cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.547d7wmbz
title: Data from: Preston’s universal formula for avian egg shape

description: The main data are 50 photographs of eggs, one from each of 50
 species.  25 of these species have pyriform eggs, based on the
 traditional usage of this descriptive term. The photographs were taken to
 allow an investigation of egg shape, so they are lit from behind to
 provide a clear silhouete and were arranged to have the plane containing
 their longest axis parallel to the 'film' plane. A csv file
 contains basic information about each egg. A second csv file contains the
 results of processing these photographs (using the script GetErrors.R) to
 assess the error associated with various methods of summarising egg shape,
 including Preston's universal formula. A third csv file conatins some
 summary information on many more eggs obtained from a different study.
description: The eggs are in Museum collections. They were photographed and
 measured on site. The photographs are processed using
 GetErrors.R  For each egg, this produces the errors
 arising from various methods of summarising the egg's
 shape. The output from GetErrors.R provides the
 'raw' data for various comparisons of the methods for sumamrsing
 shape. Using this output, FigTables.R performs the
 analysis reported.
DOI: 10.15468/dl.9wgj39
title: Occurrence Download

description: A dataset containing 183 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Portugal",
 "OccurrenceStatus is Present",
 "TaxonKey is Lissotriton maltzani"
 ]
}

 The dataset includes 183 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003158-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.1rn8pk0x5
title: Resource modification by ecosystem engineers generates hotspots of stream community assembly and ecosystem function

description: Ecosystem engineers can generate hotspots of ecological structure and
 function by facilitating the aggregation of both resources and consumers.
 However, nearly all examples of such engineered hotspots come from
 long-lived foundation species, such as marine and freshwater mussels,
 intertidal cordgrasses, and alpine cushion plants, with less attention
 given to small-bodied, and short-lived taxa. Insects often have rapid life
 cycles and high population densities and are among the most diverse and
 ubiquitous animals on earth. Although these taxa have the potential to
 generate hotspots and heterogeneity comparable to that of foundation
 species, few studies have examined this possibility. We conducted a
 mesocosm experiment to examine the degree to which a stream insect
 ecosystem engineer, the net-spinning caddisfly
 (Tricoptera:Hydropsychidae), creates hotspots of ecosystem function by
 facilitating invertebrate community assembly. Our experiment used two
 treatments: (1) stream benthic habitat with patches of caddisfly engineers
 present and (2) a control treatment with no caddisflies present. We show
 that compared to controls, caddisflies increased local resource
 availability, measured as particulate organic matter (POM) by 43%,
 ecosystem respiration (ER) by 70%, and invertebrate density, biomass and
 richness by 96%, 244%, and 72%, respectively. These changes resulted in
 increased spatial variation of POM by 25%, invertebrate density by 76%,
 and ER by 29% compared to controls, indicating a strong effect of
 caddisflies on ecological heterogeneity. We found a positive relationship
 between invertebrate density and ammonium concentration in the caddisfly
 treatment, but no such relationship in the control, indicating that either
 caddisflies themselves or the invertebrate aggregations they create
 increased nutrient availability. When accounting for the amount of POM,
 caddisfly treatments increased invertebrate density by 48% and richness by
 40% compared to controls, suggesting that caddisflies may also enhance the
 nutritional quality of resources for the invertebrate assemblage. The
 caddisfly treatment also increased the rate of ecosystem respiration as a
 function of increasing POM compared to the control. Our study demonstrates
 that insect ecosystem engineers can generate heterogeneity by
 concentrating local resources and consumers, with consequences for carbon
 and nutrient cycling.
DOI: 10.5061/dryad.tht76hf26
title: Innovafrica project data on agricultural food value chains

description: A dataset was generated using the baseline survey data of the project
 entitled "Innovations in Technology, Institutional and Extension
 Approaches towards Sustainable Agriculture and enhanced Food and Nutrition
 Security in Africa (Acronym - Innovafrica)", which involved 16
 istitutions from Europe and Africa and was implemented in six countries
 namely Ethiopia, Kenya, Malawi, Rwanda, South Africa and Tanzania. It
 includes the following information: smallholders' socio-demographic
 and economic characteristics; improved agriculture practices and seed
 systems adopted; climate change related aspects; membership in
 agricultural associations, and access to subsidies, agricultural inputs
 and credit. 
description: The dataset was created by selecting and generating variables
 based on the baseline survey data of Innovafrica project. 
description: Microsoft Excel
DOI: 10.5061/dryad.15dv41p0z
title: Data for: Phylogenetics and the Cenozoic radiation of lampreys

description: Jawed vertebrates rapidly eclipsed jawless fishes in species diversity
 after they appeared approximately 450 million years ago. Only two jawless
 clades comprising less than 1% of living vertebrate diversity have
 survived: the lampreys and hagfishes. Here, we present a new phylogeny and
 historical biogeographic reconstruction of lampreys that includes all
 living species. We show that whereas the early diversification of living
 lampreys tracks Pangaean fragmentation, lampreys rapidly diversified in
 the northern hemisphere during the mid-Cretaceous turnovers and directly
 after the Cretaceous-Paleogene mass extinction. These radiations mirrored
 concurrent adaptive radiations in other lineages of animals and plants and
 coincided with changes to lamprey ecology and feeding behavior. Our
 time-calibrated phylogeny suggests that 80% of living lamprey clades
 appeared in the last 20 million years of Earth history. The age of the
 lamprey common ancestor inferred by our phylogeny is markedly younger than
 the oldest fossil occurrences of stem-group lampreys during the initial
 dominance of jawless fishes in the early Paleozoic, indicating living
 lamprey biodiversity is the result of lineage diversification extending
 from the Cretaceous to present.
description: All information is in the main text.
description: Required software applications are RStudio and BEAST 2.6.6.
 suite.
DOI: 10.5061/dryad.jsxksn0cp
title: Evolutionary changes in the chromatin landscape contribute to reorganization of a developmental gene network during rapid life history evolution in sea urchins

description: Chromatin configuration is highly dynamic during embryonic development in
 animals, exerting an important point of control in transcriptional
 regulation. Yet there exists remarkably little information about the role
 of evolutionary changes in chromatin configuration to the evolution of
 gene expression and organismal traits. Genome-wide assays of chromatin
 configuration, coupled with whole-genome alignments, can help address this
 gap in knowledge in several ways. In this study, we present a comparative
 analysis of regulatory element sequences and accessibility throughout
 embryogenesis in three sea urchin species with divergent life histories: a
 lecithotroph Heliocidaris erythrogramma, a closely related planktotroph H.
 tuberculata, and a distantly related planktotroph Lytechinus variegatus.
 We identified distinct epigenetic and mutational signatures of
 evolutionary modifications to the function of putative cis-regulatory
 elements in H. erythrogramma that have accumulated non-uniformly
 throughout the genome, suggesting selection, rather than drift, underlies
 many modifications associated with the derived life history. Specifically,
 regulatory elements composing the sea urchin developmental gene regulatory
 network are enriched for signatures of positive selection and
 accessibility changes which may function to alter binding affinity and
 access of developmental transcription factors to these sites. Furthermore,
 regulatory element changes often correlate with divergent expression
 patterns of genes involved in cell type specification, morphogenesis, and
 development of other derived traits, suggesting these evolutionary
 modifications have been consequential for phenotypic evolution in H.
 erythrogramma. Collectively, our results demonstrate that selective
 pressures imposed by changes in developmental life history rapidly reshape
 the cis-regulatory landscape of core developmental genes to generate novel
 traits and embryonic programs.
DOI: 10.5061/dryad.v6wwpzgzv
title: Differential changes in lifecycle-event phenology provide a window into regional population declines

description: Climate change affects the phenology of annual lifecycle events of
 organisms, such as reproduction and migration. Shifts in the timing of
 these events could have important population implications directly, or
 provide information about the mechanisms driving population trajectories,
 especially if they differ between lifecycle event. We examine if such
 shifts occur in a declining migratory passerine bird (Willow Warbler,
 Phylloscopus trochilus), which exhibits latitudinally diverging population
 trajectories. We find evidence of phenological shifts in breeding
 initiation, breeding progression and moult that differ across geographic
 and spring temperature gradients. Moult initiation following warmer
 springs advances faster in the south than in the north, resulting in
 proportionally shorter breeding seasons, reflecting higher nest failure
 rates in the south and in warmer years. Tracking shifts in multiple
 lifecycle events allowed us to identify points of failure in the breeding
 cycle in regions where the species has negative population trends, thereby
 demonstrating the utility of phenology analyses for illuminating
 mechanistic pathways underlying observed population trajectories.
description: We leverage observations of
 three lifecycle events (egg laying, brood patch re-feathering, moult) from
 two large-scale citizen science schemes, the UK Nest Record Scheme (Crick
 et al. 2003) and the British and Irish Ringing Scheme (Baillie et al.
 1999), collected from 2000 – 2018 across Great Britain and operated by the
 British Trust for Ornithology (BTO) in partnership with the Joint Nature
 Conservation Committee (JNCC). Nest recording and ringing occur at
 volunteer selected sites, with brood patch and moult records generally
 originating at ringing sites. Both schemes achieve broad coverage across
 Great Britain, although records south of 51˚N and north of 57˚N were
 excluded for both schemes due to low sample sizes and inconsistent
 sampling in these areas.
description: All files are in text based formats.
DOI: 10.5061/dryad.sn02v6x70
title: Spatiotemporal connectivity dynamics in spatially structured populations

description: Connectivity is a fundamental concept linking dispersal to the emergent
 dynamics and persistence of spatially structured populations. Functional
 measures of connectivity typically seek to integrate aspects of landscape
 structure and animal movement to describe ecologically meaningful
 connectedness at the landscape and population scale. Despite this focus on
 function, traditional measures of landscape connectivity assume it is a
 static property of the landscape, hence abstracting out the underlying
 spatiotemporal population dynamics. Connectivity is, arguably, a dynamic
 property of landscapes, and is inherently related to the spatial
 distribution of individuals and populations across the landscape. Static
 representations of connectivity potentially overlook this variation and
 therefore adopting a dynamic approach should offer improved insights about
 connectivity and associated ecological processes. Using a large scale,
 long-term time-series of occupancy data from a metapopulation of water
 voles (Arvicola amphibius), we tested competing hypotheses about how
 considering the dynamic nature of connectivity improves the ability of
 spatially-explicit occupancy models to recover population dynamics.
 Iteratively relaxing standing assumptions of connectivity metrics, these
 models ranged from spatially and temporally fixed connectivity metrics
 that are widely applied, to the more flexible, but lesser used model that
 allowed temporally-varying connectivity measures that incorporate
 spatiotemporally dynamic patch occupancy states. Our results provide
 empirical evidence that demographic-weighting using patch occupancy
 dynamics and temporal variability in connectivity measures are important
 for describing metapopulation dynamics. We highlight the implications of
 commonly held assumption in connectivity modeling and demonstrate how they
 result in different and highly variable predictions of metapopulation
 capacity. Thus, we argue that the concept of connectivity and its
 potential applications would benefit from recognizing inherent
 spatiotemporal variation in connectivity that is explicitly linked to
 underlying ecological state variables. 
description: Data set collection and analysis procedures may be found in Drake
 et al. 2022. "Spatiotemporal connectivity dynamics in spatially
 structured populations". These analyses contain location data
 requiring spatial censoring to protect sensitive species populations and
 their habitat. XY coordinates are the same relative distribution to allow
 replication, but with northing and easting values changed to mask specific
 locations.
description: Follow details in README document, in brief, program R is
 required to access the full context of the .RData files provided, but
 preview datasets of .csv are also provided.
DOI: 10.25338/b8d354
title: Climate change is predicted to reduce sympatry among North American wood-warblers

description: Abstract Anthropogenic climate change will dramatically alter species
 distributions. The rate and magnitude of range shifts, however, will
 differ among taxa, resulting in altered patterns of co-occurrence and
 interspecific interactions. We examined potential climate-mediated
 breeding range shifts among North American wood-warblers (Parulidae), a
 speciose avian family likely to be especially impacted by such changes due
 to high levels of interspecific competition and hybridization. We used
 publicly available species distribution model (SDM) range outputs to
 compare current ranges and patterns of sympatry among warbler species to
 future ranges and sympatry under 1.5°C, 2.0°C, and 3.0°C of average global
 warming. Range overlap among species and number of sympatric species are
 expected to decrease significantly in future warming scenarios, and
 unequal range shifts will alter the composition of warbler communities. On
 average, climate change will result in net decreases in the local species
 diversity; each warbler species is predicted to gain sympatry with
 approximately 1 new species and lose sympatry with approximately 2
 species. Climate-mediated changes are predicted to differ among warblers
 in different regions of North America, with greatest impacts on eastern
 and boreal forest species. Our findings suggest that climate change will
 alter the diversity of wood-warbler communities during this century.
 Targeted monitoring of these changing interspecific relationships,
 especially for antagonistic interactions or hybridization between newly
 sympatric species, will be crucial for prioritizing particular species and
 regions in future conservation or management efforts.
description: We used publicly available species distribution model (SDM) range
 outputs to compare current ranges and patterns of sympatry among warbler
 species to future ranges and sympatry under 1.5 °C, 2.0 °C, and 3.0 °C of
 average global warming. We used these outputs to calculate average
 breeding range area, range overlap among species, number of sympatric
 species, and distances of breeding range shifts. We additionally
 calculated the number gained and lost sympatric interactions under each
 warming scenario. 
description: Any software to open and manipulate spreadsheets - file extension
 .csv - (e.g., R, Python, Excel), as well as spatial data - file extension
 .shp - (e.g., R, ArcGIS) are required to open data files included here. A
 Python compiler (e.g., ArcGIS [what we used], Jupyter) is required to open
 .ipynb files and R/RStudio is required to open .Rmd files.
DOI: 10.5061/dryad.37pvmcvp1
title: Molecular and electrophysiological features of GABAergic neurons in the dentate gyrus reveal limited homology with cortical interneurons

description: GABAergic interneurons tend to diversify into similar classes across
 telencephalic regions. However, it remains unclear whether the
 electrophysiological and molecular properties commonly used to define
 these classes are discriminant in the hilus of the dentate gyrus. Here,
 using patch-clamp combined with single cell RT-PCR, we compare the
 relevance of commonly used electrophysiological and molecular features for
 the clustering of GABAergic interneurons sampled from the mouse hilus and
 primary sensory cortex. While unsupervised clustering groups cortical
 interneurons into well-established classes, it fails to provide a
 convincing partition of hilar interneurons. Statistical analysis based on
 resampling indicates that hilar and cortical GABAergic interneurons share
 limited homology. While our results do not invalidate the use of classical
 molecular marker in the hilus, they indicate that classes of hilar
 interneurons defined by the expression of molecular markers do not exhibit
 strongly discriminating electrophysiological properties.
DOI: 10.6078/d1jt6s
title: The phylogeny of Syntrichia: An ecologically diverse clade of mosses with an origin in South America

description: Premise: To address the biodiversity crisis, we need to understand the
 evolution of all organisms and how they fill geographic and ecological
 space. Syntrichia is one of the most diverse and dominant genera of
 mosses, ranging from alpine habitats to desert biocrusts, yet its
 evolutionary history remains unclear.    Results: We
 found 10 major well-resolved subclades of Syntrichia that possess
 geographical or morphological coherence, in some cases representing
 previously accepted genera. We infer that the extant species diversity of
 Syntrichia likely originated in South America in the early Eocene
 (56.5–43.8 mya), subsequently expanded its distribution to the neotropics,
 and finally dispersed to the northern hemisphere. There, the clade
 experienced a recent diversification (15–12 mya) into a broad set of
 ecological niches (e.g., the S. caninervis and S. ruralis complexes). The
 transition from terricolous to either saxicolous or epiphytic habitats
 occurred more than once and was associated with changes in water-related
 traits. Conclusions: Our study provides a framework for understanding the
 evolutionary history of Syntrichia through the combination of
 morphological and molecular characters, revealing that migration events
 that shaped the current distribution of the clade have implications for
 morphological character evolution in relation to niche diversity.
description: We present a comprehensive phylogenetic analysis of Syntrichia,
 based on both molecular and morphological data, with most of the named
 species and closest outgroups represented. In addition, we provide
 ancestral-state reconstructions of water-related traits and a global
 biogeographic analysis.
DOI: 10.5061/dryad.tqjq2bw2m
title: Data from: Contrasting patterns of disparity suggest differing constraints on the evolution of trilobite cephalic structures during the Cambrian ‘explosion’

description: Trilobites are an abundant group of Palaeozoic euarthropods that appear
 abruptly in the fossil record c. 521 million years ago. Quantifying the
 development of morphological variation (or ‘disparity’) through time in
 fossil groups like trilobites is critical in understanding evolutionary
 radiations such as the Cambrian ‘explosion’. Here, I use geometric
 morphometrics to quantify ‘cumulative disparity’ in functionally-important
 structures within the trilobite cephalon across their initial radiation
 during Cambrian Series 2. Overall cephalic disparity increased rapidly and
 attained a maximum within several million years. This pattern is dominated
 by the cephalic outline (in particular the genal spines), reflecting
 rapid, convergent expansion to the extremes of morphospace in a few early
 families. In contrast, removing the outline and focusing on structures
 such as the glabella and eye ridges (associated with feeding and vision,
 respectively) showed a more gradual increase in disparity, closer in line
 with taxonomic diversity and supporting the hypothesis of a relatively
 accurate trilobite fossil record. These contrasting patterns suggest that
 disparity in different structures was constrained in different ways, with
 extrinsic (ecological) factors likely having the biggest impact on overall
 disparity. It also implies that patterns of disparity in isolated
 substructures cannot necessarily be taken individually as representative
 of overall morphologies.
description: Methods are described in the main text of the article and in the
 'Detailed Methods' section of Appendix S1.
description: The data files included are for use in the statistical
 programming environment R v.4.1.1 (used in conjunction with RStudio v.
 1.4.1717 in the analysis conducted here).
DOI: 10.5061/dryad.2fqz612rt
title: Systemic racial disparities in funding rates at the National Science Foundation

description: Concerns about systemic racism at academic and research institutions have
 increased over the past decade. Here, we investigate data from the
 National Science Foundation (NSF), a major funder of research in the
 United States, and find evidence for pervasive racial disparities. In
 particular, white principal investigators (PIs) are consistently funded at
 higher rates than most non-white PIs. Funding rates for white PIs have
 also been increasing relative to annual overall rates with time. Moreover,
 disparities occur across all disciplinary directorates within the NSF and
 are greater for research proposals. The distributions of average external
 review scores also exhibit systematic offsets based on PI race. Similar
 patterns have been described in other research funding bodies, suggesting
 that racial disparities are widespread. The prevalence and persistence of
 these racial disparities in funding have cascading impacts that perpetuate
 a cumulative advantage to white PIs across all of science, technology,
 engineering and mathematics.
description: All data were collated from publicly available annual merit
 review reports published by the National Science Foundation, which can be
 accessed online at the following link: https://www.nsf.gov/nsb/publications/pubmeritreview.jsp