cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.kr6hg
title: Data from: Traditional forest management practices stop forest succession and bring back rare plant species

description: Past management practices may continue to influence ecosystem functions
 and processes for decades, centuries or even longer after they have been
 abandoned. Until now, few researchers have attempted experiments which
 test the effects of restoring some of these past management practices on
 long-term community developmental trajectories. Strong evidence indicates
 that the diversity of various taxonomic groups declined in European
 lowland forests in the second half of the 20th century, following the
 abandonment of some traditional forest management practices. We carried
 out a five-year field trial in a lowland thermophilous oak forest to
 describe the effects of restoration of litter raking and grass cutting on
 the long-term developmental trajectory of species composition and the
 diversity of understorey vegetation. We used target species groups, i.e.
 species specific to thermophilous forests and dry grassland vegetation and
 plant functional traits to evaluate the restoration success using both
 compositional and functional outcomes. Dissimilarity in species
 composition between the managed plots and controls increased significantly
 during the five years of the trial. Litter raking increased the richness
 and cover of the thermophilous forest and dry grassland species, whereas
 grass cutting increased the richness and cover of only the dry grassland
 species. We did not record any overall trends in divergence of functional
 trait composition between managed and control plots. In the litter raking
 plots, we recorded increases in community-weighted means of specific leaf
 area, in lateral spread and in Ellenberg indicator values for nutrients
 and soil reaction. In contrast, we found little evidence for
 predictability of species functional trait composition subjected to grass
 cutting. Synthesis and applications. Following the restoration of
 traditional forest management practices we were able to change the
 community's developmental trajectory towards higher richness and
 cover of target species. The evaluation of community developmental
 trajectories using species and functional trait composition supports the
 idea that restoration of traditional forest management practices should
 carefully distinguish among possible interventions.
description: vegetation_dataVegetation data of plots treated with the restored management practices.
DOI: 10.5061/dryad.1pg48
title: Data from: The effects of selective history and environmental heterogeneity on inbreeding depression in experimental populations of Drosophila melanogaster

description: Inbreeding depression varies considerably among populations, but only some
 aspects of this variation have been thoroughly studied. Because inbreeding
 depression requires genetic variation, factors that influence the amount
 of standing variation can affect the magnitude of inbreeding depression.
 Environmental heterogeneity has long been considered an important
 contributor to the maintenance of genetic variation, but its effects on
 inbreeding depression have been largely ignored by empiricists. Here we
 compare inbreeding depression, measured in two environments, for 20
 experimental populations of Drosophila melanogaster that have been
 maintained under four different selection regimes, including two types of
 environmentally homogeneous selection and two types environmentally
 heterogeneous selection. In line with theory, we find considerably higher
 inbreeding depression in populations from heterogeneous selection regimes.
 We also use our data set to test whether inbreeding depression is
 correlated with either stress or the phenotypic coefficient of variation
 (CV), as suggested by some recent studies. Though both of these factors
 are significant predictors of inbreeding depression in our study, there is
 an effect of assay environment on inbreeding depression that cannot be
 explained by either stress or CV.
description: Survivorship &
 Fecundity Data from assays conducted on salt-supplemented
 mediaThis data file
 contains data used in the study “The effects of
 selective history and environmental heterogeneity on inbreeding depression
 in experimental populations of Drosophila melanogaster” by Tristan A.F.
 Long, Locke Rowe and Aneil Agrawal. For details on how these data were
 obtained, please consult original article. The data consist of data
 collected from females obtained from experimentally evolved populations of
 fruit flies that had been cultured under protocols differing in their
 amount and type of environmental homogeneity. The
 file contains data from individuals assayed on
 salt-supplemented media.export_ID_SALT.xlsSurvivorship & Fecundity Data from assays conducted on cadmium-supplemented mediaThis data file contains data used in the study “The effects of selective history and environmental heterogeneity on inbreeding depression in experimental populations of Drosophila melanogaster” by Tristan A.F. Long, Locke Rowe and Aneil Agrawal. For details on how these data were obtained, please consult original article. The data consist of data collected from females obtained from experimentally evolved populations of fruit flies that had been cultured under protocols differing in their amount and type of environmental homogeneity. The file contains data from individuals assayed on cadmium-supplemented media.export_ID_CAD.xls
DOI: 10.5061/dryad.fg500
title: Data from: Strength and variability of postmating reproductive isolating barriers between four European white oak species

description: The identification and quantification of the relative importance of
 reproductive isolating barriers is of fundamental importance to understand
 species maintenance in the face of interspecific gene flow between
 hybridizing species. Yet, such assessments require extensive experimental
 fertilisations that are particularly difficult when dealing with more than
 two hybridizing and long generation time species such as oaks. Here we
 quantify the relative contribution of four postmating reproductive
 isolating barriers consisting of two prezygotic barriers (gametic
 incompatibility, conspecific pollen precedence) and two postzygotic
 barriers (germination rate, early survival) from extensive controlled
 pollinations between four oak species (Quercus robur, Q. petraea, Q.
 pubescens and Q. pyrenaica) that have been shown to frequently hybridize
 in natural populations. We found high variation in the strength of total
 reproductive isolation between species, ranging from total reproductive
 isolation to advantage toward hybrid formation. As previously found, Q.
 robur pollen was unable to fertilize Q. petraea due to a strong
 reproductive isolating mechanism. On the contrary, Q. pubescens pollen was
 more efficient at fertilizing Q. petraea than conspecific pollen. Overall,
 prezygotic barriers contribute far more than postzygotic barriers to
 isolate species reproductively, suggesting a role for reinforcement in the
 development of prezygotic barriers. Conspecific pollen precedence reduced
 hybrid formation when pollen competition was allowed, however presence of
 conspecific pollen did not totally prevent hybridization. Our results
 suggest that pollen competition depends on multiple ecological and
 environmental parameters, including species local abundance, and that it
 may be of uppermost importance to understand interspecific gene flow among
 natural multispecies populations.
description: Lepais-et-al_TGG_ResultsForm-4OakSpecies-ControlledCrossesLepais-et-al_4OakSpecies-ControlledCrosses_DataForDryad.xls
DOI: 10.5281/zenodo.10989854
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by George Campbell Eickwort, http://www.wikidata.org/entity/Q55030504. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q55030504
DOI: 10.5281/zenodo.18381803
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by George Campbell Eickwort, http://www.wikidata.org/entity/Q55030504. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q55030504
DOI: 10.5061/dryad.td8kt
title: Data from: Colorimetric detection of hydrogen peroxide by dioxido-vanadium(V) complex containing hydrazone ligand: synthesis and crystal structure

description: Dioxidovanadium(V) complex has been synthesized in good yield, the complex
 was characterized by IR, UV-Visible and 1H NMR spectroscopy. Single
 crystal X-ray Crystallography techniques was used to assign the structure
 of the complex. Complex crystallized with monoclinic P2/c space group with
 cell parameters a/Å = 39.516(5), b/Å = 6.2571(11), c/Å = 17.424(2), α/° =
 90, β/° = 102.668(12), and γ/° = 90. The hydrazone ligand is coordinate to
 metal ion in tridentate fashion through -ONO- donor atoms forming a
 distorted square pyramidal geometry around the metal ion.
description: XRD-FILE
DOI: 10.5061/dryad.fg15tg2
title: Data from: Maize-nutrient response functions for Eastern and Southern Africa

description: Information is scarce for maize (Zea mays L.) response to nutrient
 application for many production areas in tropical Africa. Research was
 conducted to determine macronutrient response functions and to diagnose
 Mg–S–Zn–B deficiencies. Site–year × N-rate interactions within countries
 often accounted for little variation in yield relative to the N-rate
 effect. Country mean grain yield responses to N-rate were curvilinear to
 plateau, but linear in Malawi. Although mean yields differed, the response
 to N was similar for Kenya, Tanzania, and Zambia with a mean yield
 increase of 0.94 Mg ha–1 due to 50 kg ha–1 N compared with 1.59 Mg ha–1
 for Malawi and Rwanda. Response to N was related to yield with no
 fertilizer applied (r = 0.40). Only Rwanda had mean responses to P and K
 with respective yield increases of 0.99 and 0.22 Mg ha–1 due to 15 kg
 ha–1. Application of Mg–S–Zn–B caused a mean yield increase of 0.73 Mg
 ha–1 in Rwanda but had no effect in other countries. Application of
 affordable fertilizer to twice as much land at 50% compared with 100% of
 the economically optimum rate results in mean gains of 50% for production
 and agronomic efficiency and 72% for profit/cost ratio. Soil test results
 were not related to response to applied nutrients but historical yield
 appears to be weakly predictive of N response. The determined
 country-level P and K response functions can be widely applied, except for
 Kenya, in consideration of other available information. The response to
 Mg–S–Zn–B in Rwanda needs further investigation.
description: ESA Maize Fertilizer
 Response DataThis data was generated
 from collaborative research in five countries of eastern and southern
 Africa using a similar treatment structure for determination of maize
 response functions to fertiizer N, P, and K and for the diagnosis of
 deficiencies for Mg, S, Zn and B.
DOI: 10.5061/dryad.qt3m8jv7
title: Data from: The expression of self-incompatibility in angiosperms is bimodal

description: Self-incompatibility is expressed by nearly one half of all angiosperms. A
 large proportion of the remaining species are self-compatible, and they
 either outcross using various contrivances or self-fertilize to some
 extent. Because of the common occurrence of populations and individuals
 with intermediate levels of self-incompatibility, categorization of the
 expression of self-incompatibility as an approximately binary trait has
 become controversial. We collect a widely reported index (ISI) used to
 asses the strength and variation of self-incompatibility from over 1200
 angiosperm taxa. Its distribution is bimodal and positively associated
 with outcrossing rate, albeit with a weak relationship within
 self-compatible taxa. A substantial fraction of species have intermediate
 mean values of ISI. Their occurrence can be caused by segregating
 ephemeral self-compatible mutations, averaging artifacts, and experimental
 biases, in addition to the often invoked stabilizing selection acting on
 the expression of self-incompatibility. Selection may also generally favor
 taxa with high ISI values through increased lineage birth and death rates,
 and it may counter lower-level selection advantages within taxa expressing
 intermediate and low values of ISI. Such a null hypothesis is nearly
 universally overlooked, despite the fact that it could adequately explain
 the observed distribution of mating and breeding systems.
description: ISI.dryad
DOI: 10.5061/dryad.m5t20
title: Data from: The role of preservation on the quantification of morphology and patterns of disparity within Paleozoic echinoderms

description: The loss of information resulting from taphonomic degradation could
 represent a significant bias in the study of morphological diversity. This
 potential bias is even more concerning given the uneven effect of
 taphonomy across taxonomic groups, depositional facies, and stratigraphic
 successions and in response to secular changes through the Phanerozoic.
 The effect of taphonomic degradation is examined using character-based
 morphological data sets describing disparity in Paleozoic crinoids and
 blastozoans. Characters were sequentially excluded from the analyses
 following progressive taphonomic loss to determine how morphologic
 metrics, such as the relative distribution of taxa in morphospace and
 partial disparity, changed with increasing taphonomic alteration.
 Blastozoans showed very little change in these metrics with decreasing
 preservational quality, which is a result of characters that create
 distance in morphospace being recognizable in isolated plates. The
 opposite result is present in crinoids as the characters that are
 important in structuring the morphospace require intact modules (i.e., the
 calyx) to accurately assess. Temporal and stratigraphic trends produced
 encouraging results in that patterns could be largely recovered even with
 exaggerated taphonomic biases. However, certain parts of a stratigraphic
 sequence should be avoided and morphological outliers could potentially
 play a larger role through time, though both of these biases can be easily
 identified and avoided. The methods presented in this study provide a way
 to assess potential taphonomic biases in character-based studies of
 morphological diversity.
description: Supplemental Data
 1AEToL Crinoid character
 list. Variations of this character list have previously been used in
 Ausich et al. 2015 and Deline and Ausich in print.Supplemental Data
 2Crinoid codings using
 the AEToL character suite. If a crinoid was used in the stratigraphic
 analysis in either the test (x) or control (xc) group it is
 noted.Supplemental Data
 3Taphonomic Codings for
 the AETOL dataset. X denotes that the character would likely be preserved.
 TG: Taphonomic Grade, Sequence Stratigraphic abbreviations are descibed in
 the main manuscript.Supplemental Data
 4Taphonomic codigs for
 Blastozoan data set. TG= Taphonomic Grade for Type one, two, and three
 blastozoans. X denotes the character was included in the
 analyses
DOI: 10.5061/dryad.1405
title: Data from: The evolution of sexual and parthenogenetic Warramaba: a window onto Plio-Pleistocene diversification processes in an arid biome

description: Environmental changes over the Plio-Pleistocene have been key drivers of
 speciation patterns and genetic diversification in high-latitude and mesic
 environments, yet comparatively little is known about the evolutionary
 history of species in arid environments. We applied phylogenetic and
 phylogeographic analyses to understand the evolutionary history of
 Warramaba grasshoppers from the Australian arid zone, a group including
 sexual and parthenogenetic lineages. Sequence data (mitochondrial COI)
 showed that the four major sexual lineages within Warramaba most likely
 diverged in the Pliocene, around 2-7 million years ago. All sexual
 lineages exhibited considerable phylogenetic structure. Detailed analyses
 of the hybrid parthenogenetic species W. virgo and its sexual progenitors
 showed a pattern of high phylogenetic diversity and phylogeographic
 structure in northern lineages, and low diversity and evidence for recent
 expansion in southern lineages. Northern sexual lineages persisted in
 localized refugia over the Pleistocene, with sustained barriers promoting
 divergence over this period. Southern parts of the present range became
 periodically unsuitable during the Pleistocene, and it is into this region
 that parthenogenetic lineages have expanded. Our results strongly parallel
 those for sexual and parthenogenetic lineages of the gecko Heteronotia
 from the same region, indicating a highly general effect of
 Plio-Pleistocene environmental change on diversification processes in arid
 Australia.
description: Warramaba sp. COI
 sequencesCOI sequences in MEGA
 format, grouped according to species/lineageCOI_Sequences_All_Grouped_Final.meg
DOI: 10.5061/dryad.dn584
title: Data from: Molecular identification of natural mangrove hybrids of Rhizophora in Peninsular Malaysia

description: Natural hybridization is common in plants. Very often, the identity of a
 putative hybrid is inferred based on the observation of morphological
 features intermediate between two possible parental species occurring in a
 specific location. However, due to plasticity of morphological features
 and the co-occurrence of more than two possible parental species,
 molecular markers would be most useful to establish the origin of a
 putative hybrid. In mangroves, three Rhizophora species (Rhizophora
 apiculata, Rhizophora mucronata, and Rhizophora stylosa) and two putative
 hybrids (Rhizophora × lamarckii and Rhizophora × annamalayana) are
 distributed in the Indo-West Pacific region. Leaf samples of Rhizophora
 were obtained from two locations in Peninsular Malaysia, namely, Bagan
 Lalang and Pulau Burung, where all three species grow in sympatry. We
 analyzed sequences of one chloroplast and six nuclear DNA regions. Our
 results confirmed earlier claims that the morphologically identified
 putative hybrids growing in Pulau Burung are R. × lamarckii, a cross
 between R. apiculata and R. stylosa. Our data also pointed to the possible
 discovery of a new Rhizophora hybrid—a cross between R. mucronata and R.
 stylosa—the identification of which would have been difficult based on
 morphological features alone. The directions and the stages of
 hybridization are also discussed.
description: cpDNA atpB-rbcL
 sequencescpDNA sequences (.fas)
 of the atpB-rbcL intergenic spacer and rbcL gene, partial cds. 48
 sequences. Alignment length: 840bp.atpB-rbcL_840bp.fasnDNA DLDH sequencesnDNA sequences (.fas) of the dihydrolipoamide dehydrogenase (DLDH) gene, partial cds. 48 sequences. Alignment length: 1221bp.DLDH_1221bp.fasnDNA FMRrm11 sequencesnDNA sequences (.fas) of the microsatellite RM11. 68 sequences. Alignment length: 609bp.FMRrm11_609bp.fasnDNA mang-1 sequencesnDNA sequences (.fas) of the mangrin (mang-1) gene, partial cds. 48 sequences. Alignment length: 438bp.mang-1_438bp.fasnDNA PAL1 sequencesnDNA sequences (.fas) of the phenylalanine ammonia-lyase (PAL1) gene, partial cds. 48 sequences. Alignment length: 940bp.PAL1_940bp.fasnDNA RPB2 sequencesnDNA sequences (.fas) of the putative RNA polymerase II second largest subunit (RPB2) gene, partial cds. 68 sequences. Alignment length: 126bp.RPB2_126bp.fasnDNA SBE2 sequencesnDNA sequences (.fas) of the starch branching enzyme II (SBE2) gene, partial cds. 48 sequences. Alignment length: 947bp.SBE2_947bp.fas
DOI: 10.5281/zenodo.17479525
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by John Burton Cleland, http://www.wikidata.org/entity/Q4223546. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q4223546
DOI: 10.5281/zenodo.18381777
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by John Burton Cleland, http://www.wikidata.org/entity/Q4223546. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q4223546
DOI: 10.5061/dryad.2b1r2sh
title: Data from: Diversity of opisthokont septin proteins reveals structural constraints and conserved motifs

description: Background: Septins are cytoskeletal proteins important in cell division
 and in establishing and maintaining cell polarity. Although septins are
 found in various eukaryotes, septin genes had the richest history of
 duplication and diversification in the animals, fungi and protists that
 comprise opisthokonts. Opisthokont septin paralogs encode modular proteins
 that assemble into heteropolymeric higher order structures. The
 heteropolymers can create physical barriers to diffusion or serve as
 scaffolds organizing other morphogenetic proteins. How the paralogous
 septin modules interact to form heteropolymers is still unclear. Through
 comparative analyses, we hoped to clarify the evolutionary origin of
 septin diversity and to suggest which amino acid residues were responsible
 for subunit binding specificity. Results: Here we take advantage of newly
 sequenced genomes to reconcile septin gene trees with a species phylogeny
 from 22 animals, fungi and protists. Our phylogenetic analysis divided 120
 septins representing the 22 taxa into seven clades (Groups) of paralogs.
 Suggesting that septin genes duplicated early in opisthokont evolution,
 animal and fungal lineages share septin Groups 1A, 4 and 2. Group 1B
 septins were present in animals and early diverging fungi but missing from
 Ascomycota and Basidiomycota. Protein homology folding showed that
 previously identified conserved septin motifs were all located near
 interface regions between the adjacent septin modules of a dimer. We found
 specific interface residues associated with each septin Group that are
 candidates for providing subunit binding specificity. Conclusions: This
 work reveals that duplication of septin genes began in an ancestral
 opisthokont more than a billion years ago and continued through the
 diversification of animals and fungi. Evidence for evolutionary
 conservation of ~49 interface residues will inform mutagenesis experiments
 and lead to improved understanding of the rules guiding septin
 heteropolymer formation and from there, to improved understanding of
 development of form in animals and fungi.
description: Full Septin
 AlignmentAlignment of whole
 septin protein sequences from included species.Septin.Cobalt.Alignment.faa.nexUltrametric Species TreeSpecies tree made ultrametric with r8s based on orthologous protein sequences.dated.Opistho.species.treAlicut processed septin alignmentSeptin alignment after processing with Alicut using window size of 12Septin.alignment.Alicut.12window.faajPrime MCCT septin phylogenyjPRIME.MCCT.septin.treMrBayes septin phylogenyMrBayes.septin.con.treRAxML Septin phylogenyRAxML.septin.with.support.tre