cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.t0553
title: Data from: Trait-specific processes of convergence and conservatism shape ecomorphological evolution in ground-dwelling squirrels

description: Our understanding of mechanisms operating over deep timescales to shape
 phenotypic diversity often hinges on linking variation in one or few
 trait(s) to specific evolutionary processes. When distinct processes are
 capable of similar phenotypic signatures, however, identifying these
 drivers is difficult. We explored ecomorphological evolution across a
 radiation of ground-dwelling squirrels whose history includes convergence
 and constraint, two processes that can yield similar signatures of
 standing phenotypic diversity. Using 4 ecologically-relevant trait
 datasets (body size, cranial, mandibular, and molariform tooth shape), we
 compared and contrasted variation, covariation, and disparity patterns in
 a new phylogenetic framework. Strong correlations existed between body
 size and 2 skull traits (allometry) and among skull traits themselves
 (integration). Inferred evolutionary modes were also concordant across
 traits (Ornstein-Uhlenbeck with 2 adaptive regimes). However, despite
 these broad similarities, we found divergent dynamics on the
 macroevolutionary landscape, with phenotypic disparity being
 differentially shaped by convergence and conservatism. Such among-trait
 heterogeneity in process (but not always pattern) reiterates the mosaic
 nature of morphological evolution, and suggests ground squirrel evolution
 is poorly captured by single process descriptors. Our results also
 highlight how use of single traits can bias macroevolutionary inference,
 affirming the importance of broader trait-bases in understanding
 phenotypic evolutionary dynamics.
description: Supp_Data_1_mtDNASpreadsheet list of mitochondrial DNA sequences used in phylogenetic inference, with publication names and web location accessed.Supp_Data_2_UCE_backbonesList of UCE-derived backbone topologies used in this study, in Newick format.Supp_Data_3_bootstrapped_treesList of species-level phylogenetic hypotheses used in this study, in Newick format, with branch lengths.Supp_Data_4_cranial_shapeSpreadsheet containing new cranial morphometric data published in this study. Tabs contain 1) list of museum specimens used along with housing institutions and provenance; 2) list of codes describing those housing institutions, and; 3) centroid sizes and Procrustes-aligned landmark data for all specimens.Supp_Data_5_evol_model_parametersList of macroevolutionary process model parameters inferred in this study for all morphological structures. These parameters were also used as the input for trait simulation.
DOI: 10.7910/dvn/hm0xpf
title: Replication Data for: Mixing with viscoelastic waves at low Reynolds numbers

description: This dataset contains the data for the scientific article titled "Mixing with viscoelastic waves at low Reynolds numbers". Authors are Enrico Turato, Christelle N. Prinz, Jason P. Beech and Jonas O. Tegenfeldt.

ABSTRACT

Mixing at microfluidic scale is challenging due to the low Reynolds numbers.
Without turbulence, mixing replies solely on diffusion, resulting in slow and inefficient mixing. We demonstrate enhanced mixing in a simple Y-shaped microfluidic
channel using viscoelastic turbulence in fluids containing macromolecules, such
as DNA and polyethylene oxide. We investigated mixing at two distinct scales: the
mixing of small molecules and the mixing of polymers. We show how the viscoelastic fluctuations fold the solvent, resulting in enhanced reaction rate between
two reagents. We also show how the viscoelastic turbulence enhances the mixing
of the macromolecules. We discuss optimization strategies taking into account
mixing efficiency, mixing time, mixing length and energy efficiency. Viscoelastic
turbulence unlocks rapid mixing in microfluidic channels where conventional
turbulence cannot operate, offering a versatile platform for applications ranging
from chemical synthesis to biomedical assays.
DOI: 10.5061/dryad.tn390
title: Data from: Molecular phylogeny of the horse flies: a framework for renewing tabanid taxonomy

description: Horse flies, family Tabanidae, are the most diverse family-level clade of
 bloodsucking insects, but their phylogeny has never been thoroughly
 explored using molecular data. Most adult female Tabanidae feed on nectar
 and on the blood of various mammals. Traditional horse fly classification
 tends towards large heterogeneous taxa, which impede much-needed taxonomic
 work. To guide renewed efforts in the systematics of horse flies and their
 relatives, we assembled a dataset of 110 exemplar species using nucleotide
 data from four genes—mitochondrial CO1, and nuclear 28S, CAD and AATS. All
 commonly recognized tribes in Tabanidae are represented, along with
 outgroups in Tabanomorpha. The phylogeny is reconstructed using Bayesian
 inference, and divergence times are estimated using Bayesian relaxed clock
 methods with time constraints from tabanid fossils. Our results show
 Athericidae strongly supported as the lineage most closely related to
 Tabanidae, and Pangoniinae and Tabaninae as monophyletic lineages.
 However, Chrysopsinae is nonmonophyletic, with strong support for both a
 nonmonophyletic Bouvieromyiini and for Rhinomyzini as sister to Tabaninae.
 Only the tribes Philolichini, Chrysopsini, Rhinomyzini and Haematopotini
 are recovered as monophyletic, although Scionini is monophyletic with
 exclusion of the peculiar genus Goniops Aldrich. Mycteromyia Philippi and
 Adersia Austen, two enigmatic genera sometimes placed in separate
 family-level groups, are recovered inside Pangoniini and Chrysopsini,
 respectively. Several species-rich genera are not recovered as
 monophyletic, including Esenbeckia Rondani, Silvius Meigen, Dasybasis
 Macquart and Tabanus L. Tabanidae likely originated in the Cretaceous, and
 all major extant groups were present by the early Palaeogene. This newly
 revised phylogenetic framework for Tabanidae forms the basis for a new
 assessment of tabanid diversification and provides context for
 understanding the evolution of trophic specialization in horse flies.
description: Morita et al. full
 concatenated data setNexus formatted,
 phylogenetic data set for Tabanidae of Morita et al. 2015. Alignment of
 five gene fragments, two from CPSase (=CAD1 and CAD5), 28S rDNA, AATS1,
 and mtCOI, concatenated into single data block. Gene boundaries are
 indicated in a character sets block. For phylogenetic analysis some
 alignment-ambiguous regions were excluded--these are denoted in the set
 block with by 'genename' +'trim'.tab2015.03.14.alignment.nexMorita_etal_TaxonCodesSpecies and taxon names corresponding to labcodes used in the phylogenenetic data set and trees.tab_2_1500_bootCONSML tree topology from 1500 bootstrap replicates perfomed in RaXML_v8 (figure 4).
DOI: 10.5061/dryad.p1g31
title: Data from: Molecular and quantitative signatures of biparental inbreeding depression in the self-incompatible tree species Prunus avium

description: Genetic diversity strongly influences populations’ adaptability to
 changing environments and therefore survival. Sustainable forest
 management practices have multiple roles including conservation of genetic
 resources and timber production. In this study, we aimed at better
 understanding the variation in genetic diversity among adult and offspring
 individuals, and the effects of mating system on offspring survival and
 growth in wild cherry, Prunus avium. We analysed adult trees and open
 pollinated seed-families from three stands in Germany at eight
 microsatellite loci and one incompatibility system locus and conducted
 paternity analyses. Seed viability testing and seed sowing in a nursery
 allowed further testing for the effects of pollen donor diversity and
 genetic similarity between mates on the offspring performance at the seed
 and seedling stages. Our results were contrasting across stands. Loss of
 genetic diversity from adult to seedling stages and positive effect of
 mate diversity on offspring performance occurred in one stand only,
 whereas biparental inbreeding depression and significant decrease in
 fixation index from adults to seedlings was detected in two stands. We
 discussed the effects of stand genetic diversity on the magnitude of
 biparental inbreeding depression at several life-stages and its
 consequences on the management of genetic resources in P. avium.
description: Bayern_CorrdBayern_FamiliesBayern_GenBrandenburg_CoordBrandenburg_FamiliesBrandenburg_GenNRW_CoordNRW_FamiliesNRW_GenInbreeding_Prunusavium_ReadMe
DOI: 10.5061/dryad.7g6v3
title: Data from: Multi-scale heterogeneity in vegetation and soil carbon in exurban residential land of southeastern Michigan, USA

description: Exurban residential land (one housing unit per 0.2–16.2 ha) is growing in
 importance as a human-dominated land use. Carbon storage in the soils and
 vegetation of exurban land is poorly known, as are the effects on C
 storage of choices made by developers and residents. We studied C storage
 in exurban yards in southeastern Michigan, USA, across a range of parcel
 sizes and different types of neighborhoods. We divided each residential
 parcel into ecological zones (EZ) characterized by vegetation, soil, and
 human behavior such as mowing, irrigation, and raking. We found a
 heterogeneous mixture of trees and shrubs, turfgrasses, mulched gardens,
 old-field vegetation, and impervious surfaces. The most extensive zone
 type was turfgrass with sparse woody vegetation (mean 26% of parcel area),
 followed by dense woody vegetation (mean 21% of parcel area). Areas of
 turfgrass with sparse woody vegetation had trees in larger size classes
 (&gt; 50 cm dbh) than did areas of dense woody vegetation. Using
 aerial photointerpretation, we scaled up C storage to neighborhoods.
 Varying C storage by neighborhood type resulted from differences in
 impervious area (8–26% of parcel area) and area of dense woody vegetation
 (11–28%). Averaged and multiplied across areas in differing neighborhood
 types, exurban residential land contained 5240 ± 865 g C/m2 in vegetation,
 highly sensitive to large trees, and 13 800 ± 1290 g C/m2 in soils (based
 on a combined sampling and modeling approach). These contents are greater
 than for agricultural land in the region, but lower than for mature forest
 stands. Compared with mature forests, exurban land contained more shrubs
 and less downed woody debris and it had similar tree size-class
 distributions up to 40 cm dbh but far fewer trees in larger size classes.
 If the trees continue to grow, exurban residential land could sequester
 additional C for decades. Patterns and processes of C storage in exurban
 residential land were driven by land management practices that affect soil
 and vegetation, reflecting the choices of designers, developers, and
 residents. This study provides an example of human-mediated C storage in a
 coupled human–natural system.
description: Carbon storage in
 exurban residential land in SE MichiganIncluded are field and
 GIS-derived data related to C storage in exurban yards in Southeastern MI,
 USA. Thorough descriptions of tabs, columns, units and variable codes are
 included in the excel spreadsheet.Currie-RLSS-2009-DryadArchived-sitestransects-022516.xlsx
DOI: 10.5061/dryad.d08h6
title: Data from: In vivo tracking of dendritic cell using MRI reporter gene, ferritin

description: The noninvasive imaging of dendritic cells (DCs) migrated into lymph nodes
 (LNs) can provide helpful information on designing DCs-based
 immunotherapeutic strategies. This study is to investigate the influence
 of transduction of human ferritin heavy chain (FTH) and green fluorescence
 protein (GFP) genes on inherent properties of DCs, and the feasibility of
 FTH as a magnetic resonance imaging (MRI) reporter gene to track DCs
 migration into LNs. FTH-DCs were established by the introduction of FTH
 and GFP genes into the DC cell line (DC2.4) using lentivirus. The changes
 in the rate of MRI signal decay (R2*) resulting from FTH transduction were
 analyzed in cell phantoms as well as popliteal LN of mice after
 subcutaneous injection of those cells into hind limb foot pad by using a
 multiple gradient echo sequence on a 9.4 T MR scanner. The transduction of
 FTH and GFP did not influence the proliferation and migration abilities of
 DCs. The expression of co-stimulatory molecules (CD40, CD80 and CD86) in
 FTH-DCs was similar to that of DCs. FTH-DCs exhibited increased iron
 storage capacity, and displayed a significantly higher transverse
 relaxation rate (R2*) as compared to DCs in phantom. LNs with FTH-DCs
 exhibited negative contrast, leading to a high R2* in both in vivo and ex
 vivo T2*-weighted images compared to DCs. On histological analysis FTH-DCs
 migrated to the subcapsular sinus and the T cell zone of LN, where they
 highly expressed CD25 to bind and stimulate T cells. Our study addresses
 the feasibility of FTH as an MRI reporter gene to track DCs migration into
 LNs without alteration of their inherent properties. This study suggests
 that FTH-based MRI could be a useful technique to longitudinally monitor
 DCs and evaluate the therapeutic efficacy of DC-based vaccines.
description: Ferritin-based MRI of
 dendritic cellFigure 1. Analysis of
 dendritic cell (DC) transduced with myc-tagged human ferritin heavy chain
 (FTH) and green fluorescence prtein (GFP) using lentivirus. Figure 2.
 Analyses of proliferation and migration activities and co-stimulatory
 molecules expressions in dendritic cell (DC) and human ferritin heavy
 chain-transduced DC (FTH-DC). Figure. 3. Cellular iron staining, iron
 amount measurement and in vitro MRI analysis of dendritic cell (DC) and
 human ferritin heavy chain-transduced DC (FTH-DC). Figure 4. in vivo and
 ex vivo MRI of popliteal lymph nodes (LNs) of mouse injected with
 dendritic cell (DC) and ferritin heavy chain-transduced DC (FTH-DC).
 Figure 5. Histological analysis of cryosectioned popliteal lymph nodes
 (LNs) with dendritic cell (DC) and ferritin heavy chain-transduced DC
 (FTH-DC).Datadryad-FTH-DC_PLOS
 ONE.pdf
DOI: 10.5061/dryad.dp7b8
title: Data from: Partner associations across sympatric broad-headed bug species and their environmentally acquired bacterial symbionts

description: Many organisms have intimate associations with beneficial microbes
 acquired from the environment. These host–symbiont associations can be
 specific and stable, but they are prone to lower partner specificity and
 more partner-switching than vertically transmitted mutualisms. To
 investigate partner specificity in an environmentally acquired insect
 symbiosis, we used 16S rRNA gene and multilocus sequencing to survey the
 bacterial population in the bacteria-harbouring organ (crypts) of 49
 individuals across four sympatric broad-headed bug species (Alydus
 calcaratus, A. conspersus, A. tomentosus and Megalotomus quinquespinosus).
 Similar to other insect–bacteria associations, Burkholderia spp. were the
 most common residents of the crypts in all four insect species (77.2% of
 recovered sequences). Burkholderia presence was associated with prolonged
 survival to adulthood in A. tomentosus, suggesting a beneficial role of
 these specialized associations. Burkholderia were also found in
 environmental reservoirs in the insects’ habitat, which may facilitate
 acquisition by insects by increasing Burkholderia–insect encounters.
 Symbiont establishment could also be facilitated by resistance to insect
 defences; zone of inhibition assays demonstrated that Burkholderia and
 other bacteria isolated from crypts are resistant to insect defences that
 limit growth of Escherichia coli. Alternatively, the insects’ defences may
 not efficiently kill a broad range of bacteria. Although the symbiosis is
 targeted to Burkholderia, the insects’ crypts housed other bacteria,
 including non-Burkholderiaceae species. There is no significant effect of
 host insect species on Burkholderia distribution, suggesting a lack of
 strong partner specificity at finer scales. The presence of frequent
 partner-switching between sympatric insects and their symbionts likely
 prevents tight co-evolutionary dynamics.
description: readmeDescription of each data
 file.survival.developmentSurvival and development in Burkholderia-positive and -negative Alydus tomentosus. Includes separate .csv files with survival and time to development data and the R script used to analyze these data.16SphylogenyNexus file with Greengenes-aligned sequences presented inthe 16S phylogeny.mlstSeparate .fasta files for each mlst gene and nexus file used to make mlst phylogeny.PERMANOVASample x OTU matrix and R script used to perform PERMANOVA analysis.AMOVASequences and corresponding variables for amova in mothur.heatmapAligned sequence file and sequence identifiers for the heatmap command in mothur.ZOIassaysClearance zone data for zone of inhibition experiments.
DOI: 10.5061/dryad.6d250
title: Data from: Long-term culture at elevated atmospheric CO2 fails to evoke specific adaptation in seven freshwater phytoplankton species

description: The concentration of CO2 in the atmosphere is expected to double by the
 end of the century. Experiments have shown that this will have important
 effects on the physiology and ecology of photosynthetic organisms, but it
 is still unclear if elevated CO2 will elicit an evolutionary response in
 primary producers that causes changes in physiological and ecological
 attributes. In this study, we cultured lines of seven species of
 freshwater phytoplankton from three major groups at current (approx. 380
 ppm CO2) and predicted future conditions (1000 ppm CO2) for over 750
 generations. We grew the phytoplankton under three culture regimes:
 nutrient-replete liquid medium, nutrient-poor liquid medium and solid agar
 medium. We then performed reciprocal transplant assays to test for
 specific adaptation to elevated CO2 in these lines. We found no evidence
 for evolutionary change. We conclude that the physiology of carbon
 utilization may be conserved in natural freshwater phytoplankton
 communities experiencing rising atmospheric CO2 levels, without
 substantial evolutionary change.
description: data and
 scriptsComplete data and R
 script.
DOI: 10.5061/dryad.35fh0
title: Data from: Protected areas buffer the Brazilian semi-arid biome from climate change

description: The Caatinga is a botanically unique semi-arid ecosystem in northeast
 Brazil whose vegetation is adapted to the periodic droughts that
 characterize this region. However, recent extreme droughts events caused
 by anthropogenic climate change have challenged its ecological resilience.
 Here, we evaluate how deforestation and protection status affect the
 response of the Caatinga vegetation to drought. Specifically, we compared
 vegetation responses to drought in natural and deforested areas as well as
 inside and outside protected areas, using a time-series of
 satellite-derived Normalized Difference Vegetation Index (NDVI) and
 climatic data for 2008–2013. We observed a strong effect of deforestation
 and land protection on overall vegetation productivity and in productivity
 dynamics in response to precipitation. Overall, deforested areas had
 significantly lower NDVI and delayed greening in response to
 precipitation. By contrast, strictly protected areas had higher
 productivity and considerable resilience to low levels of precipitation,
 when compared to sustainable use or unprotected areas. These results
 highlight the importance of protected areas in protecting ecosystem
 processes and native vegetation in the Caatinga against the negative
 effects of climate change and deforestation. Given the extremely small
 area of the Caatinga currently under strict protection, the creation of
 new conservation areas must be a priority to ensure the sustainability of
 ecological processes and to avoid further desertification.
description: Deforestation model
 datasetData used to model
 satellite-derived Normalized Difference Vegetation Index (NDVI) in
 response to precipitation in deforested and non-deforested areas of the
 Brazilian semi-arid Caatinga biome. Variables: cell_id - Numeric ID of the
 pixel included in the analysis ndvi - Montlhy Normalized Difference
 Vegetation Index (NDVI) score of the pixel prec - Monhtly precipitation
 value of the pixel long - Longitude of the pixel centroid lat - Latitude
 of the pixel centroid deforestation - Catogrical variable indicating
 existance (YES or NO) of deforestation in the pixeldefor_model.csvLand protection model datasetData used to model satellite-derived Normalized Difference Vegetation Index (NDVI) in response to precipitation on areas of the Brazilian semi-arid Caatinga biome under different protection levels. Variables: cell_id - Numeric ID of the pixel included in the analysis ndvi - Montlhy Normalized Difference Vegetation Index (NDVI) score of the pixel prec - Monhtly precipitation value of the pixel long - Longitude of the pixel centroid lat - Latitude of the pixel centroid protection_type - Catogrical variable indicating the level of land protection in the pixel, including no protection, sustainable use or full protection status.prot_model.csv
DOI: 10.5061/dryad.bv689
title: Data from: Specialization and generalization in the diversification of phytophagous insects: tests of the musical chairs and oscillation hypotheses

description: Evolutionary biologists have often assumed that ecological generalism
 comes at the expense of less intense exploitation of specific resources
 and that this trade-off will promote the evolution of ecologically
 specialized daughter species. Using a phylogenetic comparative approach
 with butterflies as a model system, we test hypotheses that incorporate
 changes in niche breadth and location into explanations of the taxonomic
 diversification of insect herbivores. Specifically, we compare the
 oscillation hypothesis, where speciation is driven by host-plant
 generalists giving rise to specialist daughter species, to the musical
 chairs hypothesis, where speciation is driven by host-plant switching,
 without changes in niche breadth. Contrary to the predictions of the
 oscillation hypothesis, we recover a negative relationship between
 host-plant breadth and diversification rate and find that changes in host
 breadth are seldom coupled to speciation events. By contrast, we present
 evidence for a positive relationship between rates of host switching and
 butterfly diversification, consonant with the musical chairs hypothesis.
 These results suggest that the costs of trophic generalism in
 plant-feeding insects may have been overvalued and that transitions from
 generalists to ecological specialists may not be an important driver of
 speciation in general.
description: Hardy-Otto-2014-DataThis is an archive containing the phylogenies (newick), trait data (CSV) and R scripts used in Hardy and Otto 2014. Cheers!