cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.w0vt4b8t7
title: Experimental cross species transmission of a major viral pathogen in bees is predominantly from honeybees to bumblebees

description: Cross-species transmission of a pathogen from a reservoir to a recipient
 host species, spillover, can have major impacts on biodiversity, domestic
 species and human health. Deformed wing virus (DWV) is a panzootic RNA
 virus in honeybees that is causal in their elevated colony losses, and
 several correlative field studies have suggested spillover of DWV from
 managed honeybees to wild bee species such as bumblebees. Yet unequivocal
 demonstration of DWV spillover is lacking whilst spillback, the
 transmission of DWV from a recipient back to the reservoir host, is rarely
 considered. Here we show in fully crossed laboratory experiments that
 transmission of DWV (genotype A) from honeybees to bumblebees occurs
 readily, yet we neither detected viral transmission from bumblebees to
 honeybees nor onward transmission from experimentally infected to
 uninoculated bumblebees. Our results support the potential for viral
 spillover from honeybees to other bee species in the field when robbing
 resources from heterospecific nests or when visiting the same flowers.
 They also underscore the importance of studies on the virulence of DWV in
 wild bee species so as to evaluate viral impact on individual and
 population fitness as well as viral adaption to new host species.
DOI: 10.5061/dryad.w0vt4b8t8
title: Plant biodiversity declines with increasing coffee yield in Ethiopia’s coffee agroforests

description: 1. Tropical agroforestry systems provide farmers with resources for their
 livelihoods, but are also well recognized as refuges for biodiversity.
 However, the relationship between yield and biodiversity might be negative
 in these systems, reflecting a potential trade-off between managing for
 increased yield or biodiversity. The potential for synergies will depend
 partly on the shape of the biodiversity-yield relationship, where a
 concave relationship suggests a faster decline of biodiversity with
 increasing yields than a linear or convex shape. 2. We studied the
 relationship between biodiversity (plant species richness and composition)
 and coffee yield along a gradient of management in southwestern Ethiopia,
 coffee’s native range. We inventoried species richness and community
 composition of woody plants, herbaceous plants and bryophytes at 60 sites.
 We also measured coffee management-related variables and assessed coffee
 yield for three consecutive years at each site. 3. Species richness of
 woody plants had a concave relationship with coffee yield, i.e. tree
 richness declined fast initially before levelling out at higher yields,
 whereas there was no relationship between coffee yield and species
 richness of herbaceous plants or bryophytes. Species composition of woody
 plants, herbaceous plants and bryophytes all had a concave relationship
 with coffee yield. 4. From a methodological perspective, we found that
 multi-year data on yield was necessary to reliably assess the relationship
 between biodiversity and yield, and that the number of coffee shrubs or
 coffee dominance were poor proxies for yield when trying to capture the
 biodiversity-yield relationship. 5. Synthesis and applications: The
 concave relationship between biodiversity components (species richness and
 composition) and yield suggests that there is a strong conflict between
 the goals of increasing production and conserving biodiversity. However,
 it is important to recognize that this pattern is largely driven by the
 very low-yielding sites in natural forests. Here, even minor
 intensification of coffee management seems to rapidly erode biodiversity.
 Along the rest of the productivity gradient, there was generally no
 negative relationship between yield and biodiversity, implying
 opportunities for developing strategies for increasing yields without
 biodiversity loss.
DOI: 10.5061/dryad.b2rbnzsh2
title: Data from: Population size mediates the contribution of high-rate and large-benefit mutations to parallel evolution

description: The study "Population size mediates the contribution of
 high-rate and large-benefit mutations to parallel
 evolution" by Schenk et al. explores the phenotypic
 and genotypic changes in Escherichia coli after 500
 generations of laboratory adaptation to increasing concentrations of an
 antibiotic (CTX). The source data files and scripts pertaining to the
 figures in the main manuscript and the extended data are available on the
 publishers webiste. Here we provide the source data files and scripts
 pertaining to the supplementary materials, organized according the figures
 in the supplementary material. Data are provided for Figures S2-S4, S6-S8,
 and S10-S12.
description: We characterized evolved clones and populations with different
 methods, with both phenotypic and genotypic characterization.
 Antibiotic resistance was determined with minimal inhibitory
 concentration (MIC) assays, but we also measured their beta-lactamase
 activity with nitrocefin assays. The competitive fitness of selected
 mutations was determined by competitions with flourescently marked
 strains, followed by flow cytometry. Illumina
 sequencing was performed on a randomly selected clone from each evolved
 population. In addition, we sequenced meta-populations from 5 large and 5
 small populations at 100, 200, 300, 400 and 500 generations. Raw
 sequencing data are available in the Sequencing Read Arhive (PRJNA790633),
 of the NCBI. Mutations were called from the sequencing data using
 different methods, and the set of mutations was manually curated to remove
 any sequencing or mapping artefacts. The set of mutations was used for
 subsequent analyses, such as determining the occurence of mutations in
 different classes, the repeatability of evolution, and the co-occurence of
 adaptive mutations.
description: An overview of the data files provided and how they are organized
 is given in ReadMe.rtf To make the submission coherent
 and complete, we have included a PDF of the supplementary materials
 (Supplementary Materials Schenk Zwart et al Nature Ecology and
 Evolution.pdf).
DOI: 10.5061/dryad.zcrjdfndw
title: Sequences of Staudtia kamerunensis obtained through low coverage whole genome skimming

description: The impact of Pleistocene climatic oscillations on the biodiversity of
 African tropical rain forests remains poorly understood, and the Congo
 Basin is particularly understudied. We aim to elucidate how Pleistocene
 climatic oscillations shaped lowland tropical rain forests by
 investigating the intraspecific diversity and evolutionary history of a
 widespread tree species, Staudtia kamerunensis Warb. We sequenced 88
 individuals of Staudtia kamerunensis and 1 of Staudtia pterocarpa using a
 genome skimming approach. We used maximum likelihood and Bayesian
 inference to infer the plastid phylogeny. We estimated the time of
 speciation and differentiation, genetic diversity, and we employed a
 continuous phylogeographic approach to infer the dispersal history of its
 plastid lineages. We identified five plastid lineages that diverged during
 the Early or Middle Pleistocene and are parapatric, suggesting past
 population fragmentation. Four lineages are endemic to Lower Guinea, and
 one spans the Congo Basin. We found contrasting patterns of expansion in
 the two regions, with a rapid and recent range expansion of the Congolian
 lineage in the last 200,000 years, while the spread of the Lower Guinean
 lineages was substantially slower. The contrasting demographic histories
 between eastern and western lineages, associated with contrasted levels of
 plant species richness and rates of endemism, suggest that forest cover
 was more stable in Lower Guinea during the Late Pleistocene than in
 Congolia, where the biodiversity might have been eroded before the forest
 re-expanded in the Congo basin. This study illustrates how a continuous
 phylogeographic inference approach, mostly applied so far for inferring
 the spread of fast-evolving pathogens over months or years, can provide
 new insights to reconstruct the dispersal history of tropical tree species
 over thousands or millions of years.
description: Sequencing was performed on an Illumina NovaSeq sequencer at the
 GIGA platform in Liége, Belgium. Demultiplexing was done by the GIGA
 platform. 
description: Files are paired-end. Certain files have a small amount of reads,
 or are better treated as single-end data.
DOI: 10.5061/dryad.c866t1g8d
title: Spatiotemporal variation in hatching success and nestling sex ratios track rapid movement of a songbird hybrid zone

description: Hybridization often occurs at the parapatric range interface between
 closely related species, but fitness outcomes vary: hybrid offspring
 exhibit diverse rates of viability and reproduction when compared to their
 parental species. The mobile hybrid zone between two chickadee congeners (
 Poecile atricapillus x P. carolinensis ) has been well studied
 behaviorally and genetically but the viability of hybrids, as well as the
 underlying mechanisms contributing to hybrid fitness, have remained
 unclear. To better characterize the fitness costs of hybridization in this
 system, we analyzed 21 years of data from four sites, including over 1,400
 breeding attempts by the two species, to show that rates of hatching
 success changed substantially as the zone of hybridization moved across
 the landscape. Admixture-associated declines in hatching success
 correlated with reduced proportions of heterogametic (female) offspring as
 predicted by Haldane’s rule. Our data support an underlying mechanism
 implicating genetic admixture of the homogametic (male) parent as the
 primary determinant of offspring sex ratio, via incompatibilities on the
 hemizygous Z chromosome. Our long-term study is the first to directly
 measure changes in fitness costs as a vertebrate hybrid zone moves, and it
 shows that changes in these costs are a way to track the distribution of a
 hybrid zone across the landscape.
DOI: 10.5061/dryad.hx3ffbgg4
title: Hair phenotype diversity across Indriidae lemurs

description: Objectives: Hair (i.e., pelage/fur) is a salient feature of primate
 (including human) diversity and evolution—serving functions tied to
 thermoregulation, protection, camouflage, and signaling—but wild primate
 pelage evolution remains relatively understudied. Specifically, assessing
 multiple hypotheses across distinct phylogenetic scales is essential but
 is rarely conducted. We examine whole body hair color and density
 variation across Indriidae (Avahi, Indri, Propithecus)—a lineage that,
 like humans, exhibits vertical posture (i.e., their whole bodies are
 vertical to the sun). Materials and Methods: Our analyses considers
 multiple phylogenetic scales (family-level, genus-level) and hypotheses
 (e.g., Gloger’s rule, the body cooling hypotheses). We obtain hair color
 and density from museum and/or wild animals, opsin genotypes from wild
 animals, and climate data from WorldClim. To analyze our data, we use
 phylogenetic generalized linear mixed models (PGLMM) using Markov chain
 Monte Carlo algorithms. Results: Our results show that across the
 Indriidae family, darker hair is typical in wetter regions. However,
 within Propithecus, dark black hair is common in colder forest regions.
 Results also show pelage redness increases in populations exhibiting
 enhanced color vision. Lastly, we find follicle density on the crown and
 limbs increases in dry and open environments. Discussion: This study
 highlights how different selective pressures across distinct phylogenetic
 scales have likely acted on primate hair evolution. Specifically, our data
 across Propithecus may implicate thermoregulation and is the first
 empirical evidence of Bogert’s rule in mammals. Our study also provides
 rare empirical evidence supporting an early hypothesis on hominin hair
 evolution.
description: See the README file.
DOI: 10.5061/dryad.kh1893273
title: Physiological acclimatization in high-latitude zooplankton

description: How individual organisms adapt to non-optimal conditions through
 physiological acclimatization is central to predicting the consequences of
 unusual abiotic and biotic conditions such as those produced by marine
 heat waves. The Northeast Pacific, including the Gulf of Alaska
 experienced an extreme warming event (2014-2016, “The Blob”) that affected
 all trophic levels leading to large-scale changes in the community. The
 marine copepod Neocalanus flemingeri is one key member
 of the subarctic Pacific pelagic ecosystem. During the spring
 phytoplankton bloom this copepod builds substantial lipid stores as it
 prepares for its non-feeding adult phase. A three-year comparison of gene
 expression profiles of copepods collected in Prince William Sound in the
 Gulf of Alaska between 2015 and 2017 included two high-temperature years
 (2015 and 2016) and one year with very low phytoplankton abundances
 (2016). The largest differences in gene expression were between high and
 low chlorophyll years, and not between warm and cool years. The observed
 gene expression patterns are indicative of physiological acclimatization.
 The predominant signal in 2016 was the down-regulation of genes involved
 in glycolysis and its incoming pathways, consistent with the modulation of
 metabolic rates in response to prolonged low food conditions. Despite the
 down-regulation of genes involved in metabolism, there was no evidence of
 suppression of protein synthesis based on gene expression or behavioral
 activity. Genes involved in muscle function were up-regulated, and the
 copepods were actively swimming and responsive to stimuli at collection.
 However, genes involved in fatty acid metabolism were down-regulated in
 2016, suggesting reduced lipid accumulation.
DOI: 10.5061/dryad.37pvmcvmq
title: Chloroplast genome of the invasive Pyrus calleryana

description: The complete chloroplast genome of Pyrus calleryana (BioSample
 SAMC013142) was developed by de novo assembly from whole-genome sequencing
 data. Reference-guided (P. phaeocarpa) read mapping and assembly
 were followed by annotation and phylogenetic comparisons. The Pyrus
 calleryana chloroplast genome of 159,965 bp in length (36,56% of
 GC content) represents a classical quadripartite architecture, with two
 inverted repeats regions (IRs; each 26,392 bp in length)
 separating the large single-copy region (LSC; 87,942 bp) and the
 small single-copy region (SSC; 19.239 bp). In total, 115 unique
 genes were predicted and annotated in that genome, including 81 protein
 coding genes, 30 tRNA coding genes, and 4 rRNA coding genes. Phylogenetic
 analyses based on the whole chloroplast genome sequences places the
 P. calleryana among other Rosaceae plants, specifically among the
 Asian species of Pyrus.
description: Ubuntu 20.4 code used for processing of P. calleryana SRA
 paired-end files:   bwa-mem2 index
 ../cp*.txt #Reference indexing bwa-mem2 mem -t 12
 ../cp*.txt ../*F.fastq.gz ../*R.fastq.gz &gt; draft1.sam  #Reference
 mapping samtools view --threads 12 -b -o draft1.bam -S
 draft1.sam #Samtools modification of mapped reads into .bam file
 samtools sort --threads 12 draft1.bam &gt; draft1.sorted.bam
 #Samtool sorting of the mapped reads samtools index -@
 12 draft1.sorted.bam #Samtools indexing of the sorted mapped
 reads pilon --genome ../cp*.txt --frags
 draft1.sorted.bam --tracks --threads 12 #Reference-guided assembly of the
 indexed, sorted mapped reads into a circular genome
DOI: 10.5061/dryad.rfj6q57c9
title: Intra‐season variations in distribution and abundance of humpback whales in the West Antarctic Peninsula using cruise vessels as opportunistic platforms

description: Following the near collapse of several whale populations in the Southern
 Ocean, some baleen whale stocks are on the rise again. Combined with the
 recent increase in fishery of Antarctic Krill (Euphausiia superba) around
 the Western Antarctic Peninsula (WAP) there is a growing need to quantify
 several aspects of some of these whale species in this area. In this study
 we use data collected from tourist vessels performing several trips during
 the Austral summer to quantify the beginning of the foraging season for
 Antarctic Humpback whales, estimate abundance, as well as use predictive
 habitat model to identify potential areas for interaction between this
 species and fishing vessels. The following dataset includes the GPS track
 of both vessels and all marine mammal and seabird observations collected
 on two ships between late November 2019 and mid-January 2020. These data
 were gathered following standard Distance Sampling protocols, recorded in
 Logger2010
 software (http://www.marineconservationresearch.co.uk/downloads/logger-2000-rainbowclick-software-downloads/), stored in MS Access database files and subset in .RData files for analysis.
description: Data was collected in the Antarctic Peninsula and greater Scotia
 Sea using standard distance sampling methodology. The dataset includes
 both raw data in Microsoft Access format, as well as processed R
 objects.
DOI: 10.5061/dryad.bcc2fqzdp
title: Data for: The interplay of environmental cues and wood density in the vegetative and reproductive phenology of seasonally dry tropical forest trees

description: The great phenological diversification characteristic of seasonally dry
 tropical forests (SDTF) suggests that these patterns result from a complex
 interplay between exogenous (e.g., climatic) and endogenous (e.g.,
 morphological, physiological, anatomical) factors. Based on the
 well-established relationships of wood density with water-storing capacity
 and cavitation vulnerability in woody plants, we hypothesized differential
 vegetative and reproductive phenological responses to environmental cues
 for hardwood and softwood species. To test this hypothesis, we compared
 phenological patterns of pairs of conspecific populations of 10 species
 differing in wood density, occurring in two localities with slightly
 different climatic regimes, and evaluated the influence of three
 environmental variables (rainfall, photoperiod, temperature) on them. Our
 results, based on the assessment of the overlap of the phenological curves
 of conspecific populations occurring in different sites and on linear
 modeling, showed different effects of the environmental factors on
 phenophase attributes, depending on wood density of the study species,
 thus supporting our hypothesis. Leaf out in softwood species took place in
 the dry season, they shed the foliage at the first signs of drought, and
 once leafless, they flowered and fruited shortly after. By contrast,
 hardwood species bore leaves and flowers in the rainy season, shed their
 leaves several months after the rain ceased, and produced fruits during
 the dry season. We conclude that the role of environmental variables in
 cueing growth and reproduction cycles in SDTF tree species is interrelated
 with their wood density, a key endogenous factor crucially linked to plant
 hydraulics in these water-limited ecosystems.
description: Please see article in Biotropica for a detailed description of
 field and analytical methods.
description: Luna-Nieves et al
 DataBase This
 database contains phenological observations for ten tropical dry forest
 tree species recorded over a one-year period (March 2012 - February 2013)
 in two localities from the Pacific watershed of Mexico. The ten species
 were monitored at the two localities. The format is an Excel Book
 containing three pages. Page 'Contact' contains names and
 e-mails of authors to be contacted for use of the database. Page
 'Metadata' includes the names and descriptions of the 13
 variables recorded on page 'Database'. These variables are Site
 (categorical), Species (categorical), Individual (numeric), Wood density
 (numeric), Wood density group (categorical), Phenophase (categorical),
 Month (categorical), Year (categorical), Relative intensity (numeric),
 Photoperiod (numeric), Precipitation (numeric), Precipitation -1
 (numeric), and Tmax (numeric).
DOI: 10.15468/dl.8kun5y
title: Occurrence Download

description: A dataset containing 5885 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Cupressus dupreziana atlantica, Lomandra micrantha teretifolia, Astelia alpina alpina, Labichea lanceolata brevifolia, Acacia aemula muricata, Euphorbia tannensis eremophila)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 5885 records from 63 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003028-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.zw3r22893
title: Chronic Ca2+ imaging of cortical neurons with long-term expression of GCaMP-X

description: Dynamic Ca2+ signals reflect acute changes in membrane excitability and
 also mediate signaling cascades in chronic processes. In both cases,
 chronic Ca2+ imaging is often desired but challenged by the cytotoxicity
 intrinsic to calmodulin (CaM)-based GCaMP, a series of genetically-encoded
 Ca2+ indicators that have been widely applied. Here, we demonstrate the
 performance of GCaMP-X in chronic Ca2+ imaging of cortical neurons, where
 GCaMP-X by design is to eliminate the unwanted interactions between the
 conventional GCaMP and endogenous (apo)CaM-binding proteins. By expressing
 in adult mice at high levels over an extended time frame, GCaMP-X showed
 less damage and improved performance in two-photon imaging of sensory
 (whisker-deflection) responses or spontaneous Ca2+ fluctuations, in
 comparison with GCaMP. Chronic Ca2+ imaging of one month or longer was
 conducted for cultured cortical neurons expressing GCaMP-X, unveiling that
 spontaneous/local Ca2+ transients progressively developed into
 autonomous/global Ca2+ oscillations. Along with the morphological indices
 of neurite length and soma size, the major metrics of oscillatory Ca2+,
 including rate, amplitude and synchrony were also examined. Dysregulations
 of both neuritogenesis and Ca2+ oscillations became discernible around 2–3
 weeks after virus injection or drug induction to express GCaMP in newborn
 or mature neurons, which were exacerbated by stronger or prolonged
 expression of GCaMP. In contrast, neurons expressing GCaMP-X were
 significantly less damaged or perturbed, altogether highlighting the
 unique importance of oscillatory Ca2+ to neural development and neuronal
 health. In summary, GCaMP-X provides a viable solution for Ca2+ imaging
 applications involving long-time and/or high-level expression of Ca2+
 probes. 
description: Please see the manuscript
 for details.
description: Please see README.
DOI: 10.5061/dryad.g4f4qrfs0
title: Humpback whale song comparison for the Atlantic sector of the Southern Ocean

description: The results of comparative song analyses between the ASSO and the
 Ecuadorian and Brazilian breeding populations and recordings from the
 Chilean, South African and Namibian migration routes revealed that
 individuals from at least three humpback whale breeding populations most
 likely migrate to shared feeding grounds in the ASSO. Humpback whales from
 different populations potentially mix at different times (i.e., years) at
 feeding hotspots of variable locations.