cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.mpg4f4qwx
title: Riverscape properties contribute to the origin and structure of a hybrid zone in a Neotropical freshwater fish

description: Understanding the structure of hybrid zones provides valuable insights
 about species boundaries and speciation, such as the evolution of barriers
 to gene flow and the strength of selection. In river networks, studying
 evolutionary processes in hybrid zones can be especially challenging,
 given the influence of past and current river properties along with
 biological species-specific traits. Here, we suggest that a natural hybrid
 zone between two divergent lineages of the sexually dimorphic Neotropical
 fish Nematocharax venustus was probably established by secondary contact
 as a result of a river capture event between the Contas and Pardo river
 basins. This putative river capture is supported by hydrogeological
 evidence of elbows of capture, wind gaps, and geological faults. The
 morphological (color pattern) and genetic (mtDNA and RADseq) variation
 reveal a clinal transition between parental lineages along the main river,
 with predominance of F2 hybrids at the centre of the hybrid zone, absence
 of early generation backcrosses, and different levels of hybridization in
 the tributaries. We highlight that different sources of information are
 crucial for understanding how the riverscape spatial history influences
 the connectivity between and within rivers systems and, consequently, the
 dynamics of gene flow between freshwater lineages/species.
description: Four folders:
 <strong>(1)
 faststructure and gghybrid: </strong>input files for fastSTRUCTURE
 (.str) and gghybrid (.csv) analyses. The gghybrid file contains two
 columns to the left of the marker columns, which correspond to the
 individual references and the sample population (see Figure 1 in Barreto
 et al. 2020). <strong>(2)
 parallelnewhybrid: </strong>contains a file in the NewHybrids format
 and its associated individuals file. Two other copies of the genotype file
 were used to run parallelnewhybrid. <strong>(3) hzar
 morphological data:</strong> input files for HZAR cline analyses
 using the caudal peduncle and eye coloration marks. <strong>(4) hzar genomic
 data:</strong> input files for HZAR cline analyses using the mtDNA
 haplotypes, the ancestry coefficients estimated in fastSTRUCTURE (K = 2),
 and the 99 putatively unlinked SNPs (i.e., one SNP per locus) from which
 we estimated cline parameter values independently.
DOI: 10.5061/dryad.wm37pvmkb
title: Data from: A cross-kingdom conserved ER-phagy receptor maintains endoplasmic reticulum homeostasis during stress

description: Eukaryotes have evolved various quality control mechanisms to promote
 proteostasis in the ER. Selective removal of certain ER domains via
 autophagy (termed as ER-phagy) has emerged as a major quality control
 mechanism. However, the degree to which ER-phagy is employed by other
 branches of ER-quality control remains largely elusive.  Here, we
 identify a cytosolic protein, C53, that is specifically recruited to
 autophagosomes during ER-stress, in both plant and mammalian cells. C53
 interacts with ATG8 via a distinct binding epitope, featuring a shuffled
 ATG8 interacting motif (sAIM). C53 senses proteotoxic stress in the ER
 lumen by forming a tripartite receptor complex with the ER-associated
 ufmylation ligase UFL1 and its membrane adaptor DDRGK1. The
 C53/UFL1/DDRGK1 receptor complex is activated by stalled ribosomes and
 induces the degradation of internal or passenger proteins in the ER.
 Consistently, the C53 receptor complex and ufmylation mutants are highly
 susceptible to ER stress. Thus, C53 forms an ancient quality control
 pathway that bridges selective autophagy with ribosome-associated quality
 control in the ER.
description: Please see materials and methods section of the associated
 manuscript.
description: This is the source data linked to the manuscript. All the raw
 data are labelled with the numbers of the corresponding figures. I have
 now added a readme file explaining this.
DOI: 10.5061/dryad.05qfttf14
title: Genomic insights into Raffaelea lauricola pathogenesis

description: Laurel wilt caused by Raffaelea lauricola is a lethal vascular
 disease of North American members of the Lauraceae plant family. This
 fungus and its primary ambrosia beetle vector Xyleborus glabratus
 originated from Asia; however, there is no report of laurel wilt causing
 widespread mortality on native Lauraceae trees in Asia. To gain insight
 into why R. lauricola is a tree-killing plant pathogen in North America,
 we generated and compared high quality draft genome assemblies of R.
 lauricola and its closely related non-pathogenic species R. aguacate.
 Relative to R. aguacate, the R. lauricola genome uniquely encodes several
 small-secreted proteins that are associated with virulence in other
 pathogens and is enriched in secondary metabolite biosynthetic clusters,
 particularly polyketide synthase (PKS), non-ribosomal peptide synthetase
 (NRPS) and PKS-NRPS anchored gene clusters. The two species also exhibit
 significant differences in secreted proteins including CAZymes that are
 associated with polysaccharide binding including the chitin binding CBM50
 (LysM) domain. Transcriptomic comparisons of inoculated redbay trees and
 in vitro-grown fungal cultures further revealed a number of secreted
 protein genes, secondary metabolite clusters and alternative sulfur uptake
 and assimilation pathways that are coordinately up-regulated during
 infection. Through these comparative analyses we have identified potential
 adaptations of R. lauricola that may enable it to colonize and cause
 disease on susceptible hosts. How these adaptations have interacted with
 co-evolved hosts in Asia, where little to no disease occurs, and
 non-co-evolved hosts in North America, where lethal wilt occurs, requires
 additional functional analysis of genes and pathways.
description: These data represent whole genome
 shotgun assemblies and gene predictions of <i>Raffaelea
 lauricola</i> RL4 (CBS 127349) and <i>R.</i>
 <i>aguacate</i> PL1004 (CBS 141672) . Sequencing was performed
 on the Ion Torrent Personnel Genome machine (PGM) and by Illumina Hiseq
 technology. Ion torrent reads were assembled using the de Bruijn algorithm
 implemented in the CLC Genomics Workbench version 5.0.1, MIRA 4, and
 Spades 3.7.1. The Illumina reads were assembled using the ALLPATHS-LG
 assembler. Assemblies generated from Ion Torrent and Illumina reads were
 merged using Metassembler to achieve final assemblies. These Whole Genome
 Shotgun projects have been deposited at DDBJ/ENA/GenBank under accessions
 JACBXF000000000 and JACCPH000000000.  
 <i>Raffaelea</i> <i>spp.</i> genes were predicted
 through two cycles of the Maker pipeline using the Uniprot reveiwed
 protein database for protein evidence, and transcripts from PASA pipeline
 as additional EST evidence for gene prediction. Data
 files with "RL4" designations are from
 <i>Raffaelea lauricola</i> RL4 (CBS
 127349) Data files with "Rsp272"
 designations are genetrated from <i>Raffaelea
 aguacate</i> PL1004 (CBS 141672)
DOI: 10.5061/dryad.fttdz08qp
title: Water availability drives fine root dynamics in a Eucalyptus woodland under elevated atmospheric CO2 concentration

description: Fine roots are a key component of carbon and nutrient dynamics in forest
 ecosystems. Rising atmospheric [CO2] (eCO2) is likely to alter the
 production and activity of fine roots, with important consequences for
 forest carbon storage. Yet empirical evidence of the role of eCO2 in
 driving root dynamics in low-nutrient forested ecosystems is limited,
 particularly for grassy woodlands, an ecosystem type of global importance.
 We sampled fine roots across seasons over a two-year period to examine the
 effects of eCO2 on their biomass, production, turnover and functional
 traits in a native mature grassy Eucalyptus woodland in eastern Australia
 (EucFACE). Fine root biomass, production and turnover varied greatly
 through time, increasing as soil water content declined. Despite a lack of
 persistent effects of eCO2 on fine root biomass, production or turnover
 across the two-year sampling period, we found enhanced production pulses
 under eCO2 between 10-30 cm soil depth. These eCO2-driven production
 pulses were associated with large changes in abiotic conditions. In
 addition, eCO2 led to greater carbon and phosphorus concentrations in fine
 roots and increased root diameter, but no detectable effects on other
 morphological traits. Synthesis. We found minor quantitative effects of
 eCO2 on fine root biomass dynamics that were largely driven by temporal
 variations in soil water availability. Our results suggest that in this
 mature grassy woodland, and perhaps also in other similar forested
 ecosystem types characterized by low phosphorus content in the soil, eCO2
 effects are small and transient. This suggests limited belowground fine
 root productivity responses to rising atmospheric CO2 concentrations and,
 thus, perhaps also a limited ability of these systems to mitigate climate
 change through belowground mechanisms.
description: The methods used to collect the data are detailed in the article.
 Metadata and units for each variable are given in the dataset
 itself. 
description: Any missing values are time periods data was not collected.
DOI: 10.5061/dryad.w9ghx3fmp
title: The genera Helvella and Dissingia (Ascomycota: Pezizomycetes) in Europe – Notes on species from Spain

description: Phylogenetic analyses of 115 newly collected Helvella specimens from Spain
 using three genetic markers [heat shock protein 90 (hsp), RNA polymerase
 II second largest subunit (rpb2) and the nuclear large subunit ribosomal
 DNA (LSU)] confirm the assignment of the Spanish collections to one
 Dissingia and 30 Helvella species. The analyses were supplemented with an
 additional sample of 65 Spanish and extralimital Helvella specimens from
 the fungaria of Oslo (O), Trondheim (TRH), Copenhagen (C), Uppsala (UPS),
 Stockholm (S) and Venice (MCVE). Nine species are described as new, i.e.
 Helvella fuscolacunosa, H. hispanica, H. iberica, H. inexpectata, H.
 neopallescens, H. phlebophoroides, H. poculiformis, H. retinervis, and H.
 terricola. We present photographs of a selection of fresh specimens and
 provide descriptions of all species of this diverse South European
 Mediterranean element of the genera in Europe.
description: This is a concatenated alignment of three molecular markers and
 125 Helvella individuals. bp 1-280 is HSP
 bp 281-626 is RPB2 bp 627-1163 is
 LSU See publication for further details about genbank
 accession numbers and the origin of individuals
DOI: 10.5061/dryad.59zw3r25d
title: Data from: Evidence for normal novel object recognition abilities in developmental prosopagnosia

description: The issue of the face specificity of recognition deficits in developmental
 prosopagnosia (DP) is fundamental to the organisation of high-level visual
 memory and has been increasingly debated in recent years. Previous DP
 investigations have found some evidence of object recognition impairments,
 but have almost exclusively used familiar objects (e.g., cars), where
 performance may depend on acquired object-specific experience and related
 visual expertise. An object recognition test not influenced by experience
 could provide a better, less contaminated measure of DPs’ object
 recognition abilities. To investigate this, in the current study we tested
 30 DPs and 30 matched controls on a novel object memory test (NOMT
 Ziggerins) and the Cambridge Face Memory Test (CFMT). DPs were impaired on
 the CFMT but showed no differences in accuracy or reaction times to
 controls on the NOMT. We found similar results when comparing DPs to a
 larger sample of 274 web-based controls. Additional individual analyses
 demonstrated that the rates of object recognition impairment in DPs did
 not differ from the rate of impairment in either control group. Together,
 these results demonstrate unimpaired object recognition in DPs for a class
 of novel objects that serves as a powerful index for broader novel object
 recognition capacity.
description: This dataset was collected from participants online and in the
 Boston area. Developmental prosopagnosics and in-lab controls were
 recruited from a database of previous DP participants in the Boston area
 (Dr. Matthew Peterson, MIT; Dr. Brad Duchaine, Dartmouth College), and web
 controls were acquired from TestMyBrain.org with the help of Dr. Jeremy
 Wilmer (Richler, Wilmer, and Gauthier, 2017). All in-lab participants were
 tested on either a Lenovo laptop (34.5 x 19.5 cm display, 1920 x 1080
 pixels, 60 Hz) or a Sony Vaio (34.29 x 19.05 cm, 1920 x 1080 pixels, 59
 Hz). Data was analyzed using IBM SPSS Statistics for Mac, version
 25.0.0.2. 
description: Some participants declined to provide their age, gender, or
 education level. DP participants acquired from Drs. Matthew Peterson or
 Brad Duchaine may be missing reaction time data.
DOI: 10.5061/dryad.pc866t1m6
title: Data from: Species richness and redundancy promote persistence of exploited mutualisms in yeast

description: Mutualisms, or reciprocally beneficial interspecific interactions,
 constitute the foundation of many ecological communities and agricultural
 systems. Mutualisms come in different forms, from pairwise interactions to
 extremely diverse communities, and they are continually challenged with
 exploitation by non-mutualistic community members (exploiters). Thus,
 understanding how mutualisms persist remains an essential question in
 ecology. Theory suggests that high species richness and functional
 redundancy could promote mutualism persistence in complex mutualistic
 communities. Using a yeast system (Saccharomyces cerevisiae), we
 experimentally show that communities with the greatest mutualist richness
 and functional redundancy are nearly two times more likely to survive
 exploitation than are simple communities. Persistence increased because
 diverse communities were better able to mitigate the negative effects of
 competition with exploiters. Thus, large mutualistic networks may be
 inherently buffered from exploitation.
description: See supplementary materials for details on methods.
description: Community datasheets were produced following a custom script that
 summarized the strain data. Scripts can be provided by request.
DOI: 10.5061/dryad.0p2ngf1z1
title: The diversity and function of sourdough starter microbiomes

description: Humans have relied on sourdough starter microbial communities to make
 leavened bread for thousands of years, but only a small fraction of global
 sourdough biodiversity has been characterized. Working with a
 citizen-scientist network of bread bakers, we determined the microbial
 diversity of 500 sourdough starters from four continents. In sharp
 contrast with widespread assumptions, we found little evidence for
 biogeographic patterns in starter communities. Strong co-occurrence
 patterns observed in situ and recreated in vitro demonstrate that
 microbial interactions shape sourdough community structure. Variation in
 dough rise rates and aromas were largely explained by acetic acid
 bacteria, a mostly overlooked group of sourdough microbes. Our study
 reveals the full extent of microbial diversity in an ancient fermented
 food across diverse cultural and geographic backgrounds.
DOI: 10.5061/dryad.18931zcv7
title: Lack of head sparing following third-trimester caloric restriction among Tanzanian Maasai

description: The reduction of food intake during pregnancy is part of many cultural and
 religious traditions around the world. The impact of such practices on
 fetal growth and development are poorly understood. Here, we examined the
 patterns of diet intake among Maasai pregnant women and assessed their
 effect on newborn morphometrics. We recruited 141 mother-infant pairs from
 Ngorongoro Conservation Area (NCA) in Northern Tanzania and quantified
 dietary intake and changes in maternal diet during pregnancy. We obtained
 measurements of body weight (BW) and head circumference (HC) at birth. We
 found that Maasai women significantly reduced their dietary intake during
 the third trimester, going from an average of 1601 kcal/day during the
 first two trimesters to 799 kcal/day in the final trimester. The greatest
 proportion of nutrient reduction was in carbohydrates. Overall, 40% of HC
 Z-scores of the NCA sample were more than 2 standard deviations below the
 WHO standard. Nearly a third of neonates classify as low birth weight
 (&lt; 2500g). HC was smaller relative to BW in this cohort than
 predicted using the WHO standard. This contrasts markedly to a Tanzanian
 birth cohort obtained at the same time in an urban context in which only
 12% of infants exhibited low weight, only two individuals had HC Z-scores
 &lt; 2 and HC’s relative to birth weight were larger than predicted
 using the WHO standards. The surprising lack of head sparing in the NCA
 cohort suggests that the impact of third trimester malnutrition bears
 further investigation in both animal models and human populations,
 especially as low HC is negatively associated with long term health
 outcomes.
DOI: 10.5061/dryad.sqv9s4n23
title: Quantifying shell outline variability in extant and fossil Laqueus (Brachiopoda: Terebratulida): are outlines good proxies for long-looped brachidial morphology and can they help us characterize species?

description: Extant and extinct terebratulide brachiopod species have been defined
 primarily on the basis of morphology. What is the fidelity of
 morphological species to biological species? And how can we test this
 fidelity with fossils? Taxonomically and phylogenetically, the most
 informative internal feature in the brachiopod suborder Terebratellidina
 is the geometrically complex long-looped brachidium, which, given their
 fragile nature, are not commonly preserved in the fossil record. In their
 absence, it is essential to test other sources of morphological data when
 trying to recognize and identify species. We analyzed valve outlines and
 brachidia in the genus Laqueus to explore the utility of
 shell shape in discriminating extant and fossil species. Using geometric
 morphometric methods, we quantified valve outline variability using
 elliptical Fourier methods and tested whether long-looped brachidial
 morphology correlates with shell outline shape. We then built
 classification models based on machine learning algorithms using outlines
 as shape variables to predict fossil species’ identities. Our results
 demonstrate that valve outline shape is significantly correlated with
 long-looped brachidial shape and that even relatively simple outlines are
 sufficiently morphologically distinct to enable
 extant Laqueus species to be identified, validating
 current taxonomic assignments. These are encouraging results for the study
 and delimitation of fossil terebratulide species, and their recognition as
 biological species. In addition, machine learning algorithms can be
 successfully applied to help solve species recognition and delimitation
 problems in paleontology, especially when morphology can be characterized
 quantitatively and analyzed statistically.
DOI: 10.15468/dl.c4j2d9
title: Occurrence Download

description: A dataset containing 28230 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((67.36802 22.6592,75.88092 6.51988,79.1288 8.79705,75.36328 21.5387,73.67215 24.99448,67.36802 22.6592))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Squamata"
 ]
}

 The dataset includes 28230 records from 88 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002498-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.5mkkwh73x
title: Bergmann's rule is followed at multiple stages of post-embryonic development in a long-distance migratory songbird

description: Aim: We assessed the presence of Bergmann’s rule in a model migratory
 species across all life stages on their breeding grounds. We then compared
 historic and contemporary egg sizes to understand if the biogeographic
 patterns during this developmental life stage have changed over time.
 Location: Eastern North America. Time period: 1865 to 2019. Major taxa:
 Prothonotary warbler, Protonotaria citrea Methods: We measured the size of
 eggs, young and old nestlings, and adults (of two age classes and both
 sexes) from across the full latitudinal breeding range of the species to
 assess the relationship between latitude and body size across several life
 stages in this altricial migratory species. We also assessed potential
 changes in this pattern over time by comparing historic eggs (museum
 specimens collected across a similarly broad latitudinal range) with the
 contemporary latitudinal-egg size relationship.  Results: In
 accordance with Bergmann’s rule, we found a positive relationship between
 breeding latitude and body mass during all post-embryonic life stages,
 from early nestlings through the oldest adults. We observed this same
 pattern with historic eggs, but contemporary eggs exhibited a negative
 relationship between latitude and egg size. Main conclusions: A positive
 latitude-body size relationship was present just after hatching,
 suggesting a genetic component to this pattern. As latitude increases,
 selection for larger altricial nestlings may help explain the existence of
 this pattern in adults of migratory species, as even rare extreme cold
 weather events may cause mortality during this sensitive stage. Although
 this pattern was present in all contemporary post-embryonic stages and
 historic eggs, the reversal observed in contemporary eggs may be related
 to a complicated (and dynamic) selective landscapes that may be associated
 with ongoing global climate change. Although speculative, global changes
 may be in the process of altering this long-standing ecological principle,
 but more research is necessary.
DOI: 10.15468/dl.yneffu
title: Occurrence Download

description: A dataset containing 94 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Anolis urraoi"
 ]
}

 The dataset includes 94 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002501-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17605/osf.io/ec8xz
title: Qualitative data (sample) on teacher competency in online multicultural teaching

description: Anonymous responses from 6 respondents regarding online multicultural teaching competencies.