cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7fc8c
title: Data from: Signatures of human impact: size distributions and spatial organization of wetlands in the prairie pothole landscape

description: More than 50% of global wetland area has been lost over the last 200
 years, resulting in losses of habitat and species diversity as well as
 decreased hydrologic and biogeochemical functionality. Recognition of the
 magnitude of wetland loss as well as the wide variety of ecosystem
 services provided by wetlands has in recent decades led to an increased
 focus on wetland restoration. Restoration activities, however, often
 proceed in an ad-hoc manner, with a focus on maximizing the total restored
 area rather than on other spatial attributes of the wetland network, which
 are less well understood. In this study, we have addressed the question of
 how human activities have altered the size distribution and spatial
 organization of wetlands over the Prairie Pothole Region of the Des Moines
 Lobe using high-resolution LIDAR data. Our results show that as well as
 the generally accepted 90% loss of depressional wetland area, there has
 been a disproportionate loss of both smaller and larger wetlands, with a
 marked alteration of the historical power-law relationship observed
 between wetland size and frequency and a resulting homogenization of the
 wetland size distribution. In addition, our results show significant
 decreases in perimeter-to-area ratios, increased mean distances between
 wetlands, particularly between smaller wetlands, and a reduced likelihood
 that current wetlands will be located in upland areas. Such patterns of
 loss can lead to disproportionate losses of ecosystem services, as smaller
 wetlands with larger perimeter-to-area ratios have been found to provide
 higher rates of biogeochemical processing and groundwater recharge, while
 increased mean distances between wetlands hinder species migration and
 thus negatively impact biodiversity. These results suggest the need to
 gear restoration efforts towards understanding and recreating the size
 distribution and spatial organization of historical wetlands, rather than
 focusing primarily on an increase in overall area.
description: Des Moines Lobe Wetland
 DataThis geodatabase
 contains lidar data and NWI wetland data for the Des Moines Lobe of the
 North American Prairie Pothole region.DML_Data.zipx
DOI: 10.5061/dryad.8k0m3
title: Data from: The limited contribution of reciprocal gene loss to increased speciation rates following whole-genome duplication

description: Hybrid incompatibilities contribute to reproductive isolation between
 species, allowing them to follow independent evolutionary trajectories.
 Since hybrid incompatibilities are by definition deleterious, they cannot
 be selected for directly and must arise as a by-product of evolutionary
 divergence. Divergent resolution of duplicate genes, a special case of
 Dobzhansky-Muller incompatibilities, is one mechanism by which hybrid
 incompatibility can evolve. Following whole-genome duplication, loss of
 gene copies could possibly increase the opportunity for divergent
 resolution and, hence, the evolution of hybrid incompatibilities. However,
 divergent resolution can take place only when populations are isolated in
 allopatry; genes lost within a species cannot contribute to future
 speciation. Furthermore, nearly complete allopatry is necessary for
 passive divergent resolution. Using mathematical models, we demonstrate
 that these two factors severely impede the ability of divergent resolution
 alone to increase speciation rates, except under very particular
 conditions. Instead, we find that the population dynamics of diverging
 lineages dominate this process, leading to a larger role for ecology
 relative to genetics in the origin of new species, even by passive
 mechanisms. Divergent resolution of duplicate genes might increase
 speciation rates in some clades at some times, but our results indicate
 that it alone is unlikely to account for the macroevolutionary success of
 polyploid clades.
description: DatasetsCode
DOI: 10.5061/dryad.mf278
title: Data from: Optimisation of AFLP for extremely large genomes over 70 Gb.

description: Here, we present an improved amplified fragment length polymorphism (AFLP)
 protocol using restriction enzymes (AscI and SbfI) that recognise 8-base
 pair sequences to provide alternative optimisation suitable for species
 with a genome size over 70 Gb. This cost-effective optimisation massively
 reduces the number of amplified fragments by using only +3 selective bases
 per primer during selective amplification. We demonstrate the effects of
 the number of fragments and genome size on the appearance of non-identical
 co-migrating fragments (size homoplasy), which has a negative impact on
 the informative value of AFLP genotypes. We also present various reaction
 conditions and their effects on reproducibility and the band intensity of
 the extremely large genome of Viscum album. The reproducibility of this
 octo-cutter protocol was calculated using several species with genome
 sizes ranging from 1 Gb (Carex panicea) to 76 Gb (Viscum album). The
 improved protocol also succeeded in detecting high intraspecific
 variability in species with large genomes (Viscum album, Galanthus nivalis
 and Pinus pumila).
description: Example of AFLP profiles
 in .fsa filesAFLP-samples.rarAFLP in silico size homoplasyThe file contains a script for R package that simulate size homoplasy for AFLP fragments.AFLP_in_silico_size_homoplasy.R
DOI: 10.5061/dryad.34vq1
title: Data from: Phylogenomic analysis of glycogen branching and debranching enzymatic duo

description: Branched polymers of glucose are universally used for energy storage in
 cells, taking the form of glycogen in animals, fungi, Bacteria, and
 Archaea, and of amylopectin in plants. Some enzymes involved in glycogen
 and amylopectin metabolism are similarly conserved in all forms of life,
 but some, interestingly, are not. In this paper we focus on phylogeny of
 glycogen branching and debranching enzymes, respectively involved in
 introducing and removing of the alpha(1-&gt;6) bonds in glucose
 polymers, bonds that provide the unique branching structure to glucose
 polymers. Results: We performed a large scale phylogenomic analysis of
 branching and debranching enzymes in over 400 completely sequenced
 genomes, including more than 200 from eukaryotes. We show that branching
 and debranching enzymes can be found in all kingdoms of life, including
 all major groups of eukaryotes, and thus were likely to have been present
 in the last universal common ancestor (LUCA) but have been lost in
 seemingly random fashion in numerous single celled eukaryotes. We also
 show how animal branching and debranching enzymes evolved from their LUCA
 ancestors by acquiring additional domains. Furthermore, we show that
 enzymes commonly perceived as orthologous, such as human branching enzyme
 GBE1 and E. coli branching enzyme glgB, are in fact related by a gene
 duplication and consequently paralogous. Conclusions: Despite its well
 known association with animal liver cells and plant starch, energy storage
 in the form of branched glucose polymers is clearly an ancient process and
 has been present in the earliest cells. The evolution of enzymes enabling
 this form of energy storage is more complex than previously thought and
 illustrates the need for explicit phylogenomic analysis in the study of
 even seemingly "simple" metabolic enzymes. Patterns of
 conservation and divergence in the evolution of the glycogen/starch
 branching and debranching enzymes have interesting biomedical
 connotations, as mutations in these enzymes lead to a variety of
 inheritable diseases in humans and other mammals.
description: Bayesian phylogeny of
 CBM_48—Alpha-amylase containing branching and debranching
 enzymesData file for Figure
 4.Figure_4_CBM_48_lim2_mafft_09_40_mb_con_50_majrule_phyml_fme.phylo.xmlBayesian phylogeny of GDE_C domain containing (putative) debranching enzymes (EC 3.2.1.33).Data file for Figure 5.Figure_5_GDE_C_lim_mafft_09_40_mb_con_50_majrule_phyml_fme.phylo.xmlMinimal evolution phylogeny of CBM_48 containing proteinsAlignment: hmmalign; pairwise distances: Tree-Puzzle; tree inference: FastMECBM_48__CBM_48__ee2_50_hmmalign_09_40_fme.phylo.xml
DOI: 10.5061/dryad.n28rf
title: Data from: Changes in sexual signals are greater than changes in ecological traits in a dichromatic group of fishes

description: Understanding the mechanisms by which phenotypic divergence occurs is
 central to speciation research. These mechanisms can be revealed by
 measuring differences in traits that are subject to different selection
 pressures; greater influence of different types of selection can be
 inferred from greater divergence in associated traits. Here, we address
 the potential roles of natural and sexual selection in promoting
 phenotypic divergence between species of snubnose darters by comparing
 differences in body shape, an ecologically relevant trait, and male color,
 a sexual signal. Body shape was measured using geometric morphometrics,
 and male color was measured using digital photography and visual
 system-dependent color values. Differences in male color are larger than
 differences in body shape across 8 allopatric, phylogenetically
 independent species pairs. While this does not exclude the action of
 divergent natural selection, our results suggest a relatively more
 important role for sexual selection in promoting recent divergence in
 darters. Variation in the relative differences between male color and body
 shape across species pairs reflects the continuous nature of speciation
 mechanisms, ranging from ecological speciation to speciation by sexual
 selection alone.
description: Body Shape
 DataLandmark coordinates for
 geometric morphometric analysis. Both raw data and data following
 procrustes fitting and body arching correction are
 included.Color Opponency
 DataColor data as
 interpreted in a color opponency framework. Raw color data are provided
 along with normalized response values and a color opponency score for each
 sampling location on the body. These scores are averaged within sampling
 areas and form the data used in PCA analysis.MWS-LWS
 DataColor data as
 interpreted using MWS and LWS as independent values. Raw data are given
 along with averages for each sampling area that were then used in
 subsequent PCA.
DOI: 10.6084/m9.figshare.30095521.v2
title: Cor-CA5-Original data.rar

description: <b>Cordycepin Suppresses the Growth and Virulence of </b><b><i>Magnaporthe oryzae</i></b><b> by Targeting Mitochondrial Carbonic Anhydrases</b>
DOI: 10.5061/dryad.jf142
title: Data from: Empirical Bayesian elastic net for multiple quantitative trait locus mapping

description: In multiple quantitative trait locus (QTL) mapping, a high-dimensional
 sparse regression model is usually employed to account for possible
 multiple linked QTLs. The QTL model may include closely linked and thus
 highly correlated genetic markers, especially when high-density marker
 maps are used in QTL mapping because of the advancement in sequencing
 technology. Although existing algorithms, such as Lasso, empirical
 Bayesian Lasso (EBlasso) and elastic net (EN) are available to infer such
 QTL models, more powerful methods are highly desirable to detect more QTLs
 in the presence of correlated QTLs. We developed a novel empirical
 Bayesian EN (EBEN) algorithm for multiple QTL mapping that inherits the
 efficiency of our previously developed EBlasso algorithm. Simulation
 results demonstrated that EBEN provided higher power of detection and
 almost the same false discovery rate compared with EN and EBlasso.
 Particularly, EBEN can identify correlated QTLs that the other two
 algorithms may fail to identify. When analyzing a real dataset, EBEN
 detected more effects than EN and EBlasso. EBEN provides a useful tool for
 inferring high-dimensional sparse model in multiple QTL mapping and other
 applications. An R software package ‘EBEN’ implementing the EBEN algorithm
 is available on the Comprehensive R Archive Network (CRAN).
description: simulation_datasetsThis dataset contains three datasets corresponding to the example, simI and simII in the following paper:Anhui Huang; Shizhong Xu; Xiaodong Cai, Empirical Bayesian Elastic Net for Multiple Quantitative Trait Locus Mapping. Heredity(2014) Accpeted.
DOI: 10.5061/dryad.fv921
title: Data from: Loss of avian phylogenetic diversity in neotropical agricultural systems

description: Habitat conversion is the primary driver of biodiversity loss, yet little
 is known about how it is restructuring the tree of life by favoring some
 lineages over others. We combined a complete avian phylogeny with 12 years
 of Costa Rican bird surveys (118,127 detections across 487 species)
 sampled in three land uses: forest reserves, diversified agricultural
 systems, and intensive monocultures. Diversified agricultural systems
 supported 600 million more years of evolutionary history than intensive
 monocultures but 300 million fewer years than forests. Compared with
 species with many extant relatives, evolutionarily distinct species were
 extirpated at higher rates in both diversified and intensive agricultural
 systems. Forests are therefore essential for maintaining diversity across
 the tree of life, but diversified agricultural systems may help buffer
 against extreme loss of phylogenetic diversity.
description: 1254610supplementdata
DOI: 10.5061/dryad.92cr7
title: Data from: Hydrogen sulfide regulates cardiovascular function by influencing the excitability of subfornical organ neurons

description: Hydrogen sulfide (H2S), a gasotransmitter endogenously found in the
 central nervous system, has recently been suggested to act as a signalling
 molecule in the brain having beneficial effects on cardiovascular
 function. This study was thus undertaken to investigate the effect of NaHS
 (an H2S donor) in the subfornical organ (SFO), a central nervous system
 site important to blood pressure regulation. We used male Sprague-Dawley
 rats for both in vivo and in vitro experiments. We first used RT-PCR to
 confirm our previous microarray analyses showing that mRNAs for the
 enzymes required to produce H2S are expressed in the SFO. We then used
 microinjection techniques to investigate the physiological effects of NaHS
 in SFO, and found that NaHS microinjection (5 nmol) significantly
 increased blood pressure (mean AUC = 853.5±105.7 mmHg*s, n = 5). Further,
 we used patch-clamp electrophysiology and found that 97.8% (88 of 90) of
 neurons depolarized in response to NaHS. This response was found to be
 concentration dependent with an EC50 of 35.6 µM. Coupled with the
 depolarized membrane potential, we observed an overall increase in
 neuronal excitability using an analysis of rheobase and action potential
 firing patterns. This study has provided the first evidence of NaHS and
 thus H2S actions and their cellular correlates in SFO, implicating this
 brain area as a site where H2S may act to control blood pressure.
description: miSFOH2S for plos
 paperRaw data for blood
 pressure recordingsH2S SFO Data
 AnalysisData summarizing every
 recording for current clamp and rheobase analyses
DOI: 10.5061/dryad.8qp37
title: Data from: Natural genetic variation in Arabidopsis thaliana defense metabolism genes modulate field fitness

description: Natural populations persist in complex environments, where biotic
 stressors, such as pathogen and insect communities, fluctuate temporally
 and spatially. These shifting biotic pressures generate heterogeneous
 selective forces that can maintain standing natural variation within a
 species. To directly test if genes containing causal variation for the
 Arabidopsis thaliana defensive compounds, glucosinolates (GSL) control
 field fitness and are therefore subject to natural selection, we conducted
 a multi-year field trial using lines that vary in only specific causal
 genes. Interestingly, we found that variation in these naturally
 polymorphic GSL genes affected fitness in each of our environments but the
 pattern fluctuated such that highly fit genotypes in one trial displayed
 lower fitness in another and that no GSL genotype or genotypes
 consistently out-performed the others. This was true both across locations
 and within the same location across years. These results indicate that
 environmental heterogeneity may contribute to the maintenance of GSL
 variation observed within Arabidopsis thaliana.
description: Master File eLife Dryad
 Submission-FinalMaster File eLife Dryad
 Submission - FINAL.xlsx
DOI: 10.6073/pasta/3a839f2b05c017040043e95d092cd352
title: Decomposition and lignin content of wooden dowels deployed in a saltmarsh for 3, 5, or 7 years at Goat Island, North Inlet, Georgetown SC, 2017-2024.

description: Wooden dowels were used to examine organic matter decomposition in saltmarsh soils. Dowels were inserted to a depth of 45cm in control and fertilized marsh plots. They were harvested after 3, 5 or 7 years and sectioned into 5-cm segments. Weight loss of the dowel segments was used to quantify the fate of labile organic matter, while change in lignin content was used to quantify the fate of refractory organic matter.
DOI: 10.5061/dryad.v6qj0
title: Data from: Sexual selection in true fruit flies (Diptera: Tephritidae): transcriptome and experimental evidences for phytochemicals increasing male competitive ability

description: In male tephritid fruit flies of the genus Bactrocera, feeding on
 secondary plant compounds (sensu lato male lures = methyl eugenol,
 raspberry ketone and zingerone) increases male mating success. Ingested
 male lures alter the male pheromonal blend, normally making it more
 attractive to females and this is considered the primary mechanism for the
 enhanced mating success. However, the male lures raspberry ketone and
 zingerone are known, across a diverse range of other organisms, to be
 involved in increasing energy metabolism. If this also occurs in
 Bactrocera, then this may represent an additional benefit to males as
 courtship is metabolically expensive and lure feeding may increase a
 fly's short-term energy. We tested this hypothesis by performing
 comparative RNA-seq analysis between zingerone-fed and unfed males of
 Bactrocera tryoni. We also carried out behavioural assays with zingerone
 and cuelure-fed males to test if they became more active. RNA-seq analysis
 revealed, in zingerone-fed flies, up regulation of 3183 genes with
 homologues transcripts to those known to regulate inter-male aggression,
 pheromone synthesis, mating and accessory gland proteins, along with
 significant enrichment of several energy metabolic pathways and GO terms.
 Behavioural assays show significant increases in locomotor activity,
 weight reduction and successful mating after mounting; all direct/indirect
 measures of increased activity. These results suggest that feeding on
 lures leads to complex physiological changes, which result in more
 competitive males. These results do not negate the pheromone effect, but
 do strongly suggest that the phytochemical-induced sexual selection is
 governed by both female preference and male competitive mechanisms.
description: Full list of
 differentially expressed genes Kumaran.xlsThe data file contains
 complete list of transcripts that are differentially expressed in
 Queensland fruit fly, Bactrocera tryoni male flies fed on a phytochemical,
 zingerone.Full list of diff exp genes
 Kumaran.xls.xlsxRT-PCR fold change
 expressionFold change expression
 of candidate genes in zingerone-fed males when compared to unfed males of
 Bactrocera tryoniEnriched GO
 termsEnriched GO terms and
 their classes in Bactrocera tryoni transcriptomeEnriched metabolic
 pathwaysKEGG Metabolic pathways
 in Bactrocera tryoni transcriptomeWing beat
 frequencyRaw data on wing beat
 frequency, total time rested, mid-point crosses and number of calling
 boutsDistance
 crawledRaw data of total
 distance walked, resting time and mid-point crossesWeight
 lossRaw data on weight of
 the flies, weight loss. water content and metabolismsProportion of success to
 failure attemptsRaw data on
 proportionate successful mating attemptsRT-PCRRaw data on delta ct
 values for candidate genes
DOI: 10.5061/dryad.gn577
title: Data from: Paternal care in a fish: epigenetics and fitness enhancing effects on offspring anxiety

description: In many animals, including humans, interactions with caring parents can
 have long-lasting effects on offspring sensitivity to stressors. However,
 whether these parental effects impact offspring fitness in nature is often
 unclear. In addition, despite evidence that maternal care can influence
 offspring behaviour via epigenetic alterations to the genome, it remains
 unclear whether paternal care has similar effects. Here, we show in
 three-spined sticklebacks, a fish in which fathers are the sole provider
 of offspring care, that the direct care provided by fathers affects
 offspring anxiety and the potential for epigenetic alterations to the
 offspring genome. We find that families are differentially vulnerable to
 early stress and fathers can compensate for this differential sensitivity
 with the quality of their care. This variation in paternal care is also
 linked to the expression in offspring brains of a DNA methyltransferase
 (Dnmt3a) responsible for de novo methylation. We show that these paternal
 effects are potentially adaptive and anxious offspring are unlikely to
 survive an encounter with a predator. By supplying offspring care, fathers
 reduce offspring anxiety thereby increasing the survival of their
 offspring—not in the traditional sense through resource provisioning but
 through an epigenetic effect on offspring behavioural development.
description: McGhee&Bell_data1_offspring_behavior_dnmt3aThis is data on the behavior and gene expression of each individual stickleback offspring. These are data collected in the lab. See Readme file.McGhee&Bell_data2_father_averagesThis is data on the paternal care behavior, the average offspring behavior and gene expression for each father. This is data collected in the lab. See Readme file.McGhee&Bell_data3_survival_controltrtThis is data on each individual stickleback and each predator-prey interaction from the predation experiment. This is data collected in the lab. See Readme file.