cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.p2ngf1vmq
title: Remotely sensed forest understory density and nest predator occurrence interact to predict suitable breeding habitat and the occurrence of a resident boreal bird species

description: Habitat suitability models (HSM) based on remotely sensed data are useful
 tools in conservation work. However, they typically use species occurrence
 data rather than robust demographic variables, and their predictive power
 is rarely evaluated. These shortcomings can result in misleading guidance
 for conservation. Here, we develop and evaluate a HSM based on correlates
 of long term breeding success of an open nest building boreal forest bird,
 the Siberian jay. In our study site in northern Sweden, nest failure of
 this permanent resident species is driven mainly by visually hunting
 corvids that are associated with human settlements. Parents rely on
 understory nesting cover as protection against these predators.
 Accordingly, our HSM includes a light detection and ranging (LiDAR) based
 metric of understory density around the nest and the distance of the nest
 to the closest settlement to predict breeding success. It reveals that a
 high understory density 15-80 m around nests is associated with increased
 breeding success in territories close to settlements (&lt;1.5 km).
 Farther away from human settlements breeding success is highest at nest
 sites with a more open understory providing a favourable warmer
 microclimate. We validated this HSM by comparing the predicted breeding
 success with landscape-wide census data on Siberian jay occurrence. The
 correlation between breeding success and occurrence was strong up to 40 km
 around the study site. However, the HSM appears to overestimate breeding
 success in regions with a milder climate, and therefore higher corvid
 numbers. Our findings suggest that maintaining patches of small diameter
 trees may provide a cost-effective way to restore the breeding habitat for
 Siberian jays up to 1.5 km from human settlements. This distance is
 expected to increase in the warmer, southern, and coastal range of the
 Siberian jay where the presence of other corvids is to a lesser extent
 restricted to settlements.
description: See the methods part of the article for more information.
description: See the methods part of the article for more information.
DOI: 10.5061/dryad.qfttdz0cq
title: Lineage-specific adaptation to climate involves flowering time in North American Arabidopsis lyrata

description: Adaptation to local climatic conditions is commonly found within species,
 but whether it involves the same intraspecific genomic variants is
 unknown. We studied this question in North American Arabidopsis lyrata,
 whose current distribution is shaped by post-glacial range expansion from
 two refugia, resulting in two distinct genetic clusters covering
 comparable climatic gradients. Using whole-genome pooled sequence data of
 41 outcrossing populations, we identified loci associated with three
 niche-determining climatic variables in the two clusters and compared
 these outliers. Little evidence was found for parallelism in climate
 adaptation for single nucleotide polymorphisms (SNPs) and for genes with
 an accumulation of outlier SNPs. Significantly increased selection
 coefficients supported them as candidates of climate adaptation. However,
 the fraction of gene ontology (GO) terms shared between clusters was
 higher compared to outlier SNPs and outlier genes, suggesting that
 selection acts on similar pathways but not necessarily the same genes.
 Enriched GO terms involved responses to abiotic and biotic stress,
 circadian rhythm and development, with flower development and reproduction
 being among the most frequently detected. In line with GO enrichment,
 regulators of flowering time were detected as outlier genes. Our results
 suggest that while adaptation to environmental gradients on the genomic
 level are lineage-specific in A. lyrata, similar biological processes seem
 to be involved. Differential loss of standing genetic variation – likely
 driven by genetic drift – can in part account for the lack of parallel
 evolution on the genomic level.
description: Details of data collection and processing can be obtained from
 the publication. In short, this dataset consists of four files:
 (1) Results of six GWAS analyses (eastern and western genetic
 cluster of North American <em>Arabidopsis lyrata</em> subsp.
 <em>lyrata </em>with three climatic variables each - minimum
 temperature in early spring, precipitation of the wettest quarter, and
 moisture availability). The table contains genomic coordinates (bed file
 format) and Bayes factors obtained for each climatic variable/genetic
 cluster using the software BayPass. (2) An excel sheet
 listing gene ontology outliers obtained using the snp2go and REVIGO
 software. The REVIGO output including false discovery rates and p-values
 is given. (3) An excel sheet listing outlier genes
 obtained following the method described by Yeaman et al., 2016 (Science)
 including test statistics. (4) A table containing all
 genes, for which SNPs were detected in the dataset, including SNP content
 and gene length.
DOI: 10.5061/dryad.pzgmsbcgg
title: Synchronous and asynchronous root and shoot phenology in temperate woody seedlings

description: Understanding variation in root and shoot growth phenology among species
 is crucial to understanding underlying mechanisms of temporal niche
 differentiation. However, little is known about the relationship between
 root and shoot phenology, or how this relationship varies among functional
 traits. We examined fine root and shoot phenology of 42 seedlings
 representing a variety of woody species that inhabit the cool temperate
 forests of northern Japan. Some aspects of phenology were common to the
 pool of species examined: we found positive relationships between root and
 shoot phenology for the end of growth, and for the duration of growth, but
 not for the start of growth. Further, seedlings that started root growth
 relatively early also ended root growth relatively late. Other aspects of
 phenology varied predictably with functional traits, i.e. leaf habit and
 successional status: first, root growth in evergreen species started
 significantly earlier and ended later than in deciduous species; second,
 early successional species had the longest duration of shoot growth among
 all successional types. Our results suggest that niche differentiation may
 be promoted by differences in phenology between root and shoots, likely
 contributing to the co-existence of woody seedlings in temperate forests.
description: The relative growth rate was measured every 1-2 weeks over one
 yea in Hokkaido, Japan. The root growth was measured by using
 rhizobox.
description: The year of investirgation ranged over 4 years. For the analysis,
 the year was identified as factor data (not numeric data).
DOI: 10.5061/dryad.rbnzs7h7f
title: Categorical versus geometric morphometric approaches to characterising the evolution of morphological disparity in Osteostraci (Vertebrata, stem-Gnathostomata)

description: Morphological variation (disparity) is almost invariably characterised by
 two non-mutually exclusive approaches: (i) quantitatively, through
 geometric morphometrics, and (ii) in terms of discrete, ‘cladistic’, or
 categorical characters. Uncertainty over the comparability of these
 approaches diminishes the potential to obtain nomothetic insights into the
 evolution of morphological disparity and the few benchmarking studies
 conducted so far show contrasting results. Here, we apply both approaches
 to characterising morphology in the stem-gnathostome clade Osteostraci in
 order to assess congruence between these alternative methods as well as to
 explore the evolutionary patterns of the group in terms of temporal
 disparity and the influence of phylogenetic relationships and habitat on
 morphospace occupation. Our results suggest that both approaches yield
 similar results in morphospace occupation and clustering, but also some
 differences indicating that these metrics may capture different aspects of
 morphology. Phylomorphospaces reveal convergence towards a generalised
 ‘horseshoe’-shaped cranial morphology and two strong trends involving
 major groups of osteostracans (benneviaspidids and thyestiids), which
 probably reflect adaptations to different lifestyles. Temporal patterns of
 disparity obtained from categorical and morphometric approaches appear
 congruent, however disparity maxima are recorded at very different times
 in the evolutionary history of the group when increasing the number of
 taxa and characters in the categorical dataset. The results of our
 analyses indicate that categorical and continuous datasets may
 characterize different patterns of morphological disparity and that
 discrepancies could reflect preservational limitations of morphometric
 data and differences in the potential of each data type for characterizing
 more or less inclusive aspects of overall phenotype.
DOI: 10.15468/dl.m3y3ds
title: Occurrence Download

description: A dataset containing 4544 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-115.19683 49.1877,-115.33308 45.04945,-104.79659 44.95311,-104.56951 49.1877,-115.19683 49.1877))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Ericameria nauseosa, Grindelia squarrosa, Heterotheca villosa, Rosa arkansana, Rosa arkansana, Allium textile, Cirsium undulatum, Cleome serrulata, Cleome serrulata, Ratibida columnifera, Astragalus crassicarpus, Astragalus crassicarpus, Dalea candida, Echinacea angustifolia, Liatris ligulistylis, Liatris ligulistylis, Liatris ligulistylis, Linum lewisii, Monarda fistulosa, Monarda fistulosa, Monarda fistulosa, Monarda fistulosa, Solidago missouriensis, Vicia americana, Vicia americana, Symphoricarpos occidentalis, Frasera speciosa, Frasera speciosa, Frasera speciosa, Campanula rotundifolia, Coleosporium campanulae-rotundifoliae, Campanula rotundifolia, Campanula rotundifolia, Campanula rotundifolia, Campanula rotundifolia, Penstemon albidus, Penstemon albidus)",
 "Year 2015-2026"
 ]
}

 The dataset includes 4544 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002147-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.8kprr4xjk
title: Strong sexual selection despite spatial constraints on extra-pair paternity

description: Extra-pair paternity should contribute to sexual selection by increasing
 the number of potential mates available to each individual. Potential
 copulation partners are, however, limited by their proximity. Spatial
 constraints may therefore reduce the impact of extra-pair paternity on
 sexual selection. We tested the effect of spatial constraints on sexual
 selection by simulating extra-pair copulations for 15 species of socially
 monogamous songbirds with varying rates of extra-pair paternity. We
 compared four metrics of sexual selection between simulated populations
 without spatial constraints and populations where extra-pair copulations
 were restricted to first- and second-order neighbors. Counter to
 predictions, sexual selection as measured by the Bateman gradient (the
 association between number of copulation partners and offspring produced)
 increased under spatial constraints. In these conditions, repeated
 extra-pair copulations between the same individuals led to more offspring
 per copulation partner. In contrast, spatial constraints did somewhat
 reduce sexual selection – as measured by the opportunity for selection,
 s’max, and the selection gradient on male quality – when the association
 between simulated male quality scores and copulation success (e.g., female
 preferences or male-male competition) was strong.  Sexual
 selection remained strong overall in those populations, even under spatial
 constraints. Spatial constraints did not substantially reduce sexual
 selection when the association between male quality and copulation success
 was moderate or weak. Thus, spatial constraints on extra-pair copulations
 are insufficient to explain the absence of strong selection on male traits
 in many species.
description: One data file shows the distribution of extra-pair offspring
 among clutches, with extra-pair paternity identified using genetic tools.
 These data were compiled from published studies in some cases and for
 other species, they represent unpublished additional information connected
 to publications. Sources are provided in the associated manuscript.
 Permission to provide the unpublished data were provided by the authors of
 that information. The second data file shows the
 estimated values of m and s, two parameters used in the simulation
 code. Finally, the simulation code is
 included. 
description: Please see readme file.
DOI: 10.5061/dryad.gtht76hh9
title: Plant response to habitat amount and configuration in Swedish forests

description: Aim: There is an intense debate about whether habitat fragmentation has a
 negative or positive effect on biodiversity. We examined whether species
 richness and incidence of forest plants were negatively or positively
 associated with fragmented forest configuration. We also analysed whether
 the results support the fragmentation threshold hypothesis with
 fragmentation effects only in landscapes with small habitat amount.
 Location: Södermanland province, south-eastern Sweden (8,388 km2).
 Methods: Data consisted of plant distribution maps and landscape data on
 forest amount and configuration in 2.5 km × 2.5 km quadrats. We carried
 out models including forest area together with clumpiness index (CL
 models) or edge density (ED models) as the measure of habitat
 configuration. We focused on plant taxa with positive association between
 incidence and forest area (163 taxa in CL models; 119 taxa in ED models).
 Results: Responses to fragmented configuration were negative more often
 than by random (33 and 22 taxa in CL and ED models, respectively; includes
 only models without significant forest area × configuration interaction),
 whereas positive responses were rare (four taxa in both models). When
 forest area × configuration interaction was significant, the most common
 response had a negative effect of fragmented configuration when forest
 area was low and no effect of configuration when forest area was high,
 which agrees with the fragmentation threshold hypothesis. Species richness
 also had this type of response. In another common interactive response,
 the effect of fragmented configuration was negative at low forest area and
 positive at high forest area. Main conclusions: Responses to fragmented
 forest configuration, when significant, were usually negative. When
 responses to fragmented configuration were modulated by forest area, they
 were negative when forest area was low. The findings of complex
 interaction between forest area and configuration have implications for
 selection of appropriate patch sizes in sustainable forest management.
description: Data collection and processing methods are described in Lehtilä
 et al. (2020), Plant response to habitat amount and configuration in
 Swedish forests. Diversity and Distributions.
DOI: 10.5061/dryad.3xsj3txbt
title: Integrating stable isotopes, parasite and ring-reencounter data to quantify migratory connectivity - a case study with Barn Swallows breeding in Switzerland, Germany, Sweden and Finland

description: Ecosystems around the world are connected by seasonal migration. The
 migrant animals themselves are influenced by migratory connectivity
 through effects on the individual and the population level. Measuring
 migratory connectivity is notoriously difficult due to the simple
 requirement of data conveying information about the non-breeding
 distribution of many individuals from several breeding populations.
 Explicit integration of data derived from different methods increases the
 precision and the reliability of parameter estimates. We combine
 ring-reencounter, stable isotope and blood parasite data of Barn Swallows
 Hirundo rustica in a single integrated model to estimate migratory
 connectivity for three large scale breeding populations across a
 latitudinal gradient from Central Europe and Scandinavia. To this end, we
 integrated a non-Markovian multi-state mark-recovery model for the
 ring-reencounter data with normal and binomial mixture models for the
 stable isotope and parasite data. The integration of different data
 sources within a mark-recapture modelling framework enables the most
 precise quantification of migratory connectivity on the given broad
 spatial scale. The results show that northern breeding populations and
 Southern Africa as well as southern breeding populations and
 Western-Central Africa are more strongly connected through Barn Swallow
 migration than central European breeding populations with any of the
 African wintering areas. The non-breeding distribution of Barn Swallows
 from central European breeding populations seems to be a mixture of those
 populations breeding further North and South, indicating a migratory
 divide.
description: raw_isotope_data.txt: The site key defines the sampling site of
 the feather sample. Codes are given in Figure S1.
 rcode_for_running_model.r: Complete R code ready to load the data
 and run the model in Jags
 recovery_isotope_parasite_data.rda: Compiled data (ringing and
 ring re-encounter data, parasite data and z-transformed stable isotope
 data) to be read into R using the r-codefile
 "rcode_for_running_model.r". jags_code.txt:
 Jags code of the model
DOI: 10.5061/dryad.h44j0zpfz
title: A 12-month-old with hypotonia and developmental delays

description: This data shows the references cited in the case report for the diagnosis
 of a 12-month-old girl who was referred to the pediatric neuromuscular
 clinic for evaluation of hypotonia and weakness and ultimately found to
 have 2 variants of uncertain significance in the NFU1 gene (NM
 _001002755.2 c.398T&gt;C; p.Leu133Pro and NM _001002755.2
 c.299C&gt;G; p.Ala100Gly). Biochemical testing including CSF
 metabolomics confirmed her diagnosis of NFU1-related multiple
 mitochondrial dysfunctions syndrome (type 1). 
description: These are references cited in the case report: 1.        Orsini JJ, Escolar ML, Wasserstein MP, Caggana M. <i>Krabbe Disease</i>.; 2018. 2.        Srivastava S, Naidu S. <i>Alexander Disease</i>. University of Washington, Seattle; 2015. 3.        Gomez-Ospina N. <i>Arylsulfatase A Deficiency</i>. University of Washington, Seattle; 2017. 4.        Hobson GM, Kamholz J. <i>PLP1-Related Disorders</i>. University of Washington, Seattle; 2013. 5.        Raymond G V, Moser AB, Fatemi A. X-Linked Adrenoleukodystrophy. GeneReviews. https://www.ncbi.nlm.nih.gov/books/NBK1315/. Published February 15, 2018. Accessed June 26, 2019. 6.        Matalon R, Delgado L, Michals-Matalon K. <i>Canavan Disease</i>. University of Washington, Seattle; 2018.
DOI: 10.5061/dryad.z34tmpg8q
title: Detection of prey odors underpins dietary specialization in a Neotropical top-predator: how army ants find their ant prey

description: 1. Deciphering the mechanisms that underpin dietary specialization and
 niche partitioning is crucial to understanding the maintenance of
 biodiversity. New world army ants live in species-rich assemblages
 throughout the Neotropics and are voracious predators of other arthropods.
 They are therefore an important and potentially informative group for
 addressing how diverse predator assemblages partition available prey
 resources. 2. New World army ants are largely specialist predators of
 other ants, with each species specializing on different ant genera.
 However, the mechanisms of prey choice are unknown. In this study, we
 addressed whether the army ant Eciton hamatum: 1) can detect potential
 prey odors, 2) can distinguish between odors of prey and non-prey, and 3)
 can differentiate between different types of odors associated with its
 prey. 3. Using field experiments, we tested the response of army ants to
 the following four odor treatments: alarm odors, dead ants, live ants, and
 nest material. Each treatment had a unique combination of odor sources and
 included some movement in two of the treatments (alarm and live ants).
 Odor treatments were tested for both prey and non-prey ants. These data
 were used to determine the degree to which E. hamatum are using specific
 prey stimuli to detect potential prey and direct their foraging. 4. Army
 ants responded strongly to odors derived from prey ants, which triggered
 both increased localized recruitment and slowed advancement of the raid as
 they targeted the odor source. Odors from non-prey ants were largely
 ignored. Additionally, the army ants had the strongest response to the
 nest material of their preferred prey, with progressively weaker responses
 across the live ant, dead ant, and alarm odors treatments, respectively.
 5. This study reveals that the detection of prey odors, and especially the
 most persistent odors related to the prey’s nest, provides a mechanism for
 dietary specialization in army ants. If ubiquitous across the Neotropical
 army ants, then this olfaction-based ecological specialization may
 facilitate patterns of resource partitioning and coexistence in these
 diverse predator communities. 08-Jan-2020
description: See manuscript methods
DOI: 10.5061/dryad.qrfj6q5bj
title: Episodic herbivory, plant density dependence and stimulation of aboveground plant production

description: Herbivory is a major energy transfer within ecosystems; an open question
 is under what circumstances it can stimulate aboveground seasonal primary
 production. Despite multiple field demonstrations, past theory considered
 herbivory as a continuous process and found stimulation of seasonal
 production to be unlikely. Here we report a new theoretical model that
 explores the consequences of discrete herbivory events, or episodes,
 separated in time. We discovered that negative density (biomass)
 dependence of plant growth, such as might be expected from resource
 limitation of plant growth, favors stimulation of seasonal production by
 infrequent herbivory events under a wide range of herbivory intensities
 and maximum plant relative growth rates. Results converge to those of
 previous models under repeated, short-interval herbivory, which generally
 reduces seasonal production. Model parameters were estimated with new and
 previous data from the Serengeti ecosystem. Patterns of observed frequent
 and large magnitude stimulated production in these data agreed generally
 with those predicted by the episodic herbivory model. The model thus may
 provide a new framework for evaluating the sustainability and impact of
 herbivory.
description: Biomass measurements made once, on average 28 days apart, in each
 of consecutive months April, May, and June in 2000, 2001, and 2002 in
 three 4 x 4 m fenced plots at each of seven sites from the Long-Term
 Grazing Exclosure (LTGE) experiment. Four 25 x 25 cm quadrats were clipped
 to the ground surface in each 4 x 4 m plot, with green material sorted to
 stem versus leaf and green separated from litter (gray plant material)
 Different quadrats were clipped from different locations within plots in
 each month. Green material was air-dried at 45<sup>o</sup>C
 for a week and then weighed. Sites varied in mean annual rainfall from 490
 – 890 mm/yr , soil N from 0.05% to 0.22% and soil P from 0.005% to
 0.15%