cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.bvq83bk6p
title: Diversity and distribution across a large environmental and spatial gradient: evaluating the taxonomic and functional turnover, transitions and environmental drivers of benthic diatom communities

description: Aim: Global biodiversity loss has raised interest in understanding
 variation in diversity at different scales. Especially studies conducted
 across large spatial gradients are crucial, because they can increase
 perspectives on how ecological patterns change relative to environmental
 factors, and facilitate predictions of possible responses to environmental
 change. We explored the full extent of a brackish sea to test the
 hypotheses that (i) benthic communities are defined by species’ limited
 ranges, controlled by varying drivers along a large environmental
 gradient, (ii) the responses of taxonomic and functional community
 composition and turnover to the environmental gradient are different, thus
 highlighting the need to include both measures in ecological studies, and
 (iii) diversity reaches the minimum at intermediate salinities (Remane
 curve) due to the low adaptation of freshwater and marine species.
 Location: A large environmental and spatial gradient spanning the entire
 Swedish coastline (ca. 2300 km; salinity 1.2-27.6), the Baltic Sea Time
 period: August 2018 Major taxa studied: Benthic diatoms Methods: We
 assessed environmental drivers for the communities and calculated the
 taxonomic and functional alpha and beta diversity along the gradient. We
 also compared the taxonomic and functional composition and diversity of
 communities between areas with different salinity. Results: We found
 support for the hypothesis of limited species ranges, as taxonomic beta
 diversity, mainly induced by changes in salinity and climate, was high,
 whereas functional beta diversity remained considerably lower, and the
 composition and diversity of communities, as well as environmental drivers
 controlling the communities, differed between regions with different
 salinity. The lowest taxonomic diversity was found at intermediate
 salinities of 5-6. Main conclusions: These findings advance understanding
 of large-scale patterns of benthic diversity, emphasize the importance of
 large gradient studies for a better understanding of general ecological
 patterns, and highlight the vulnerability of brackish water ecosystems as
 ecologically important tipping point realms.
description: The dataset was collected from the freshwater-marine gradient
 along the Swedish coastline in northern Europe. The dataset covers ca.
 2300 km of coastline. Benthic diatoms were collected from littoral
 stones.
DOI: 10.5061/dryad.rv15dv465
title: Data from: Queuine is a nutritional regulator of Entamoeba histolytica response to oxidative stress and a virulence attenuator

description: Queuosine is a naturally occurring modified ribonucleoside found in the
 first position of the anticodon of the transfer RNAs for Asp, Asn, His and
 Tyr. Eukaryotes lack pathways to synthesize queuine, the nucleobase
 precursor to queuosine, and must obtain it from diet or gut microbiota.
 Here we describe the effects of queuine on the physiology of the
 eukaryotic parasite, Entamoeba histolytica, the causative agent of amebic
 dysentery. Queuine is efficiently incorporated into E. histolytica tRNAs
 by a tRNA-guanine transglycosylase (EhTGT) and this incorporation
 stimulates the methylation of C38 in tRNAAspGUC.  Queuine
 protects the parasite against oxidative stress (OS) and antagonizes the
 negative effect that oxidation has on translation by inducing the
 expression of genes involved in OS response, such as heat shock protein 70
 (Hsp 70), antioxidant enzymes, and enzymes involved in DNA repair. On the
 other hand, queuine impairs E. histolytica virulence by downregulating the
 expression of genes previously associated with virulence, including
 cysteine proteases, cytoskeletal proteins, and small GTPases. Silencing of
 EhTGT prevents incorporation of queuine into tRNAs and strongly impairs
 methylation of C38 in tRNAAspGUC, parasite growth, resistance to OS, and
 cytopathic activity. Overall, our data reveal that queuine plays a dual
 role in promoting OS resistance and reducing parasite virulence.
DOI: 10.5068/d11m3q
title: Identification and selection of optimal reference genes for qPCR-based gene expression analysis in Fucus distichus under various abiotic stresses

description: Quantitative gene expression analysis is an important tool in the
 scientist’s belt. The identification of evenly expressed reference genes
 is necessary for accurate quantitative gene expression analysis, whether
 by traditional RT-PCR (reverse-transcription polymerase chain reaction) or
 by qRT-PCR (quantitative real-time PCR; qPCR). In the Stramenopiles (the
 major line of eukaryotes that includes brown algae) there is a noted lack
 of known reference genes for such studies, largely due to the absence of
 available molecular tools.  Here we present a set of nine
 reference genes (Elongation Factor 1 alpha (EF1A), Elongation Factor 2
 alpha (EF2A), Elongation Factor 1 beta (EF1B), 14-3-3 Protein, Ubiquitin
 Conjugating Enzyme (UBCE2), Glyceraldehyde-3-phosphate Dehydrogenase
 (GAPDH), Actin Related Protein Complex (ARP2/3), Ribosomal Protein (40s;
 S23), and Actin) for the brown alga Fucus distichus. These reference genes
 were tested on adult sporophytes across six abiotic stress conditions
 (desiccation, light and temperature modification, hormone addition,
 pollutant exposure, nutrient addition, and wounding). Suitability of these
 genes as reference genes was quantitatively evaluated across conditions
 using standard methods and the majority of the tested genes were evaluated
 favorably. However, we show that normalization genes should be chosen on a
 condition-by-condition basis. We provide a recommendation that at least
 two reference genes be used per experiment, a list of recommended pairs
 for the conditions tested here, and a procedure for identifying a suitable
 set for an experimenter’s unique design. With the recent expansion of
 interest in brown algal biology and accompanied molecular tools
 development, the variety of experimental conditions tested here makes this
 study a valuable resource for future work in basic biology and
 understanding stress responses in the brown algal lineage.
description: See README.
DOI: 10.5061/dryad.2rbnzs7m0
title: Latitudinal gradients in population growth do not reflect demographic responses to climate

description: Spatial gradients in population growth, such as across latitudinal or
 elevational gradients, are often assumed to primarily be driven by
 variation in climate, and are frequently used to infer species’ responses
 to climate change. Here, we use a novel demographic, mixed model approach
 to dissect the contributions of climate variables vs. other latitudinal or
 local site effects on spatiotemporal variation in population performance
 in three perennial bunchgrasses. For all three species, we find that
 performance of local populations decreases with warmer and drier
 conditions, despite latitudinal trends of decreasing population growth
 towards the cooler and wetter northern portion of each species’ range.
 Thus, latitudinal gradients in performance are not predictive of either
 local or species-wide responses to climate. This pattern could be common,
 as many environmental drivers, such as habitat quality or species’
 interactions, are likely to vary with latitude or elevation, and thus
 influence or oppose climate responses.
description: Demographic data were collected by monitoring the size, survival,
 growth, and reproduction of three perennial bunchgrasses at multiple sites
 from southern Oregon to Washington from 2015-2018.
description: Missing values are indicated as 'NA' in the data files.
 ReadMe tabs in each file include descriptions of the variables. Details of
 the methods are given in the published paper and supplemental
 materials.
DOI: 10.5061/dryad.qz612jmcj
title: Aquatic beetles influence colonization of disparate taxa in small lentic systems

description: Structure of natural communities is shaped by both abiotic characteristics
 and by the ongoing processes of community assembly. Important to this
 process are the habitat selection behaviors and subsequent survival of
 colonists, both in the context of temporal changes in the abiotic
 characteristics and priority effects driven by earlier colonists. Aquatic
 beetles are prevalent in temporary freshwater systems, form speciose
 assemblages, and are often early colonists of temporary ponds. While
 beetles have the potential to influence community structure through
 post-colonization interactions (predation and competition), our goal was
 to determine whether the presence of beetle assemblages (versus patches
 without beetles) influence the colonization and oviposition of a diverse
 group of animals in a naturally-colonized experimental landscape. We
 established mesocosms that either contained existing beetle assemblages or
 contained no beetles and assessed abundances of subsequent colonists.
 Treefrogs, Hyla chrysoscelis, and mosquitoes, Culex restuans, both
 deposited fewer eggs in patches containing beetle assemblages, while two
 beetles, Copelatus glyphicus and Paracymus, colonized those patches at
 lower rates. One beetle, Helophorus linearis, colonized patches containing
 beetle assemblages at higher rates, while two beetles, Berosus infuscatus
 and Tropisternus lateralis, exhibited no colonization differences between
 treatments. Overall, there were no differences in the assemblage structure
 or richness of beetles that colonized patches. Our results illustrate the
 importance of species-specific habitat selection behavior in determining
 the species composition of habitat patches, while emphasizing the role of
 priority effects in influencing patterns of community assembly. Habitat
 selection in response to abiotic and biotic characteristics of habitat
 patches can potentially create greater spatiotemporal niche separation
 among the numerous, often closely-related species (phylogenetically and
 trophically), that can be simultaneously found in similar patches across
 landscapes.
description: Data are sums across entire duration of experiment.
description: See README file.
DOI: 10.5061/dryad.5hqbzkh42
title: Data and Code for: Isotopic Niche Size of Coregonus artedi (sensu lato) Increases in the Presence of Mysis diluviana, Expanded Habitat Use and Phenotypic Diversity

description: Post-glacial colonization of lakes in Algonquin Park, Ontario, Canada
 resulted in food webs with cisco (Coregonus artedi sensu lato) and either
 Mysis diluviana or Chaoborus spp. as the dominant diel migrator. Mysis as
 prey, its diel movements and benthic occupancy, are hypothesized to be key
 elements of ecological opportunity for cisco diversity in the Laurentian
 Great Lakes.  If correct, the hypothesis strongly implies that
 lakes with Mysis would have greater trophic niche size and drive greater
 adaptive radiation of cisco forms relative to lakes without Mysis. The
 dichotomy in diel migrator in Algonquin Park lakes was an opportunity to
 assess the isotopic niche size of cisco (δ15N and δ13C) and determine if
 niche size expands with Mysis presence. We found the presence of Mysis is
 necessary to expand isotopic niche size in our study lakes. The use of
 habitats not typically associated with the ancestral form of cisco (e.g.,
 benthic habitats) and phenotypic diversity (blackfin and cisco) also
 continue to expand niche size in Mysis-based food webs. Partial ecological
 speciation based on a large niche space appears to be present in one lake
 (Cauchon Lake) where use of alternative habitats is the only real
 difference in cisco. The presence of blackfin expands niche space in Cedar
 and Radiant Lakes. This was not matched in Hogan Lake where niche space
 was relatively smaller with similar forms. Possible reasons for this
 discrepancy may be related to the asymmetric basin of Hogan Lake and
 whether the two forms overlap during cool and cold-water periods of the
 annual temperature cycle. By comparing trophic niche size among lakes with
 and without Mysis we conclude that Mysis provides a key ecological
 opportunity for cisco diversity in our study lakes and likely more widely.
description: Lake surveys in Algonquin Provincial Park were conducted in lakes
 with and without Mysis diluviana, a glacial relict species signifying
 pro-glacial lake inundation over 10,000 years ago. Surveys were conducted
 with standardized gillnets following a depth stratified randomized design.
 Cisco muscle tissue was analyzed for trophic
 isotopes (δ<sup>15</sup>N and δ<sup>13</sup>C).
 Cisco were distinguished based on whether they were caught in pelagic nets
 (ancestral habitat) or bottom nets as well as based on morphogical
 variation. The datasets included here are summaries of the data in Figures
 in Ridgway et al (2020). This also includes the morphologial data from
 Piette-Lauziere et al (2019).
description: The datasets and R code pertain to figures in Ridgway et al
 (2020). Data are in .csv files and data labels precede R code for each
 figure.
DOI: 10.5068/d1wx0f
title: Intracrater Terminal Dune Fields in Arabia Terra, Mars

description: Craters are the most prevalent basins and potential depo-centers of
 sediment on Mars. Within these craters and extending from them, terminal
 dune fields and wind streaks are abundant, indicating active sediment
 transport and providing a way to study how wind and sediment interact with
 crater topography. Here, we explore the role of craters as both sources
 and sinks in the modern martian sedimentary cycle. Our results show that
 craters with low albedo wind streaks (indicative of sediment transport out
 of a crater and downwind dust removal) have lower crater wall slopes (9.4°
 ±5.5°) compared to craters without wind streaks (17° ±5.8°). We interpret
 that crater wall slopes play a dominant role in whether sediment is
 transported out of a crater basin, and infer, from measurements of craters
 on Mars, that a crater transitions from being a net sediment sink to a net
 sediment source when crater wall slopes decrease to ~15°. This threshold
 value is consistent with limits of bedform climb observed on Earth and
 elsewhere on Mars.
description: The enclosed table contains data collected for the 116 craters in
 Arabia Terra, Mars that are referred to in this work. All included craters
 are &gt;10 km in diameter and were selected based on terminal dune
 fields observed in their interior. Crater wall slopes were measured
 downwind of each terminal dune field using elevation data from the Mars
 Orbiter Laser Altimeter (MOLA) 128 ppd interpolated elevation map. The
 slope of each crater wall was measured at the closest location downwind of
 each terminal dune field from a wind-parallel elevation transect
 originating at the rim of the crater and ending at the dune field. The
 depth of the crater was estimated by subtracting the elevation of the
 downwind margin of the dune field from the elevation of the crater rim
 measured downwind of the dune field. Wind streak type was determined by
 observing the albedo contrast between the wind streak (if present) and the
 surrounding landscape. For more information on methods and data analysis,
 see the main text of this publication.
DOI: 10.5061/dryad.n2z34tmv1
title: Associations between socio-environmental factors and landscape-scale biodiversity recovery in naturally regenerating tropical and subtropical forests

description: Natural regeneration is key for large-scale forest restoration, yet it may
 lead to different biodiversity outcomes depending on socio-environmental
 context. We combined the results of a global meta-analysis to quantify how
 biodiversity recovery in naturally regenerating forests deviates from
 biodiversity values in reference old-growth forests, with structural
 equation modeling, to identify direct and indirect associations between
 socioeconomic, biophysical and ecological factors and deviation in
 biodiversity recovery at a landscape scale. Low deviation within a
 landscape means higher chances of multiple sites in naturally regenerating
 forests successfully recovering biodiversity compared to reference
 forests. Deviation in biodiversity recovery was directly negatively
 associated with the percentage of cropland, forest cover, and positively
 associated with the percentage of urban areas in the surrounding
 landscape. These three factors mediated the indirect associations with
 rural population size, recent gross deforestation, time since natural
 regeneration started, mean annual temperature, mean annual water deficit,
 road density, land opportunity cost, percentage cover of strictly
 protected forest areas, and human population variation in the surrounding
 landscape. We suggest that natural forest restoration should be
 prioritized in landscapes with both low socioeconomic pressures on land
 use conversion to pasturelands and urban areas, and high percentage of
 forest cover.
description: This is available in the methods section of this paper.
DOI: 10.5061/dryad.8gtht76mr
title: Silence is sexy: Soundscape complexity alters mate choice in túngara frogs

description: Many animals acoustically communicate in large aggregations, producing
 biotic soundscapes. In turn, these natural soundscapes can influence the
 efficacy of animal communication, yet little is known about how variation
 in soundscape interferes with animals that communicate acoustically. We
 quantified this variation by analyzing natural soundscapes with the
 mid-frequency cover index and by measuring the frequency ranges and call
 rates of the most common acoustically communicating species. We then
 tested female mate choice in the túngara frog (Physalaemus pustulosus) in
 varying types of background chorus noise. We broadcast two natural túngara
 frog calls as a stimulus and altered the densities (duty cycles) of
 natural calls from conspecifics and heterospecifics to form the different
 types of chorus noise. During both conspecific and heterospecific chorus
 noise treatments, females demonstrated similar preferences for
 advertisement calls at low and mid noise densities but failed to express a
 preference in the presence of high noise density. Our data also suggest
 that nights with high densities of chorus noise from conspecifics and
 heterospecifics are common in some breeding ponds, and on nights with high
 noise density, the soundscape plays an important role diminishing the
 accuracy of female decision-making.
description: Soundscape data was collected in Panama in 2018 and 2019 at two
 sites: Santa Cruz and Ocelot ponds. Frog choruses were recorded using Song
 Meter SM3s. Recordings were largely processed by inputting files into R
 and running QUT Ecoacoustics Analysis Programs (Towsey M, Truskinger A,
 Cottman-Fields M, Roe P. 2018. Ecoacoustics Audio Analysis Software
 v18.03.0.41 (Version v18.03.0.41). Zenodo. http://doi.org/10.5281/zenodo.1188744). Behavioral data was collected by running phonotaxis experiments in Panama in 2019. Data were recorded during trials, and videos of trials were saved for review.
description: Due to the nature of sound and video files taking up a lot of
 storage space, these have not been included. However, they are available
 upon request from the first author.
DOI: 10.5061/dryad.98sf7m0gv
title: Data from: Population responses to a historic drought across the range of the common monkeyflower (Mimulus guttatus)

description: This dataset contains both metadata and phenotype data for both of the
 resurrections experiments described in Kooyers et al. 2020. Datasets are
 uploaded as .csv files. Please read the readme files for descriptions of
 the data in each .csv file.
DOI: 10.25338/b8703s
title: Data and Supplemental Material from: A multifunction trade-off has contrasting effects on the evolution of form and function

description: Trade-offs caused by the use of an anatomical apparatus for more than one
 function are thought to be an important constraint on evolution. However,
 whether multifunctionality suppresses diversification of biomechanical
 systems is challenged by recent literature showing that traits more
 closely tied to trade-offs evolve more rapidly. We contrast the
 evolutionary dynamics of feeding mechanics and morphology between fishes
 that exclusively capture prey with suction and multifunctional species
 that augment this mechanism with biting behaviors to remove attached
 benthic prey. Diversification of feeding kinematic traits was, on average,
 over 13.5 times faster in suction feeders, consistent with constraint on
 biters due to mechanical trade-offs between biting and suction
 performance. Surprisingly, we found that the evolution of morphology
 contrasts directly with these differences in kinematic evolution, with
 significantly faster rates of evolution of head shape in biters. This
 system provides clear support for an often postulated, but rarely
 confirmed prediction that multifunctionality stifles functional
 diversification, while also illustrating the sometimes weak relationship
 between form and function.
description: We recommend removing shapes associated with Dactylopus
 dactylopus.
DOI: 10.5281/zenodo.18395848
title: Fair Detective 4.2v
DOI: 10.5281/zenodo.18395847
title: Fair Detective 4.2v
DOI: 10.5061/dryad.ksn02v72d
title: A survey of soil bacterial diversity across a Northeast Louisiana federal wildlife refuge

description: Soil microbial communities represent complex biological systems
 responsible for many ecosystem functions. Differences in these systems are
 attributable to a variety of factors, including soil series, plant
 communities, and anthropogenic land use. We assessed the microbial
 diversity at 30 sites covering two ecoregions, three land usages, and
 seven soil series at Black Bayou Lake National Wildlife Refuge, an over 21
 km2 site located north of Monroe, Louisiana. Based on an average of over
 47,000 amplified sequence variants per site, we found no significant
 difference in alpha diversity measures across groups but did find
 significant differences in beta diversity between ecoregions and the sites
 and soil series located within them. Bacteria associated with agricultural
 practices were significantly more abundant at the Ouachita River Backswamp
 sites, reflecting the historical land use of these areas. We found no
 significant differences between a managed prairie fragment and the
 Backswamp sites, suggesting that the microbial communities have not
 changed over twenty years post-restoration. Our data provide meaningful
 baseline measure of bacterial community diversity and abundance for the
 refuge, and highlight the necessity to manage these valuable soil
 resources in conjunction with the plant and animal communities.
description: Soil was collected at 30 sites at Black Bayou Lake NWR near
 Monroe, Louisiana. DNA extraction was carried out using the PowerSoil DNA
 isolation kit (Mo Bio Laboratories) according to manufacturer’s
 directions. DNA samples were sent to MrDNALab (Shallowater, Texas) where
 the 16S rDNA gene variable region V4 was PCR amplified using the 515/806
 primer pair (Caporaso et al. 2011). Sequencing was performed on an Ion
 Torrent PGM (Thermo Fisher), and data were de-noised and depleted of
 barcodes, sequences less than 150 bp, and homopolymer runs over 6 bp using
 a proprietary pipeline.
description: FASTA file of ASVs with the site number in each sequence header.
 Sequences have not been dereplicated nor filtered.