cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.ffbg79cs6
title: Accelerated brain shape evolution is associated with rapid diversification in an avian radiation

description: Niche expansion is a critical step in the speciation process. Large brains
 linked to improved cognitive ability may enable species to expand their
 niches and forage in new ways, thereby promoting speciation. Despite
 considerable work on ecological divergence in brain size and its
 importance in speciation, relatively little is known about how brain shape
 relates to behavioral, ecological, and taxonomic diversity at
 macroevolutionary scales. This is due, in part, to inherent challenges
 with quantifying brain shape across many species. Here, we present a
 novel, semiautomated approach for rapidly phenotyping brain shape using
 semilandmarks derived from X-ray computed micro-tomography (microCT)
 scans. We then test its utility by parsing evolutionary trends within a
 diverse radiation of birds, kingfishers (Aves: Alcedinidae). Multivariate
 comparative analyses reveal that rates of brain shape evolution, but not
 beak shape, are positively correlated with lineage diversification rates.
 Distinct brain shapes are further associated with changes in body size and
 foraging behavior, suggesting both allometric and ecological constraints
 on brain shape evolution. These results are in line with the idea of
 brains acting as a "master regulator" of critical processes
 governing speciation, such as dispersal, foraging behavior, and dietary
 niche.
DOI: 10.5061/dryad.bk3j9kd8m
title: Data and analyses from: Herbivory and time since flowering shape floral rewards and pollinator-pathogen interactions

description: Herbivory can induce chemical changes throughout plant tissues including
 flowers, which could affect pollinator-pathogen interactions. Pollen is
 highly defended compared to nectar, but no study has examined whether
 herbivory affects pollen chemistry. We assessed the effects of leaf
 herbivory on nectar and pollen alkaloids in Nicotiana tabacum, and how
 herbivory-induced changes in nectar and pollen affect pollinator-pathogen
 interactions. We damaged leaves of Nicotiana tabacum using the specialist
 herbivore Manduca sexta and compared nicotine and anabasine concentrations
 in nectar and pollen. We then pooled nectar and pollen by collection
 periods (within and after one month of flowering), fed them in separate
 experiments to bumble bees (Bombus impatiens) infected with the gut
 pathogen Crithidia bombi, and assessed infections after seven days. We did
 not detect alkaloids in nectar, and leaf damage did not alter the effect
 of nectar on Crithidia counts. In pollen, herbivory induced higher
 concentrations of anabasine but not nicotine, and alkaloid concentrations
 rose and then fell as a function of days since flowering. Bees fed pollen
 from damaged plants had Crithidia counts 15 times higher than bees fed
 pollen from undamaged plants, but only when pollen was collected after one
 month of flowering, indicating that both damage and time since flowering
 affected interaction outcomes. Within undamaged treatments, bees fed
 late-collected pollen had Crithidia counts 10 times lower than bees fed
 early-collected pollen, also indicating the importance of floral
 phenology. Our results emphasize the role of herbivores in shaping pollen
 chemistry, with consequences for interactions between pollinators and
 their pathogens.
description: File descriptions and variable explanations are all contained in
 the file metadata.txt. All R scripts will call the appropriate data file
 from user's directory.  Contents:
 metadata.txt
 pollen.bioassays.R
 pollen.bioassay.csv
 nectar.bioassays.R
 nectar.bioassay.csv
 alk.conc.tweedie.R
 pollen.jdate.simple.csv
 binomial.csv
DOI: 10.5061/dryad.tmpg4f4wq
title: Ecological and conceptual consequences of Arctic pollution

description: Though the effect of pollution on forest health and decline received much
 attention in the 1980s, it has not been considered to explain the
 ‘Divergence Problem’ in dendroclimatology; a decoupling of tree growth
 from rising air temperatures since the 1970s. Here we use physical and
 biogeochemical measurements of hundreds of living and dead conifers to
 reconstruct the impact of heavy industrialisation around Norilsk in
 northern Siberia. Moreover, we develop a forward model with surface
 irradiance forcing to quantify long-distance effects of anthropogenic
 emissions on the functioning and productivity of Siberia’s taiga. Downwind
 from the world’s most polluted Arctic region, tree mortality rates of up
 to 100% have destroyed 24,000 km2 boreal forest since the 1960s,
 coincident with dramatic increases in atmospheric sulphur, copper, and
 nickel concentrations. In addition to regional ecosystem devastation, we
 demonstrate how ‘Arctic Dimming’ can explain the circumpolar ‘Divergence
 Problem’, and discuss implications on the terrestrial carbon cycle.
description: We utilize hundreds of TRW samples from living and dead conifers
 surrounding the Norilsk industrial complex to reconstruct the sequence of
 events leading up to a historically unprecedented forest dieback and
 decline, in one of the world’s most polluted regions, since the 1930s. We
 expand our dendrochronological findings with high-resolution measurements
 of wood and soil chemistry to quantify the spatiotemporal extent of
 Norilsk’s devastating ecosystem damage. We develop a process-based forward
 model of boreal tree growth to detect and attribute the effects of changes
 in surface solar radiation (see publication for details).
description: The memo contains all information.
DOI: 10.5061/dryad.12jm63xw0
title: Physical-mental multimorbidity in children and youth: a scoping review

description: OBJECTIVE: Efforts to describe the current state of research are needed to
 advance the field of physical-mental multimorbidity (i.e., the
 co-occurrence of at least one physical illness and at least one mental
 disorder) among children and youth. Our objective was to systematically
 explore the breadth of physical-mental multimorbidity research in children
 and youth, and to provide an overview of existing literature topics.
 DESIGN: Scoping review METHODS: We conducted a systematic search of four
 key databases: PubMed, EMBASE, PsycINFO, and Scopus, as well as a thorough
 scan of relevant grey literature. We included studies of any research
 design, published in English, referring to physical-mental multimorbidity
 among children and youth aged ≤18 years. Studies were screened for
 eligibility and data were extracted, charted, and summarized narratively
 by research focus. Critical appraisal was employed using the modified
 Quality Index (QI). RESULTS: We included 431 studies and two sources of
 grey literature. Existing research emphasizes the co-occurrence of
 anxiety, mood, and attention disorders among children with epilepsy,
 asthma, and allergy. Evidence consists of mostly small, observational
 studies that use cross-sectional data. The average QI score across
 applicable studies was 9.1 (SD = 1.8). CONCLUSIONS: There is a pressing
 need for more robust research within the field of child physical-mental
 multimorbidity.
DOI: 10.5061/dryad.zkh189385
title: Data from: Spatial familial networks to infer demographic structure of wild populations

description: In social species, reproductive success and rates of dispersal vary among
 individuals resulting in spatially structured populations. Network
 analyses of familial relationships may provide insights on how these
 parameters influence population-level demographic patterns. These methods
 have however rarely been applied to genetically-derived pedigree data from
 wild populations. Here we use parent-offspring relationships to construct
 familial networks from polygamous boreal woodland caribou (Rangifer
 tarandus caribou) in Saskatchewan, Canada, to inform recovery efforts. We
 collected samples from 933 individuals at 15 variable microsatellite loci
 along with caribou-specific primers for sex identification. Using network
 measures, we assess the contribution of individual caribou to the
 population with several centrality measures and then determine which
 measures are best suited to inform on the population demographic
 structure. We investigate the centrality of individuals from eighteen
 different local areas, along with the entire population. We found
 substantial differences in centrality of individuals in different local
 areas, that in turn contributed differently to the full network,
 highlighting the importance of analyzing networks at different scales. The
 full network revealed that boreal caribou in Saskatchewan form a complex,
 interconnected familial network, as the removal of edges with high
 betweenness did not result in distinct subgroups. Alpha, betweenness, and
 eccentricity centrality were the most informative measures to characterize
 the population demographic structure and for spatially identifying areas
 of highest fitness levels and family cohesion across the range. We found
 varied levels of dispersal, fitness and cohesion in family groups.
 Synthesis and applications: Our results demonstrate the value of different
 network measures in assessing genetically-derived familial networks. The
 spatial application of the familial networks identified individuals
 presenting different fitness levels, short and long-distance dispersing
 ability across the range in support of population monitoring and recovery
 efforts.
DOI: 10.5281/zenodo.17838464
title: RD Galaxy Dynamics Phase-Transition Dataset (SPARC + ATLAS³D)

description: This dataset contains the complete analysis pipeline and results used toevaluate whether a structural phase transition may exist in galactic dynamics,as quantified by the unified dynamical parameter τ.

The dataset includes 109 SPARC spiral galaxies and 89 ATLAS³D ellipticalgalaxies with full TDGL (Time-Dependent Ginzburg–Landau) fits applied torotation curves and velocity-dispersion profiles. All derived parameters(κ₁, ξ_GL, r_core, η, τ) are provided along with the Python scripts requiredfor full reproducibility.

Across the sample analysed, all rotation-supported SPARC galaxies exhibitτ > 0, while the majority of pressure-supported ATLAS³D ellipticals exhibitτ < 0, with S0 galaxies clustering near τ ≈ 0. This separation suggests apossible dynamical phase boundary in galaxy structure, though independentvalidation is encouraged.

Files included:• Raw SPARC and ATLAS³D datasets (for transparency)• TDGL fitting code (rotation curves and Jeans modelling)• Derived parameter tables for all 194 galaxies• Publication-quality figures• Documentation describing the methods and theoretical context

This dataset is intended to support independent replication, verification,and further investigation into dynamical structure in galaxies.
DOI: 10.5061/dryad.0p2ngf1z4
title: Data from: Silence of the killers: discovery of male-killing suppression in a rearing strain of the small brown planthopper, Laodelphax striatellus

description: According to evolutionary theory, sex ratio distortions caused by
 reproductive parasites such as Wolbachia and Spiroplasma are predicted to
 be rapidly normalised by the emergence of host nuclear suppressors.
 However, such processes in the evolutionary arms race are difficult to
 observe because sex ratio biases will be promptly hidden and become
 superficially unrecognisable. The evolution of genetic suppressors has
 been reported in just two insect species so far. In the small brown
 planthopper, Laodelphax striatellus, female-biases caused by Spiroplasma,
 which is a ‘late’ male-killer, have been found in some populations. During
 the continuous rearing of L. striatellus, we noticed that a rearing strain
 had a 1:1 sex ratio even though it harboured Spiroplasma. Through
 introgression crossing experiments with a strain lacking suppressors, we
 revealed that the L. striatellus strain had the zygotic male-killing
 suppressor acting as a dominant trait. The male-killing phenotype was
 hidden by the suppressor even though Spiroplasma retained its male-killing
 ability. This is the first study to demonstrate the existence of a late
 male-killing suppressor and its mode of inheritance. Our results, together
 with those of previous studies, suggest that the inheritance modes of
 male-killing suppressors are similar regardless of insect order or early
 or late male-killing.
DOI: 10.5061/dryad.d51c5b019
title: Early-wilted forest following the Central European 2018 extreme drought

description: During the summer of 2018, Central Europe experienced the most extreme
 drought and heat wave on record, leading to widespread early leaf-shedding
 and die-offs in forest trees. We quantified such early-wilting
 responses by associating Sentinel-2 time-series statistics of
 the Normalized Difference Vegetation Index with visually
 classified orthophotos, using a random forest classifier. The predictions
 of our classifier achieved a high accuracy of
 0.90 ±0.014 and estimated the area of
 affected forest at 21’500 ±2800 km2. Early wilting was especially
 prevalent in eastern and central Germany and in the Czech
 Republic and it was related to high temperatures and low
 precipitation at large-scales, and small to medium-sized
 trees, steep slopes, and shallow soils at fine-scales. The present
 dataset includes spatial predictons of 2018 early-wilting
 presence/absence for entire Central Europe (c. 800'000 km2)
 at 10×10 m resolution. It may be used for high-resolution studies
 of early-wilting patterns, to study how factors
 like physiology or species identity relate to
 early-wilting patterns, and/or as testbed for
 alternative approaches quantifying water stress in
 forests. 
description: The data consists of spatial presence/absence predictions of a
 random forest classifier. As dependent variable, we used
 &gt;304'000 visually interpreted pixels associated with 1022
 polygons of early-wilting presence or absence. Visual interpretation was
 largely based on Google Earth aerial imagery with &lt;1 m spatial
 resoltuion. As predictors, we used ten time-series statistics of the
 2018 Normalized Difference Vegetation Index (NDVI) as sensed by the
 Sentinel-2 mission. These statistics included NDVI spring minimum, the
 fall minimum, the spring maximum, the fall maximum, the summer mean, the
 magnitude of change at the summer change point, the timing of the summer
 change point, the temporal summer trend, the significance of the temporal
 summer trend, and the mean absolute error during summer. We defined the
 forests as areas with a tree cover density of &gt;80%, as detailed by
 the Tree Cover Density Map 2015 from Copernicus.
description: Contains: 87 raster layers in GeoTIFF format corresponding to
 individual tiles of the Sentiel-2 tiling system.
 Values: 0 = early-witling absence, 1 = early-wilting presence, NA
 = non-forested area Resolution: 10x10 m
 Projection: ETRS89-extended / LAEA Europe (EPSG:3035)
DOI: 10.5061/dryad.3tx95x6dg
title: Chesapeake DolphinWatch weekly data

description: Bottlenose dolphins (Tursiops truncatus) are migratory marine mammals that
 live in both open-ocean and coastal habitats. Although widely studied,
 little is known about their occurrence patterns in the highly urbanized
 Chesapeake Bay, U.S.A. The goal of this study was to establish the spatial
 and temporal distribution of bottlenose dolphins throughout this large
 estuarine system and use statistical modeling techniques to determine how
 their distribution relates to environmental factors. Three years
 (2017-2019) of observational dolphin sighting reports from a
 citizen-science database, Chesapeake DolphinWatch, were used to determine
 relative occurrence throughout the estuary. The dolphins had a distinct
 temporal pattern, most commonly sighted during summer months with a peak
 in July. This pattern of observed occurrence was confirmed with passive
 acoustic detections of dolphin echolocation clicks. Using a Generalized
 Additive Model (GAM), dolphin presence was found to be significantly
 correlated to spring tidal phase, warm water temperature, and salinity
 ranging from 6 – 22 PPT. Further, we were able to use these GAMs with a
 test dataset to predict species occurrence in the Bay, which were
 statistically correlated to the actual number of dolphin sighting reports
 during that time. These models can be implemented as a predictive tool for
 species occurrence and help to inform management of this protected species
 within the Chesapeake Bay.
description: This dataset was collected by a citizen science initiative named
 Chesapeake DolphinWatch, which is available as a web-based application or
 a phone application for iPhones/Androids. The daily dolphin sighting
 information was summed to weekly dolphin sightings. All environmental
 data, collected from the Maryland Department of Natural Resources
 (http://eyesonthebay.dnr.maryland.gov), the National Oceanic and
 Atmospheric Admistration (https://buoybay.noaa.gov), the Chesapeake Bay
 Program (http://data.chesapeakebay.net/WaterQuality), and the Astronomical Applications Department of the US Naval Observatory (https://www.usno.navy.mil/USNO/astronomical-applications). These data, too, were summed to represent weekly values. 
description: Additional information regarding Chesapeake DolphinWatch can be
 found here: https://www.umces.edu/dolphinwatch, https://chesapeakedolphinwatch.org.
DOI: 10.5061/dryad.3tx95x6dh
title: Salinity, not genetic incompatibilities, limits the establishment of the invasive hybrid cattail Typha × glauca in coastal wetlands

description: A single pair of co-existing species that can successfully hybridize may
 produce many more hybrids in some regions than in others. The reasons for
 this are not well understood, but could help explain processes such as
 species diversification or the range expansion of invasive
 hybrids.  The widespread cattails Typha latifolia and T.
 angustifolia seldom hybridize in some parts of their range, but in other
 areas produce the dominant hybrid T. × glauca.  We used a
 combination of field and greenhouse experiments to investigate why T. ×
 glauca has invaded wetlands in the Laurentian Great Lakes region of
 southern Ontario, Canada, but is much less common in the coastal wetlands
 of NS in eastern Canada.  One potentially important environmental
 difference between these two regions is salinity.  We therefore
 tested three hypotheses: 1) T. latifolia and T. angustifolia in NS are
 genetically incompatible; 2) the germination or growth of T. × glauca is
 reduced by salinity; and 3) T. latifolia, a main competitor of T. ×
 glauca, is locally adapted to saline conditions in NS.  Our
 experiments showed that NS T. latifolia and T. angustifolia are
 genetically compatible, and that saline conditions do not impede growth of
 hybrid plants.  However, we also found that under conditions of
 high salinity, germination rates of hybrid seeds were substantially lower
 than those of NS T. latifolia.  In addition, germination rates of
 NS T. latifolia were higher than those of Ontario T. latifolia, suggesting
 local adaptation to salinity in coastal wetlands.  This study
 adds to the growing body of literature which identifies the important
 roles that local habitat and adaptation can play in the distributions and
 characteristics of hybrid zones.
DOI: 10.5061/dryad.866t1g1p1
title: Newick trees for "Within-patient phylogenetic reconstruction reveals early events in Barrett's Esophagus"

description: Newick format within-patient phylogenetic trees for a Barrett's
 Esophagus WGS dataset
description: Phylogenies were generated using the method described in the
 associated paper.  After September 30, 2020, the underlying whole-genome
 data will be archived at http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001912.v1.p1 and can be retrieved from that site.
description: Each file represents one patient and is named by the ID used in
 the study. Each file contains one or more Newick trees;
 when multiple trees are present, they represent putative independent
 origins of Barrett's Esophagus.  Branch lengths are proportional to
 inferred number of mutations.  Root branches have lengths which represent
 mutations found in all Barrett's samples but not in a blood or
 gastric control from the same patient.  Note that some Newick-reading
 software will discard these root lengths. Filenames
 containing "_all" are trees for extended data sets with two
 additional samples from a third time point.  The filename for the same
 patient ID without "_all" contains trees for only the samples
 from the first two time points. Tip names in the trees
 are sample IDs from the study.  When a single sample is inferred to
 contain two or more lineages, they are suffixed with "-1",
 "-2" etc.
DOI: 10.5061/dryad.5qfttdz32
title: Reconstructing cranial evolution in an extinct hominin

description: Homo erectus occupies a central position in human evolution as a likely
 ancestor of the modern human (Homo sapiens) and Neanderthal / Denisovan
 lineages and the first hominin species with a truly cosmopolitan
 distribution. Understanding the evolutionary population dynamics of Homo
 erectus has larger implications for the emergence of later Homo lineages
 in the Middle Pleistocene. Quantitative genetics models provide a means of
 interrogating aspects of longstanding Homo erectus population history
 narratives. For the current study, cranial fossils were sorted into six
 major paleodemes from sites across Africa and Asia spanning 1.8 to 0.1 Ma.
 Three-dimensional shape data from the occipital and frontal bones were
 used to test population genetic hypotheses. Results indicate that Homo
 erectus had higher individual and group variation than Homo sapiens,
 likely reflecting different levels of genetic diversity and population
 history in these spatially disperse species. This study also revealed
 distinct evolutionary histories for frontal and occipital bone shape in
 Homo erectus,with a larger role for natural selection in the former. One
 scenario consistent with these findings is climate-driven facial
 adaptation in Homo erectus, which is reflected in the frontal bone through
 integration with the orbits.
description: Data are 3D landmarks and semilandmarks from the frontal bone
 (all_coord_f2.csv) and occipital bone (all_coord_o2.csv) of Homo erectus
 (extinct hominin) fossils and comparative Homo sapiens (recent humans).
 Data were collected with a 3D Microscribe digitizer. Missing landmarks
 were estimated using several procedures (described in SI of original
 article). Also included are files required to
 'slide' the semilandmarks (sliders_Frt.csv and
 sliders_occ.csv) The final file is R code for
 performing anlyses presented in article.
description: The following human population abbreviations were used: Aust =
 Aboriginal Australians; Lach = Lachish, Israel; Anda = Andamanese
 Islanders; Teit = Teita, Kenya; Ngui = New Guinea; Chin = Chinese; Grgl =
 Grand Gulch, Utah (Anasazi); Ipiu = Ipiutak from Point Hope,
 Alaska. Columns in landmark files: indiv = fossil
 abbreviation; spp = species; pop = population; pop_simp = not used in
 current study; V1-V3 = x, y, and z coordinates of landmark 1, and so
 on