cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3cd2611
title: Data from: Ecological mechanisms and phylogeny shape invertebrate stoichiometry: a test using detritus-based communities across Central and South America

description: 1. Stoichiometric differences among organisms can affect trophic
 interactions and rates of nutrient cycling within ecosystems. However, we
 still know little about either the underlying causes of these
 stoichiometric differences, or the consistency of these differences across
 large geographic extents. 2. Here we analyze elemental (carbon, nitrogen,
 phosphorus) composition of 872 aquatic macroinvertebrates (71 species)
 inhabiting tank bromeliads (n = 140) from five distantly located sites
 across Central and South America to (1) test phylogenetic, trophic and
 body size scaling explanations for why organisms differ in elemental
 composition, and (2) determine if patterns in elemental composition are
 universal or context-dependent. 3. Taxonomy explained most variance in
 elemental composition, even though phylogenetic signals were weak and
 limited to regional spatial extents and to the family level. The highest
 elemental contents and lowest carbon:nutrient ratios were found in
 organisms at high trophic levels and with smaller body size, regardless of
 geographic location. 4. Carnivores may have higher nutrient content and
 lower carbon:nutrient ratios than their prey, as organisms optimize growth
 by choosing the most nutrient-rich resources to consume and then
 preferentially retain nutrients over carbon in their bodies. Smaller
 organisms grow proportionally faster than large organisms, and so are
 predicted to have higher nutrient requirements to fuel RNA and protein
 synthesis. Geography influenced the magnitude, more than the direction, of
 the ecological and/or phylogenetic effects on elemental composition. 5.
 Overall, our results show that both ecological (i.e., trophic group) and
 evolutionary drivers explain among-taxa variation in the elemental content
 of invertebrates, whereas intraspecific variation is mainly a function of
 body size. Our findings also demonstrate that restricting analyses of
 macroinvertebrate stoichiometry solely to either the local scale or
 species level affects inferences of the patterns in invertebrate elemental
 content, and their underlying mechanisms.
description: Stoichiometry.Invertebrates.2018Data on elemental content of aquatic macroinvertebrates from tank bromeliads across Central-South America
DOI: 10.3535/2nn-vvz-qv9
title: Logania martinssoni Gross, 1967

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/40k-y4t-k9t
title: Logania martinssoni Gross, 1967

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/tw8-fmm-044
title: Logania martinssoni Gross, 1967

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/1a6-h5y-vj5
title: Logania kummerovi (Gross, 1967)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/8fe-2ex-013
title: Logania kummerovi (Gross, 1967)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/svk-mrs-zdb
title: Logania martinssoni Gross, 1967

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/kqx-9t1-cx2
title: Katoporus tricavus Gross, 1967

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/x5f-xjk-l49
title: Logania martinssoni Gross, 1967

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.5061/dryad.b7sp7
title: Data from: Less is more: selective advantages can explain the prevalent loss of biosynthetic genes in bacteria

description: Bacteria that have adapted to nutrient-rich, stable environments are
 typically characterized by reduced genomes. The loss of biosynthetic genes
 frequently renders these lineages auxotroph, hinging their survival on an
 environmental uptake of certain metabolites. The evolutionary forces that
 drive this genome degradation, however, remain elusive. Our analysis of
 949 metabolic networks revealed auxotrophies are likely highly prevalent
 in both symbiotic and free-living bacteria. To unravel whether selective
 advantages can account for the rampant loss of anabolic genes, we
 systematically determined the fitness consequences that result from
 deleting conditionally essential biosynthetic genes from the genomes of
 Escherichia coli and Acinetobacter baylyi in the presence of the focal
 nutrient. Pairwise competition experiments with each of 20 mutants
 auxotrophic for different amino acids, vitamins, and nucleobases against
 the prototrophic wild type unveiled a pronounced, concentration-dependent
 growth advantage of around 13% for virtually all mutants tested.
 Individually deleting different genes from the same biosynthesis pathway
 entailed gene-specific fitness consequences and loss of the same
 biosynthetic genes from the genomes of E. coli and A. baylyi
 differentially affected the fitness of the resulting auxotrophic mutants.
 Taken together, our findings suggest adaptive benefits could drive the
 loss of conditionally essential biosynthetic genes.
description: Selective_benefits_auxotrophy_raw_dataThe file contains data containing fitness (Mathusian parameters) and productivity (Max optical density at 600nm) of different auxotrophic mutants of Escherichia coli and Acinetobacter baylyi when growing in minimal medium supplemented with either amino acids, vitamins or nucleobases.
DOI: 10.5061/dryad.mf886
title: Data from: Trophic position determines functional and phylogenetic recovery after disturbance within a community

description: 1. The roles that functional traits and/or evolutionary history of species
 from co-occuring trophic groups have in determining community recovery
 following disturbance are poorly understood. Functional traits help
 determine how species interact with their environment, thus functional
 traits are likely to change with time since logging. However, traits of
 species may also be phylogenetically constrained depending on their
 evolutionary history. Because beetles are trophically diverse, the effects
 of phylogenetic and functional aspects of community recovery can be
 compared between co-occuring trophic groups. 2. Using a chronosequence of
 forest ages following logging, we applied a novel combination of
 functional trait and phylogenetic approaches to assess the extent to which
 taxonomic, functional and phylogenetic composition recovered after
 logging, and if these dimensions of composition approached those
 characteristic of mature forests, for both predators and
 decomposers/primary consumers. We also examined to what extent functional
 traits of both trophic groups were phylogenetically conserved. 3. Predator
 functional compostion had recovered ~45 years after logging, and this
 recovery preceded taxonomic recovery. Neither taxonomic nor functional
 composition had recovered for the decomposer/primary consumer communites
 by this time. 4. In contrast to decomposers/primary consumers, predator
 community recovery had no distinct phylogenetic signature, yet predator
 functional traits were more phylogenetically conserved than
 decomposers/primary consumer functional traits. 5. Trait syndromes that
 characterise forest recovery stages are identified and provide a basis for
 future work on community re-assembly following disturbance. 6. We
 demonstrate differential recovery of co-occuring beetle trophic groups
 following disturbance. We show that functional and phylogenetic
 composition may be disconnected from taxonomic composition; highlighting
 the advantages of integrating understanding of these three potentially
 independent components of ecological diversity to enable deeper
 understanding of animal community composition.
description: Species abundance data
 for predators and decomposers/primary consumersSpecies abundance data
 for both predators (first tab, 60 species) and decomposers/primary
 consumers (second tab, 73 species). Site information (time since logging)
 is located in the last column for each data set. See Appendix S2E for
 corresponding trait data and for phylogenetic
 relationships.Fountain-Jones et al 2017
 Species abundance data.xlsx
DOI: 10.5061/dryad.411s8
title: Data from: Tree ring δ15N as validation of space-for-time substitution in disturbance studies of forest nitrogen status

description: Forest ecosystem nitrogen (N) response to disturbance has often been
 examined by space-for-time substitution, but there are few objective tests
 of the possible variation in disturbance type and intensity across
 chronosequence sites. We hypothesized that tree ring δ15N, as a record of
 ecosystem N status, could validate chronosequence assumptions and provide
 isotopic evidence to corroborate N trends. To test this we measured soil N
 availability, soil δ15N, and foliar N attributes of overstory Douglas-fir
 (Pseudotsuga menziesii) and understory western hemlock (Tsuga
 heterophylla) across three old-growth stands and nine second-growth
 plantations on southeast Vancouver Island, British Columbia (Canada).
 Increment cores for wood δ15N were retrieved from three co-dominant
 Douglas-fir per plot. Bulk soil δ15N was well aligned with both foliar and
 recent wood δ15N, demonstrating the utility of wood δ15N in monitoring
 ecosystem N status. Strongly contrasting trends in tree ring δ15N were
 evident among second-growth stands, with most trees from plantations older
 than 50 years exhibiting steep declines (3–4‰) in δ15N but with no
 temporal trends detected for younger plantations. The discrepancy in tree
 ring δ15N suggests disturbance history varied considerably among
 second-growth sites, likely because of greater slash loads and hotter
 broadcast burns on older cutblocks. As a consequence, the pattern of
 increased soil N availability and foliar N concentration with time since
 disturbance derived from the chronosequence could not be validated. Tree
 ring δ15N may provide insights into disturbance intensity, especially
 fire, and correlations with foliar N concentration could inform the extent
 of changes in stand nutrition.
description: Buried bag N
 concentrationsIn situ buried bag
 methodology to measure soil nitrogen availabilitySoil chemistry
 chronosequence plotsMineral soil and forest
 floor chemistry from chronosequence plotsFoliar chemistry
 Douglas-fir Western hemlocktree ring 15N by site
 and treeNatural 15N abundance of
 wood samples from increment cores of Douglas-fir over chronosequence
 plots
DOI: 10.5061/dryad.4045sq6
title: Data from: Fine-scale spatial homogenization of microbial habitats: a multivariate index of headwater wetland complex condition

description: With growing public awareness that wetlands are important to society,
 there are intensifying efforts to understand the ecological condition of
 those wetlands that remain, and to develop indicators of wetland
 condition. Indicators based on soils are not well developed and are absent
 in some current assessment protocols; these could be advantageous,
 particularly for soils, which are complex habitats for plants,
 invertebrates, and microbial communities. In this study, we examine
 whether multivariate soil indicators, correlated with microbial biomass
 and community composition, can be used to distinguish reference standard
 (i.e., high condition) headwater wetland complexes from impacted headwater
 wetland complexes in central Pennsylvania, USA. Our reference standard
 sites existed in forested landscapes, while our impacted sites were
 situated in multi–use landscapes and were affected by a range of land–use
 legacies in the 1900s. We found that current assessment protocols are
 likely underrepresenting sampling needs to accurately represent site mean
 soil properties. On average more samples were required to represent soil
 property means in reference standard sites compared to impacted sites.
 Reference standard and impacted sites also had noticeably different types
 of microbial habitats for the two multivariate soil indices assessed, and
 impacted sites were more homogenized in terms of the fine-scale (i.e., 1-m
 and 5-m) spatial variability of these indices. Our study shows promise for
 the use of multivariate soil indices as indicators of wetland condition
 and provides insights into the sample sizes and scales at which soil
 sampling should occur during assessments. Future work is needed to test
 the generalizability of these findings across wetland types and ecoregions
 and establish definitive links between structural changes in microbial
 habitats and changes in wetland soil functioning.
description: Headwater Wetland
 Complex DatasetThis file contains the
 raw data used to construct multivariate indices of headwater wetland
 condition. Indices were constructed from soil property information that
 has been shown to have a strong relationship with wetland microbial
 community biomass and composition. These data were the basis of the
 analyses conducted in: Fine-scale spatial homogenization of microbial
 habitats: a multivariate index of headwater wetland complex
 condition.Moon et al Headwater Wetland
 Dataset.xlsx
DOI: 10.5061/dryad.34jc0m7
title: Data from: Genetic trade-offs between male reproductive traits in Drosophila melanogaster

description: In Drosophila melanogaster, males engage in both extensive pre-and
 postcopulatory competition for the opportunity to mate with females and
 subsequently sire offspring. The selection pressure for increased male
 reproductive success has resulted in the evolution of a wide diversity of
 sexual traits. However, despite strong selection, individuals often
 exhibit considerable phenotypic variation in the expression of these
 traits, and it is unclear if any of this variation is due to underlying
 genetic trade-offs. Here, using hemiclonal flies, we examine how male
 reproductive success covaries with their ability to induce long-term
 stimulation of oogenesis and oviposition in their mates, and how this
 relationship may change over time. We found that males from hemiclone
 lines with phenotypes that were more successful in a short-term
 reproductive “scramble” environment were less effective at stimulating
 long-term fecundity in females. Furthermore, we observed that males from
 hemiclone lines that showed the most improvement over a longer
 reproductive interaction period also tended to stimulate higher long-term
 fecundity in females. Together, these results indicate the presence of
 genetic trade-offs between different male reproductive traits, and offer
 insights into the maintenance of their variation.
description: Paternity
 dataComplete data set from
 competitive paternity assayFull
 Data.csvFecundity
 DataComplete data set from
 fecundity assayMeansComputed means of all
 measurements, including fecundity, paternity success on all days, and body
 mass
DOI: 10.5061/dryad.ps46g
title: Data from: Evidence for non-allopatric speciation among closely related sympatric Heliotropium species in the Atacama Desert

description: The genetic structure of populations of closely related, sympatric species
 may hold the signature of the geographical mode of the speciation process.
 In fully allopatric speciation, it is expected that genetic
 differentiation between species is homogeneously distributed across the
 genome. In non-allopatric speciation, the genomes may remain
 undifferentiated to a large extent. In this paper, we analysed the genetic
 structure of five sympatric species from the plant genus Heliotropium in
 the Atacama Desert. We used Amplified Fragment Length Polymorphisms
 (AFLPs) to characterise the genetic structure of these species and
 evaluate their genetic differentiation as well as the number of loci
 subject to positive selection using Divergence Outlier Analysis (DOA). The
 five species form distinguishable groups in the genetic space, with zones
 of overlap, indicating that they are possibly not completely isolated.
 Among-species differentiation accounts for 35% of the total genetic
 differentiation (FST=0.35), and FST between species pairs is positively
 correlated with phylogenetic distance. DOA suggests that few loci are
 subject to positive selection, which is in line with a scenario of
 non-allopatric speciation. These results support the idea that sympatric
 species of Heliotropium sect. Cochranea are under an ongoing speciation
 process, characterised by a fluctuation of population ranges in response
 to pulses of arid and humid periods during Quaternary times.
description: Heliotropium_AFLP_DataAFLP data in genpop formatMcheza table AFLP Heliotropium.txtSpecies tree of Heliotropium sect. CochraneaSpecies tree of Heliotropium sect. Cochranea generated with star-BEASTAdditional DNA sequences of Heliotropium sect. CochraneaGenBank accession numbers KF301622:KF301628. These sequences were added to the dataset of Luebert & Wen (Syst. Bot. 33:390–402, 2008) and used for the species tree analysis in star-BEAST.NCBI_Heliotropium_DEC2013
DOI: 10.5061/dryad.2215v
title: Data from: The size of a melanin-based plumage ornament correlates with glucocorticoid receptor concentrations in the skin of that ornament

description: Glucocorticoid hormones such as corticosterone (CORT) play crucial roles
 in many physiological processes. CORT's actions are primarily
 mediated via binding to two receptors (glucocorticoid receptors (GR) and
 mineralocorticoid receptors (MR)) in different target tissues. CORT
 receptors can be independently regulated from circulating hormone titers,
 from tissue to tissue and even within different regions of the same tissue
 type. Increasing evidence has shown relationships between circulating CORT
 and melanin-based pigmentation in skin and feathers, yet to our knowledge
 there have been no studies of CORT receptors in the skin of melanized
 ornaments. Male house sparrows (Passer domesticus) have a black, melanized
 bib, and evidence suggests that bib size is an important intraspecific
 signal. We examined the relationship between bib area and tissue
 sensitivity to CORT by quantifying GR and MR in bib skin and in adjacent
 paler-feathered belly skin (as a control tissue) at different life history
 stages using radioligand binding assays. Males with larger bibs relative
 to their life history stage had less GR in bib skin, but not belly skin,
 than males with smaller bibs. These results suggest a connection between
 the size of a melanin-based ornament and the underlying tissue's
 responsiveness to CORT.
description: Bib area measurements
 from two sets of annotatorsBased on photos from
 male house sparrows at 5 times of year, photographed with a ruler for
 reference, and measured using ImageJ software.Lattin and Romero bib skin area
 data 8-17-13.xlsxReceptor concentrations
 (MR and GR) in bib skin and belly skinReceptor concentrations
 measured via radioligand binding assays in bib skin and belly skin of male
 house sparrows at 5 different times of year. All binding was standardized
 to fmol/mg protein as measured using Bradford assays.Lattin and Romero receptor and
 bib skin data 8-17-13.xlsx
DOI: 10.5061/dryad.66
title: Data from: Biogeography and floral evolution of baobabs (Adansonia, Bombacaceae) as inferred from multiple data sets

description: The phylogeny of baobab trees was analyzed using four data sets:
 chloroplast DNA restriction sites, sequences of the chloroplast rpl 16
 intron, sequences of the internal transcribed spacer ITS region of nuclear
 ribosomal DNA, and morphology. We sampled each of the eight species of
 Adansonia plus three outgroup taxa from tribe Adansonieae. These data were
 analyzed singly and in combination using parsimony. ITS and morphology
 provided the greatest resolution and were largely concordant. The two
 chloroplast data sets showed concordance with one another but showed
 significant conflict with ITS and morphology. A possible explanation for
 the conflict is genealogical discordance within the Malagasy Longitubae,
 perhaps due to introgression events. A maximum likelihood analysis of
 branching times shows that the dispersal between Africa and Australia
 occurred well after the fragmentation of Gondwana and therefore involved
 overwater dispersal. The phylogeny does not permit unambiguous
 reconstruction of floral evolution but suggests the plausible hypothesis
 that hawkmoth pollination was ancestral in Adansonia and that there were
 two parallel switches to pollination by mammals in the genus.
description: Baum et. al Data
 Matrixbaum.append.txt
DOI: 10.5061/dryad.56mv5
title: Data from: Migration tendency delays distributional response to differential survival prospects along a flyway

description: When populations grow or decline, habitat selection may change due to
 local density-dependent processes, such as site dependence and
 interference. In seasonally migrating animals, nonbreeding distributions
 may be determined through these mechanisms of density dependence, which we
 examine here at a hemispheric scale for a long-distance migrating bird.
 Using summer and winter resightings of 2,095 Eurasian spoonbills Platalea
 leucorodia leucorodia that were ringed in the Netherlands during 16 years
 of fast population growth, we show that neither site dependence nor
 interference fully explains their patterns of survival and winter
 distribution. Within their three main wintering areas, annual survival
 decreased with an increase in population size. While survival was
 consistently higher in the two European wintering areas (France, Iberia),
 most spoonbills migrated onward to winter in west Africa. The number of
 birds wintering in Europe increased, but not enough to maximize annual
 survival. We conclude that a constraint of tradition (their “migration
 tendency”) inhibits birds from changing their migratory habits. We pose
 that this phenomenon may similarly constrain other migratory populations
 from rapidly responding to large-scale climate- and/or human-driven
 habitat changes at their wintering grounds.
description: Encounter histories
 adult spoonbills 1994-2010This datafile (plain
 textfile to be imported in program E-Surge) contains the encounter
 histories of 2095 adult (&gt;3cy) Eurasian spoonbills, born between 1988
 and 2007 and resighted between summer 1994 and summer 2010. Two resighting
 periods per year are defined (summer = March-September, winter =
 December-January for France and Iberia and October-February for Mauritania
 & Senegal). Events are coded as: (0) not resighted, (1) resighted in
 summer in The Netherlands, (2) resighted in winter in France, (3)
 resighted in winter in Iberia, (4) resighted in winter in Mauritania &
 Senegal. Columns refer to encounter history (H:), sample size (S:) and
 'standardized' year of birth (COV:yb), calculated as ([year of
 birth]-2000)/10.Encounter_history_file_1994_2010.txt