cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.ng0kn
title: Data from: Subordinate plants mitigate drought effects on soil ecosystem processes by stimulating fungi

description: The subordinate insurance hypothesis suggests that highly diverse
 communities contain greater numbers of subordinate species than less
 diverse communities. It has previously been reported that subordinate
 species can improve grassland productivity during drought, but the
 underlying mechanisms remain undetermined. Using a combination of
 subordinate species removal and summer drought, we show that soil
 processes play a critical role in community resistance to drought.
 Interestingly, subordinate species drive soil microbial community
 structure and largely mitigate the effect of drought on grassland soil
 functioning. Our results highlight subordinate species in shifting the
 balance within the phospholipid fatty acid (PLFA) microbial community
 towards more fungal dominance. Fungal communities promoted by subordinate
 species were more resistant to drought and maintained higher rates of
 litter decomposition and soil respiration. These results emphasize the
 important role of subordinate species in mitigating drought effects on
 soil ecosystem functions. Reciprocal effects between fungi and subordinate
 species explain also how subordinate species better resisted to drought
 conditions. Our results point to a delayed plant–soil feedback following
 environmental perturbation. Additionally, they extend the diversity
 insurance hypothesis by showing that more diverse communities not only
 contain species well adapted to perturbations, but also species with
 higher impacts on soil microbial communities and related ecosystem
 functions.
description: Results Mariotte et al.
 2015 Func EcolData contains soil
 PLFA's, soil respiration, litter decomposition, 15N isotopes measures
 in control plots without removal and plot with removal of subordinate
 species in combination with a drought treatment (watered/drought) in
 grasslandsResults_Mariotte_Func_Ecol_2015.xlsx
DOI: 10.5061/dryad.9t0r6
title: Data from: Fine-scale belowground species associations in temperate grassland

description: Evaluating how belowground processes contribute to plant community
 dynamics is hampered by limited information on the spatial structure of
 root communities at the scale that plants interact belowground. In this
 study, roots were mapped to the nearest one mm and molecularly identified
 by species on vertical (0–15 cm deep) surfaces of soil blocks excavated
 from dry and mesic grasslands in Yellowstone National Park (YNP) to
 examine the spatial relationships among species at the scale that roots
 interact. Our results indicated that average interspecific root – root
 distances for the majority of species were within a distance (3 mm) that
 roots have been shown to compete for resources. Most species placed their
 roots at random, although low root numbers for many species probably led
 to overestimating the occurrence of random patterns. According to theory,
 we expected that most of the remaining species would segregate their root
 systems to avoid competition. Instead we found that more species
 aggregated than segregated from others. Based on previous investigations,
 we hypothesize that species aggregate to increase uptake of water,
 nitrogen and/or phosphorus made available by neighbouring roots, or as a
 consequence of a reduction in the pathogenicity of soil biota growing in
 multispecies mixtures. Our results indicate that YNP grassland root
 communities are organized as closely interdigitating networks of species
 that potentially can support strong interactions among many species
 combinations. Future root research should address the prevalence and
 functional consequences of species aggregation across plant communities.
description: Root
 coordinatesProvides coordinates and
 species ids of roots sampled from soil blocks. Variable descriptions are
 provided in the file.Dryad data file
 submitted.csv
DOI: 10.5061/dryad.c857r
title: Data from: Strong selection barriers explain microgeographic adaptation in wild salamander populations

description: Microgeographic adaptation occurs when populations evolve divergent
 fitness advantages across the spatial scales at which focal organisms
 regularly disperse. Although an increasing number of studies find evidence
 for microgeographic adaptation, the underlying causes often remain
 unknown. Adaptive divergence requires some combination of limited gene
 flow and strong divergent natural selection among populations. In this
 study, we estimated the relative influence of selection, gene flow and the
 spatial arrangement of populations in shaping patterns of adaptive
 divergence in natural populations of the spotted salamander (Ambystoma
 maculatum). Within the study region, A. maculatum co-occur with the
 predatory marbled salamander (A. opacum) in some ponds, and past studies
 have established a link between predation risk and adaptive trait
 variation in A. maculatum. Using 14 microsatellite loci, we found a
 significant pattern of genetic divergence among A. maculatum populations
 corresponding to levels of A. opacum predation risk. Additionally, A.
 maculatum foraging rate was strongly associated with predation risk,
 genetic divergence and the spatial relationship of ponds on the landscape.
 Our results indicate the sorting of adaptive genotypes by selection regime
 and strongly suggest that substantial selective barriers operate against
 gene flow. This outcome suggests that microgeographic adaptation in A.
 maculatum is possible because strong antagonistic selection quickly
 eliminates maladapted phenotypes despite ongoing and substantial
 immigration. Increasing evidence for microgeographic adaptation suggests a
 strong role for selective barriers in counteracting the homogenizing
 influence of gene flow.
description: Richardson and Urban
 2013_Evol_AMMA 13 pop genotypes_2Genepop formated
 genotype file for all 13 populations in the analyses, including the two
 outlying populations (Saltonstall and Trimountain).Richardson and Urban
 2013_Evol_AMMA genotypes_3 risk classesGenepop formated
 genotype file for the 11 Northford Ridge populations in the analyses. This
 dataset divides populations and individuals based on the three A. opacum
 predation risk categories described in the text.Richardson and Urban
 2013_Evol_AMMA pond trait dataTable with the mean pond
 and population trait data used in analyses.
DOI: 10.5061/dryad.fs798
title: Data from: Divergent trophic responses to biogeographic and environmental gradients

description: Following environmental changes, communities disassemble and reassemble in
 seemingly unpredictable ways. Whether species respond to such changes
 individualistically or collectively (e.g. as functional groups) is still
 unclear. To address this question, we used an extensive new dataset for
 the lake communities in the Azores' archipelago to test whether: 1)
 individual species respond concordantly within trophic groups; 2) trophic
 groups respond concordantly to biogeographic and environmental gradients.
 Spatial concordance in individual species distributions within trophic
 groups was always greater than expected by chance. In contrast, trophic
 groups varied non-concordantly along biogeographic and environmental
 gradients revealing idiosyncratic responses to them. Whether communities
 respond individualistically to environmental gradients thus depends on the
 functional resolution of the data. Our study challenges the view that
 modelling environmental change effects on biodiversity always requires an
 individualist approach. Instead, it finds support for the longstanding
 idea that communities might be modelled as a cohort if the functional
 resolution is appropriate.
description: Distribution of aquatic
 organisms across freshwater along the Azores ArchipelagoData consists of
 presence/absences of aquatic organisms in freshwater lakes. The dataset
 consists of a single table that was generated by combining survey data
 from the Springs of 2011 and 2012.matiasetal_divergent_trophic_responses.xlsx
DOI: 10.5061/dryad.j59jf
title: Data from: Lack of genetic isolation by distance, similar genetic structuring but different demographic histories in a fig-pollinating wasp mutualism

description: Historical abiotic factors such as climatic oscillations and extreme
 climatic events as well as biotic factors have shaped the structuring of
 species’ genetic diversity. In obligate species-specific mutualisms, the
 biogeographic histories of the interacting species are tightly linked.
 This could be particularly true for nuclear genes in the Ficus-pollinating
 wasp mutualistic association as the insects disperse pollen from their
 natal tree. In this study we compare spatial genetic structure of plant
 and pollinator for the Ficus hirta-Valisia javana association throughout
 South-East China including Hainan Island, for both nuclear and cytoplasmic
 markers. We show that dispersal of the insect leads to plant and insect
 presenting similar signatures of lack of genetic isolation by distance for
 nuclear genes on the continent over a distance of 1000 km. But we also
 show that the demographic histories of plant and insect are strikingly
 different. This is in agreement with extreme climatic events leading to
 transient regional extinctions of the insects, associated with local
 survival of the plants. We also evidence genetic differentiation for both
 wasps and fig-tree between the continent and Hainan Island, although the
 Qiongzhou Strait is only on average 30 km wide suggesting that geographic
 isolation by itself has not been sufficient to generate this
 differentiation. Hence, our results suggest that in highly dispersive
 mutualistic systems, isolation by dispersal limitation across a geographic
 barrier could be supplemented by isolation by adaptation, and maybe by
 coevolution, allowing further genetic divergence. In such systems, species
 may frequently be composed of a single population.
description: Data accessibility-for
 SSR and mtDNA dataMicrosatellite genotype
 data and mtDNA sequences for all individuals of V.
 javana.
DOI: 10.5061/dryad.hk0rt
title: Data from: Novel concordance between geographic, environmental and genetic structure in the ecological generalist prickly sculpin (Cottus asper) in California

description: Ecological generalists may contain a wealth of information concerning
 diversity, ecology, and geographic connectivity throughout their range. We
 explored these ideas in prickly sculpin (Cottus asper), a small generalist
 freshwater fish species where coastal forms have potentially undergone
 radiations into inland lacustrine and riverine environments. Using a 962bp
 cytochrome b mtDNA marker and 11 microsatellites, we estimated diversity,
 divergence times, gene flow, and structure among populations at 43
 locations throughout California. We then incorporated genetic and GIS data
 into ecological niche models to assess ecological conditions within
 identified groups. Though not reciprocally monophyletic, unique mtDNA
 haplotypes, microsatellite clustering, and measures of isolation by
 distance (Coastal: r = 0.960, P &lt; 0.001; Inland: r = 0.277, P =
 0.148) suggest 2 novel taxonomic groups, Coastal and Inland (constrained
 to Great Central Valley). Divergence estimates of 41–191 kya combined with
 the regional biogeographic history suggest geographic barriers are absent
 between groups since divergence, but ecological niche modeling revealed
 significant environmental differences (t = 10.84, P &lt; 0.001).
 Introgressed individuals were also discovered between groups in an
 ecologically and geographically intermediate region. Population structure
 was limited, predominately found in tributaries of the San Joaquin basin
 in the Inland group. Overall, C. asper exhibited substantial genetic
 diversity, despite its ecological generality, reflecting California’s
 historically unique and complex hydrology. More broadly, this study
 illustrates variable environments within the range of a generalist species
 may mask genetic divergences and should not be overlooked in biodiversity
 assessments.
description: Comprehensive
 microsatellite allele table for 11 lociMicrosatellite alleles
 used in study for each sampled site. Some individuals were less successful
 and may have been removed before final analysis. Location information can
 be found in the main paper (GPS, etc.).Final_Genotypes_Prickly.csv
DOI: 10.5061/dryad.2dv31
title: Data from: Experimental evolution with a multicellular host causes diversification within and between microbial parasite populations – differences in emerging phenotypes of two different parasite strains

description: Host-parasite coevolution is predicted to have complex evolutionary
 consequences, potentially leading to the emergence of genetic and
 phenotypic diversity for both antagonists. However, little is known about
 variation in phenotypic responses to coevolution between different
 parasite strains exposed to the same experimental conditions. We infected
 Caenorhabditis elegans with one of two strains of Bacillus thuringiensis
 and either allowed the host and the parasite to experimentally coevolve
 (coevolution treatment) or allowed only the parasite to adapt to the host
 (one-sided parasite adaptation). By isolating single parasite clones from
 evolved populations, we found phenotypic diversification of the ancestral
 strain into distinct clones, which varied in virulence towards ancestral
 hosts and competitive ability against other parasite genotypes. Parasite
 phenotypes differed remarkably not only between the two strains, but also
 between and within different replicate populations, indicating
 diversification of the clonal population caused by selection. This study
 highlights that the evolutionary selection pressure mediated by a
 multicellular host causes phenotypic diversification, but not necessarily
 with the same phenotypic outcome for different parasite strains.
description: Rawdata and z-scores for
 evolved B. thuringiensis clones and populationsFirst spreadsheet shows
 the original data for killing rate, inhibition of MYBT18247 (247) and
 MYBT18679 (679) of the evolved Bacillus thuringiensis clones. Data are
 collected for ancestral, coevolved and adapted clones in technical
 replicates / experimental runs for the B. thuringiensis strains. For 5
 evolved populations per strain and treatment, 5 clones were analyzed.
 Furthermore, z-scores of evolved clones relative to the data of the
 ancestral clones are shown. The second spreadsheet shows the raw-data and
 z-scores of killing rate for the evolved populations (before clone
 isolation).Rawdata Dryad
 clones.xlsx
DOI: 10.5061/dryad.307g0
title: Data from: The challenge of species delimitation at the extremes: diversification without morphological change in Philippine sun skinks

description: Species represent one of the fundamental units of the evolutionary
 process, and an accurate understanding of species diversity is essential
 to studies across a wide range of biological subdisciplines. However,
 delimiting species remains challenging in evolutionary radiations where
 morphological diversification is rapid and accompanied by little genetic
 differentiation or when genetic lineage divergence is not accompanied by
 morphological change. We investigate the utility of a variety of recently
 developed approaches to examine genetic and morphological diversity, and
 delimit species in a morphologically conserved group of Southeast Asian
 lizards. We find that species diversity is vastly underestimated in this
 unique evolutionary radiation, and find an extreme case where extensive
 genetic divergence among lineages has been accompanied by little to no
 differentiation in external morphology. Although we note that different
 conclusions can be drawn when species are delimited using molecular
 phylogenetics, coalescent-based methods, or morphological data, it is
 clear that the use of a pluralistic approach leads to a more comprehensive
 appraisal of biodiversity, and greater appreciation for processes of
 diversification in this biologically important geographic region.
 Similarly, our approach demonstrates how recently developed methodologies
 can be utilized to obtain robust estimates of species limits in
 “non-adaptive” or “cryptic” evolutionary radiations.
description: Species Morphological
 DataMorphological data for
 individuals utilized in study (145). All measurements were taken by hand
 using digital calipers and are given in millimeters. SVL=snout-vent
 length, Arm-Elb=distance from armpit to elbow, Elb-Hnd=distance from elbow
 to hand, Arm-knee=distance from groin to knee, knee-ft=distance from knee
 to foot, Lamellae=lamellae under toe I,II,III,IV,V
 respectively.DryadMorphData.xlsx
DOI: 10.15468/dl.rpc3vn
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Reyesia chilensis",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 5 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000985-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.3600k
title: Data from: Chronic exposure to a neonicotinoid increases expression of antimicrobial peptide genes in the bumblebee Bombus impatiens

description: Bumblebees are important pollinators in wild and agricultural settings. In
 recent decades pollinator declines have been linked to the effects of
 increased pesticide use and the spread of disease. Synergy between these
 factors has been suggested, but no physiological mechanism has been
 identified. This study examines the connection between neonicotinoid
 exposure and innate immune function in the bumblebee Bombus impatiens,
 which is an important wild and commercial pollinator in eastern North
 America. Experimental colonies in the field were enclosed and provided
 pollen and sugar syrup containing an agriculturally relevant range of
 imidacloprid concentrations. Bumblebees were collected from colonies over
 four weeks, and the expression of antimicrobial peptides was measured
 using multiplex quantitative real time PCR. Significant increases in the
 expression of abaecin, apidaecin and hymenoptaecin were found over time in
 treatments receiving moderate to high concentrations of the pesticide.
 Responses were dependent on time of exposure and dose. These results
 indicate that immune function in bumblebees is affected by neonicotinoid
 exposure and suggest a physiological mechanism by which neonicotinoids may
 impact the innate immune function of bumblebee pollinators in wild and
 agricultural habitats.
description: Supplemental Data and
 Analysis ScriptA zip files containing
 csv, xls and Rmd formats.SI.files.zip
DOI: 10.5061/dryad.t49d5
title: Data from: Mechanisms of global diversification in the brown booby (Sula leucogaster) revealed by uniting statistical phylogeographic and multilocus phylogenetic methods

description: Recent theoretical and empirical research suggests that statistical models
 based on coalescent theory can improve both phylogeographic and
 phylogenetic inference. An approach that involves elements of both
 statistical phylogeography (e.g., Isolation with Migration analyses) and
 multilocus phylogenetic inference (e.g., *BEAST) may be particularly
 useful when applied to populations with relatively old divergence times.
 Here we use such an approach in the globally distributed brown booby (Sula
 leucogaster). We sampled 215 individuals from all major breeding areas and
 genotyped them at eight microsatellite and three nuclear intron loci. We
 found that brown booby populations were highly differentiated and that
 colonies can be grouped into four major genetic populations (Caribbean
 Sea, Central Atlantic Ocean, Indo-Central Pacific, and Eastern Pacific).
 These populations apparently diverged in the absence of gene flow and,
 with one exception, currently exchange few to no migrants. The Eastern
 Pacific population diverged from all other populations approximately one
 million years ago [90% highest posterior density: 330 000 – 2 000 000
 years ago] and exhibits a distinct male plumage, relative to other
 populations. However, recent gene flow from the Indo-Central Pacific into
 the Eastern Pacific appears to have occurred, suggesting that
 approximately one million years of genetic isolation and divergence in
 male plumage colour are not sufficient to prevent interbreeding. Gene flow
 following secondary contact of the Indo-Central Pacific and Eastern
 Pacific populations was not detected in previous mitochondrial DNA (mtDNA)
 studies, and the contrast between the mtDNA results and our current
 results highlights the advantage of a multilocus phylogeographic approach.
description: S_leucogaster_sampleNames_locations_genotypes
DOI: 10.5061/dryad.43d3g
title: Data from: White-tailed deer as the last megafauna dispersing seeds in Neotropical dry forests: the role of fruit and seed traits

description: Endozoochory is a prominent form of seed dispersal in tropical dry
 forests. Most extant megafauna that perform such seed dispersal are
 ungulates, which can also be seed predators. White-tailed deer (Odocoileus
 virginianus) is one of the last extant megafauna of Neotropical dry
 forests, but whether it serves as a legitimate seed disperser is poorly
 understood. We studied seed dispersal patterns and germination after
 white-tailed deer gut passage in a tropical dry forest in southwest
 Ecuador. Over 23 mo, we recorded ca 2000 seeds of 11 species in 385 fecal
 samples. Most seeds belonged to four species of Fabaceae: Chloroleucon
 mangense, Senna mollissima, Piptadenia flava, and Caesalpinia glabrata.
 Seeds from eight of the 11 species dispersed by white-tailed deer
 germinated under controlled conditions. Ingestion did not affect
 germination of C. mangense and S. mollissima, whereas C. glabrata showed
 reduced germination. Nevertheless, the removal of fruit pulp resulting
 from ingestion by white-tailed deer could have a deinhibition effect on
 germination due to seed release. Thus, white-tailed deer play an important
 role as legitimate seed dispersers of woody species formerly considered
 autochorous. Our results suggest that more research is needed to fully
 understand the ecological and evolutionary effects of the remaining extant
 megafauna on plant regeneration dynamics in the dry Neotropics.
description: seed dispersal by deer -
 REASeeds of woody species
 dispersed by withe-tailed deer in the Arenillas Ecological Reserve,
 Southwestern Ecuador. Collection date, species and number of seeds present
 and germinated are defined for each fecal sample.data.deer.REA.xlsx