat_redML concatenated matrix tree
DOI: 10.7284/100738
title: Meteorological Station data collected during research cruise NH0906 using a SIO MET-System instrument system onboard the platform RV New Horizon

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.5061/dryad.v5375
title: Data from: Egg shape mimicry in parasitic cuckoos

description: Parasitic cuckoos lay their eggs in nests of host species. Rejection of
 cuckoo eggs by hosts has led to the evolution of egg mimicry by cuckoos,
 whereby their eggs mimic the colour and pattern of their host eggs to
 avoid egg recognition and rejection. There is also evidence of mimicry in
 egg size in some cuckoo-host systems, but currently it is unknown whether
 cuckoos can also mimic the egg shape of their hosts. In this study we test
 whether there is evidence of mimicry in egg form (shape and size) in three
 species of Australian cuckoos: the fan-tailed cuckoo Cacomantis
 flabelliformis which exploits dome nesting hosts, the brush cuckoo
 Cacomantis variolosus, which exploits both dome and cup nesting hosts, and
 the pallid cuckoo Cuculus pallidus, which exploits cup nesting hosts. We
 found evidence of size mimicry, and for the first time evidence of egg
 shape mimicry in two Australian cuckoo species (pallid cuckoo and brush
 cuckoo). Moreover, cuckoo-host similarity was higher for hosts with open
 nests than for hosts with closed nests. This finding fits well with
 theory, since it has been suggested that hosts with closed nests have more
 difficulty recognising parasitic eggs than open nests, have lower
 rejection rates, and thus exert lower selection for mimicry in cuckoos.
 This is the first evidence of mimicry in egg shape in a cuckoo-host
 system, suggesting that mimicry at different levels (size, shape, colour
 pattern) is evolving in concert. We also confirm the existence of egg size
 mimicry in cuckoo-host systems.
description: Histogram
 sizeData file to use in R
 code 'Stats_GLMMs'. This contains information on the size
 distances of all the eggs measured in the study.Histogram
 shapeData file to use in R
 code 'Stats GLMMs'. Contains information about egg shape
 distances for all the eggs measured in the study.Average size for
 random_newData file with
 information on egg size for each of the eggs in our sample. This file is
 meant to be used in the R code 'Size
 analysis_R_Step2'.Average shape for
 randomData file with
 information on egg shape for each of the eggs in our sample. This file is
 meant to be used in the R code 'Shape
 analysis_R_Step2'.Stats_GLMMs_Shape and
 SizeR
 markdown file describing all the final statistical analyses performed in
 the manuscript (e.g. shown in Table 1).Shape
 analysis_R_Step2R markdown file showing
 how we calculated shape distances between eggs.Size
 analysis_R_Step2R markdown analysis
 showing how we calculated size distances among eggs.Extraction of PCA
 shape_Step1R markdown file that
 shows how we extracted shape coordinates from outline files obtained from
 egg photographs. Input file is the whole file called 'XY
 coordinates'.XY
 coordinatesXY coordinates for each
 egg obtained from photographs.
DOI: 10.7284/100740
title: Meteorological Station data collected during research cruise NH0908 using a SIO MET-System instrument system onboard the platform RV New Horizon

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/100743
title: Meteorological Station data collected during research cruise NH0911 using a SIO MET-System instrument system onboard the platform RV New Horizon

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.5061/dryad.6fh45
title: Data from: NF-κB pathways are involved in M1 polarization of RAW 264.7 macrophage by polyporus polysaccharide in the tumor microenvironment

description: Bladder cancer is one of the most malignant tumors closely associated with
 macrophages. Polyporus polysaccharide (PPS) has shown excellent efficacy
 in treating bladder cancer with minimal side effects. However, the
 molecular mechanisms underlying the effects of PPS in inhibiting bladder
 cancer remain unclear. In this study, we used macrophages cultured alone
 or with T24 human bladder cancer cell culture supernatant as study models.
 We found that PPS enhanced the activities of IFN-γ-stimulated RAW 264.7
 macrophages, as shown by the release of inducible nitric oxide synthase
 (INOS), secretion of tumor necrosis factor (TNF)-α and interleukin (IL)-6,
 phagocytosis activity, as well as expression of M1 phenotype indicators,
 such as CD40, CD284 and CD86. PPS acted upstream in activation cascade of
 nuclear factor (NF)-κB signaling pathways by interfering with IκB
 phosphorylation. In addition, PPS regulated NF-κB (P65) signaling by
 interfering with Toll-like receptor (TLR)-4, INOS and cyclooxygenase
 (COX)-2. Our results indicate that PPS activates macrophages through
 TLR4/NF-κB signaling pathways.
description: DataPloS.zip
DOI: 10.7284/100745
title: Meteorological Station data collected during research cruise NH0913 using a SIO MET-System instrument system onboard the platform RV New Horizon

description: Original (unprocessed) data collected during a Field_expedition