cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.m0cfxpnzm
title: Mind the outgroup and bare branches in total-evidence dating: a case study of Pimpliform Darwin Wasps (Hymenoptera, Ichneumonidae)

description: Taxon sampling is a central aspect of phylogenetic study design, but it
 has received limited attention in the context of total-evidence dating, a
 widely used dating approach that directly integrates molecular and
 morphological information from extant and fossil taxa. We here assess the
 impact of commonly employed outgroup sampling schemes and missing
 morphological data in extant taxa on age estimates in a total-evidence
 dating analysis under the uniform tree prior. Our study group is
 Pimpliformes, a highly diverse, rapidly radiating group of parasitoid
 wasps of the family Ichneumonidae. We analyze a data set comprising 201
 extant and 79 fossil taxa, including the oldest fossils of the family from
 the Early Cretaceous and the first unequivocal representatives of extant
 subfamilies from the mid Paleogene. Based on newly compiled molecular data
 from ten nuclear genes and a morphological matrix that includes 222
 characters, we show that age estimates become both older and less precise
 with the inclusion of more distant and more poorly sampled outgroups.
 These outgroups not only lack morphological and temporal information, but
 also sit on long terminal branches and considerably increase the
 evolutionary rate heterogeneity. In addition, we discover an artefact that
 might be detrimental for total-evidence dating: “bare-branch attraction”,
 namely high attachment probabilities of certain fossils to terminal
 branches for which morphological data are missing. Using computer
 simulations, we confirm the generality of this phenomenon and show that
  a large phylogenetic distance to any of the extant taxa, rather
 than just older age, increases the risk of a fossil being misplaced due to
 bare-branch attraction. After restricting outgroup sampling and adding
 morphological data for the previously attracting, bare branches, we
 recover a Jurassic origin for Pimpliformes and Ichneumonidae. This first
 age estimate for the group not only suggests an older origin than
 previously thought, but also that diversification of the crown group
 happened well before the Cretaceous-Paleogene boundary. Our case study
 demonstrates that in order to obtain robust age estimates, total-evidence
 dating studies need to be based on a thorough and balanced sampling of
 both extant and fossil taxa, with the aim of minimizing evolutionary rate
 heterogeneity and missing morphological information.
DOI: 10.15468/dl.wdcvz4
title: Occurrence Download

description: A dataset containing 19053 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Araucaria angustifolia, Cyanocorax caeruleus)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 19053 records from 156 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002018-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.r2280gb8n
title: Data from: Small population size and low genomic diversity have no effect on fitness in experimental translocations of a wild fish

description: Little empirical work in nature has quantified how wild populations with
 varying effective population sizes and genetic diversity perform when
 exposed to a gradient of ecologically important environmental conditions.
 To achieve this, juvenile brook trout from 12 isolated populations or
 closed metapopulations that differ substantially in population size and
 genetic diversity were transplanted to previously fishless ponds spanning
 a wide gradient of ecologically important variables. We evaluated the
 effect of genome-wide variation, effective population size (Ne), pond
 habitat, and initial body size on two fitness correlates (survival and
 growth). Genetic variables had little effect on either fitness correlate,
 which were determined primarily by habitat (pond temperature, depth, and
 pH) and initial body size. These results suggest that some vertebrate
 populations with low genomic diversity, low Ne and long-term isolation can
 represent important sources of variation and be capable of maintaining
 fitness in, and ultimately persisting and adapting to, changing
 environments. Our results also reinforce the paramount importance of
 improving available habitat and slowing habitat degradation for species
 conservation.
DOI: 10.6078/d1mq2v
title: Data from: Species richness, endemism, and abundance patterns: tests of two fractal models in a serpentine grassland

description: From Ecology Letters: Although scaling relationships that characterize
 fractal species distributions offer an exciting potential for unification
 in biogeography, empirical support for fractal theory remains the subject
 of debate. We synthesize and test multiple predictions of two interrelated
 fractal models and a null model of random placement using Californian
 serpentine grassland data describing the spatial location of over 37 000
 individually identified plants. The endemics–area relationship and
 species‐abundance distribution recently derived from a community‐level
 fractal property performed poorly because of an inaccurate assumption of
 homogeneity among species. In contrast, a species‐level fractal model that
 incorporates species‐level differences predicted abundances well, but
 systematically overestimated endemism and predicted a species–area
 relationship that violated the observed power law. These findings indicate
 that in order to make predictions based on the existence of a power‐law
 species–area relationship, ecologists need a unifying theory of how the
 community‐level fractal property arises in the presence of species‐level
 distributional differences.
description: This data is from a census carried out over the spring and summer
 of 1998 by Jessica Green on a 64 m^2 plot at the University of
 California’s McLaughlin Reserve in Yolo county, CA. The plot was gridded
 to a smallest cell size of ¼ m^2 and in each cell the abundance of every
 plant species found there was recorded. See paper for more
 information.
description: The spreadsheet (Serpentine.csv) provided here is organized as
 follows: the columns are plant species, with each species given a code
 name that is explained in Serpentine_SpeciesList.txt. There are 256 rows
 of data, with each row corresponding to one of the ¼ m^2 cells. If the
 plot is viewed as a matrix, then the first row of data in the spreadsheet
 corresponds to the upper left cell (matrix element a1,1). The second row
 of data is the matrix element a1,2, or in other words the cell just to the
 right of a1,1. The 17th row of data then corresponds to the plot matrix
 element a2,1, and the very last row of data is the lower right cell,
 a16,16. The actual data entries are the abundances of the species in each
 cell. The data may be used by readers for any purpose,
 but any publication that includes use of the data should reference the
 data set to: Green J., J. Harte, and A. Ostling,
 2003. Species richness, endemism, and abundance patterns: tests of two
 fractal models in a serpentine grassland. <em>Ecology
 Letters</em> <strong>6</strong> 919-928.
 Moreover, the Acknowledgments should include a thanks to Jessica
 Green for use of the data.
DOI: 10.5061/dryad.8931zcrkv
title: A multimodal longitudinal study of structural brain involvement in amyotrophic lateral sclerosis

description: Objective: To understand the progressive nature of amyotrophic lateral
 sclerosis (ALS) by investigating
 differential brain patterns of gray and white
 matter involvement in clinically or genetically defined
 subgroups of patients using
 cross-sectional, longitudinal and multimodal MRI. Methods: We assessed cortical thickness, subcortical volumes and white matter connectivity from T1-weighted and diffusion-weighted MRI in 292 ALS patients (follow-up: n=150) and 156 controls (follow-up: n=72). Linear mixed-effects models were used to assess changes in structural brain measurements over time in patients compared to controls. Results: Patients with a C9orf72 mutation (n=24) showed widespread gray and white matter involvement at baseline, and extensive loss of white matter integrity in the connectome over time. In C9orf72-negative patients, we detected cortical thinning of motor and frontotemporal regions, and loss of white matter integrity of connections linked to the motor cortex. Spinal-onset patients displayed widespread white matter involvement at baseline and gray matter atrophy over time, whereas bulbar-onset patients started out with prominent gray matter involvement. Patients with unaffected cognition or behavior displayed predominantly motor system involvement, while widespread cerebral changes, including frontotemporal regions with progressive white matter involvement over time, were associated with impaired behavior or cognition. Progressive loss of gray and white matter integrity typically occurred in patients with shorter disease durations (&lt;13 months), independent of progression rate. Conclusions: Heterogeneity of phenotype and C9orf72 genotype relates to distinct patterns of cerebral degeneration. We demonstrate that imaging studies have the potential to monitor disease progression and early intervention may be required to limit cerebral degeneration.
description: Supplemental Data corresponding to research paper 'A
 multimodal longitudinal study of structural brain involvement in
 ALS' It contains appendices, supplemental figures
 and supplemental tables for this paper.
DOI: 10.15468/dl.t3bf5j
title: Occurrence Download

description: A dataset containing 830 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Onthophagus chevrolati"
 ]
}

 The dataset includes 830 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002019-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.x0k6djhf7
title: Limited phenological and pollinator-mediated isolation among selfing and outcrossing Arabidopsis lyrata populations

description: Transitions from outcrossing to selfing have been a frequent evolutionary
 shift in plants and clearly play a role in species divergence. However,
 many questions remain about the initial mechanistic basis of reproductive
 isolation during the evolution of selfing. For instance, how important are
 pre-zygotic pre-pollination mechanisms (e.g. changes in phenology and
 pollinator visitation) in maintaining reproductive isolation between newly
 arisen selfing populations and their outcrossing ancestors? To test
 whether changes in phenology and pollinator visitation isolate selfing
 populations of Arabidopsis lyrata from outcrossing populations, we
 conducted a common garden experiment with plants from selfing and
 outcrossing populations as well as their between-population hybrids.
 Specifically, we asked whether there was isolation between outcrossing and
 selfing plants and their between-population hybrids through differences in
 (1) the timing or intensity of flowering; and/or (2) pollinator
 visitation. We found that phenology largely overlapped between plants from
 outcrossing and selfing populations. There were also no differences in
 pollinator preference related to mating system. Additionally, pollinators
 preferred to visit flowers on the same plant rather than exploring nearby
 plants, creating a large opportunity for self-fertilization. Overall, this
 suggests that pre-zygotic pre-pollination mechanisms do not strongly
 reproductively isolate plants from selfing and outcrossing populations of
 Arabidopsis lyrata.
DOI: 10.5061/dryad.15dv41nsm
title: Surface indicators are correlated with soil multifunctionality in global drylands

description: 1. Multiple ecosystem functions need to be considered simultaneously to
 manage and protect the many ecosystem services that are essential to
 people and their environments. Despite this, cost effective, tangible,
 relatively simple, and globally-relevant methodologies to monitor in situ
 soil multifunctionality, i.e. the provision of multiple ecosystem
 functions by soils, have not been tested at the global scale. 2. We
 combined correlation analysis and structural equation modelling to explore
 whether we could find easily measured, field-based indicators of soil
 multifunctionality (measured using functions linked to the cycling and
 storage of soil carbon, nitrogen, and phosphorus). To do this, we gathered
 soil data from 120 dryland ecosystems from five continents. 3. Two soil
 surface attributes measured in situ (litter incorporation and surface
 aggregate stability) were the most strongly associated with soil
 multifunctionality, even after accounting for geographic location and
 other drivers such as climate, woody cover, soil pH and soil electric
 conductivity. The positive relationships between surface stability and
 litter incorporation on soil multifunctionality was greater beneath the
 canopy of perennial vegetation than in adjacent, open areas devoid of
 vascular plants. The positive associations between surface aggregate
 stability and soil functions increased with increasing mean annual
 temperature. 4. Synthesis and applications. Our findings demonstrate that
 a reduced suite of easily measured in situ soil surface attributes can be
 used as potential indicators of soil multifunctionality in drylands
 worldwide. These attributes, which relate to plant litter (origin,
 incorporation, cover), and surface stability, are relatively cheap and
 easy to assess with minimal training, allowing operators to sample many
 sites across widely varying climatic areas and soil types. The
 correlations of these variables are comparable to the influence of climate
 or soil, and would allow cost-effective monitoring of soil
 multifunctionality under changing land use and environmental conditions.
 This would provide important information for evaluating the ecological
 impacts of land degradation, desertification and climate change in
 drylands worldwide.
DOI: 10.5061/dryad.ncjsxksqs
title: Hinge and ecomorphology of Legumen Conrad, 1858 (Bivalvia, Veneridae), and the contraction of venerid morphospace following the end-Cretaceous extinction

description: The Veneridae are the most speciose modern family of bivalves, and one of
 the most morphologically conservative and homoplastic, making subfamilial
 and sometimes even genus-level classification difficult. The widespread
 Cretaceous genus Legumen Conrad, 1858 is currently placed in the subfamily
 Tapetinae of the Veneridae although it more closely resembles the
 Solenoida (razor clams, Pharidae and Solenidae) in general shell form.
 Here we provide high-resolution images of the Legumen hinge for the first
 time. We confirm from hinge morphology that Legumen belongs in Veneridae,
 but it should be referred to incertae subfamiliae, rather than retained in
 the Tapetinae, particularly in light of the incomplete and unstable
 understanding of venerid systematics. Legumen represents a unique hinge
 dentition and a shell form - and associated life habit - that is absent in
 the modern Veneridae despite their taxonomic diversity. Veneridae are
 hyperdiverse in the modern fauna but strikingly ‘under-disparate’, having
 lost forms while gaining species in the long recovery from the
 end-Cretaceous extinction.
DOI: 10.5061/dryad.9ghx3ffd2
title: Fire and grazing determined grasslands of central Madagascar represent ancient assemblages

description: The ecology of Madagascar’s grasslands is under-investigated and the
 dearth of ecological understanding of how disturbance by fire and grazing
 shapes these grasslands stems from a perception that disturbance shaped
 Malagasy grasslands only after human arrival. However, worldwide, fire and
 grazing shape tropical grasslands over ecological and evolutionary
 timescales, and it is curious Madagascar should be a global anomaly. We
 examined the functional and community ecology of Madagascar’s grasslands
 across 71 communities in the Central Highlands. Combining multivariate
 abundance models of community composition and clustering of grass
 functional traits, we identified distinct grass assemblages each shaped by
 fire or grazing. The fire-maintained assemblage is primarily composed of
 tall caespitose species with narrow leaves and low bulk density. In
 contrast, the grazer-maintained assemblage is characterized by
 mat-forming, high bulk density grasses with wide leaves. Within each
 assemblage, levels of endemism, diversity and grass ages support these as
 ancient assemblages. Grazer-dependent grasses can only have co-evolved
 with a now-extinct megafauna. Ironically, the human introduction of cattle
 likely introduced a megafaunal substitute facilitating modern day
 persistence of a grazer-maintained grass assemblage in an otherwise
 defaunated landscape, where these landscapes now support the livelihoods
 of millions of people.
DOI: 10.5061/dryad.dbrv15dx2
title: Atlantic cod recovery from the Allee effect zone: contrasting ecological and evolutionary rescue

description: The ability of a population to recover from disturbances is fundamental
 for its persistence. Impaired population recovery might be associated with
 a demographic Allee effect. Immigration from adjacent populations could
 accelerate the recovery not only by promoting population growth beyond the
 Allee effect threshold but also by bringing in advantageous genotypes. We
 explore the nature and role of ecological and evolutionary rescue in an
 Atlantic cod (Gadus morhua) population fished below its Allee effect
 threshold. We utilize an eco-evolutionary model and simulate scenarios,
 where the target population evolves in response to selective fishing and
 sample immigrants from i) a source population similarly adapted to fishing
 (post-fishing genotypes) or ii) an unexploited source population with
 natural genetic and phenotypic diversity (pre-fishing genotypes).
 Immigration of pre-fishing genotypes enhances the recovery due to the
 larger body sizes and the flow of associated genes. Post-fishing
 immigrants can promote the population abundance recovery, but they slow
 down evolutionary recovery from fishing-induced selection and increase
 uncertainty about recovery times. Our results stress the importance of
 maintaining genetic and phenotypic diversity and suggest that marine
 protected areas can serve as an important source of immigrants to promote
 both the demographic and evolutionary recovery of exploited populations.
DOI: 10.5061/dryad.dfn2z34wc
title: Fine-scale invasion genetics of the quarantine pest, Anoplophora glabripennis, reconstructed in single outbreaks

description: The xylophagous cerambycid Anoplophora glabripennis, the Asian long-horned
 beetle (ALB), is highly polyphagous and can colonize a wide range of
 broadleaved host trees causing significant economic damage. For this
 reason, it is considered a quarantine pest in Europe and North America.
 Although the global spread of ALB has been depicted recently, no
 comprehensive studies exist on the genetic pattern of populations’
 establishment and dynamics at fine-scale (i.e. within invasive outbreaks),
 before eradication measures are applied. This information may, however, be
 particularly important for an efficient management and control of invasive
 pests. Here, we characterized population genetic diversity and patterns of
 spread of ALB within and among the four outbreaks detected in Switzerland
 between 2011 and 2015. For this, we genotyped 223 specimens at 15 nuclear
 microsatellite loci and conducted specific population-based analyses. Our
 study shows: (1) At least three independent introductions and a,
 human-mediated, secondary dispersal event leading to the four outbreaks in
 the country; (2) An overall low intra-population genetic diversity in the
 viable and several years active invasive populations; (3) A colonization
 of single trees by homogeneous ALB genotypes; And (4) an establishment of
 populations several generations prior to its official discovery.
DOI: 10.5061/dryad.47d7wm38g
title: Declining freshwater mussel diversity in the middle and lower reaches of the Xin River Basin: Threat and Conservation

description: Freshwater mussels provide important functions and services for aquatic
 ecosystems, but populations of many species have been extirpated.
 Information on biodiversity plays an important role in the conservation
 and management of freshwater mussels. The Xin River Basin is a
 biodiversity hotspot for freshwater mussels in China, with more than 43
 species known, but populations of which are decreasing. Here, we quantify
 the diversity of freshwater mussels in the middle and lower reaches of the
 Xin River Basin and study the correlation of habitat characteristics and
 freshwater mussel diversity. Compared to the historical period, the number
 of species, density and biomass of freshwater mussels decreased 33%, 83%
 and 82% in the current period, respectively. 52% of recorded species were
 empty shells, and 14 native freshwater mussels were not found in the study
 area. Four species are currently listed as vulnerable species using IUCN
 criteria and their global status. The assemblage structure of freshwater
 mussels exhibits significant spatial differences, and there was a
 correlation with substrate and physicochemical parameters. The main
 tributary of the Xin River with higher freshwater mussel diversity should
 be established as one large protected area because the nestedness
 component was the main pattern of beta diversity. These results indicated
 freshwater mussel diversity was declining rapidly, which can help focus
 conservation effort for freshwater mussel biodiversity.
DOI: 10.5061/dryad.hmgqnk9c3
title: Data from: Global fern and lycophyte richness explained: how regional and local factors shape plot richness

description: Aim To disentangle the influence of environmental factors at different
 spatial grains (regional and local) on fern and lycophyte species richness
 and ask how regional and plot-level richness are related to each other.
 Location Global. Time Period Present. Major Taxa studied Ferns and
 lycophytes. Methods We explored fern and lycophyte species richness at two
 spatial grains, regional (hexagonal grid cells of 7666 km2) and plot-level
 (300–500 m2), in relation to environmental data at regional and local
 grains (the 7666-km2 hexagonal grid cells and 4-km2 square grid cells,
 respectively). For the regional grain, we obtained species richness data
 for 1243 spatial units and used them together with climatic, and
 topographical predictors to model global fern richness. For the plot-level
 grain, we collated a global dataset of nearly 83,000 vegetation plots with
 surface area in the range 300–500 m2 in which all fern and lycophyte
 species had been counted. We used structural equation modelling to
 identify which regional and local factors have the biggest effect on
 plot-level fern and lycophyte species richness worldwide. We investigate
 how plot-level richness is related to modelled regional richness at the
 plot’s location. Results Plot-level fern and lycophyte species richness
 was best explained by models allowing a link between regional environment
 and plot-level richness. A link between regional richness and plot-level
 richness was essential, as models without it were rejected, while models
 without the regional environment - plot-level richness link were still
 valid but had a worse goodness-of-fit value. Plot-level richness showed a
 hump-shaped relationship with regional richness. Main Conclusions Both
 regional environment and regional fern and lycophyte species richness each
 are important determinants of plot-level richness, and the inclusion of
 one does not substitute the inclusion of the other. Plot-level richness
 increases with regional richness until a saturation point is reached,
 after which plot-level richness decreases despite increasing regional
 richness, possibly reflecting species interactions.