cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8ht6v
title: Data from: Genome reduction and microbe-host interactions drive adaptation of a sulfur-oxidizing bacterium associated with a cold seep sponge

description: As the most ancient metazoan, sponges have established close relationships
 with particular microbial symbionts. However, the characteristics and
 physiology of thioautotrophic symbionts in deep-sea sponges are largely
 unknown. Using a tailored “differential coverage binning” method on 22-Gb
 metagenomic sequences, we recovered the nearly complete genome of a
 sulfur-oxidizing bacterium (SOB) that dominates the microbiota of the cold
 seep sponge Suberites sp. Phylogenetic analyses suggested that this
 bacterium (an unclassified gammaproteobacterium termed “Gsub”) may
 represent a new deep-sea SOB group. Microscopic observations suggest that
 Gsub is probably an extracellular symbiont. Gsub has complete sulfide
 oxidation and carbon fixation pathways, suggesting a chemoautotrophic
 lifestyle. Comparative genomics with other sponge-associated SOB and
 free-living SOB revealed significant genome reduction in Gsub,
 characterized by the loss of genes for carbohydrate metabolism, motility,
 DNA repair, and osmotic stress response. Intriguingly, this scenario of
 genome reduction is highly similar to those of the endosymbionts in
 deep-sea clams. However, Gsub has retained genes for phage defense and
 protein secretion, with the latter potentially playing a role in
 interactions with the sponge host. In addition, we recovered the genome of
 an ammonia-oxidizing archaeon (AOA), which may carry out ammonia oxidation
 and carbon fixation within the sponge body.
description: Gsub-GenomeCold seep sponge symbiont SOB, assembled using genome binning methodNsub-GenomeCold seep sponge symbiont AOA, assembled using genome binning method
DOI: 10.5061/dryad.2v075
title: Data from: Chimpanzee intellect: personality, performance and motivation with touchscreen tasks

description: Human intellect is characterized by intercorrelated psychological domains,
 including intelligence, academic performance and personality. Higher
 openness is associated with higher intelligence and better academic
 performance, yet high performance among individuals is itself attributable
 to intelligence, not openness. High conscientiousness individuals,
 although not necessarily more intelligent, are better performers. Work
 with other species is not as extensive, yet animals display similar
 relationships between exploration- and persistence-related personality
 traits and performance on cognitive tasks. However, previous studies
 linking cognition and personality have not tracked learning, performance
 and dropout over time—three crucial elements of cognitive performance. We
 conducted three participatory experiments with touchscreen cognitive tasks
 among 19 zoo-housed chimpanzees, whose personalities were assessed 3 years
 prior to the study. Performance and participation were recorded across
 experiments. High conscientiousness chimpanzees participated more, dropped
 out less and performed better, but their performance could be explained by
 their experience with the task. High openness chimpanzees tended to be
 more interested, perform better and continue to participate when not
 rewarded with food. Our results demonstrate that chimpanzees, like humans,
 possess broad intellectual capacities that are affected by their
 personalities.
description: Chimpanzee personality,
 performance, and motivation dataContains performance and
 engagement data across 3 studies. Includes personality measures for
 individuals.RSOC.tar
DOI: 10.5061/dryad.9t21c
title: Data from: Ancient recombination events between human herpes simplex viruses

description: Herpes simplex viruses 1 and 2 (HSV-1 and HSV-2) are seen as close
 relatives but also unambiguously considered as evolutionary independent
 units. Here, we sequenced the genomes of 18 HSV-2 isolates characterized
 by divergent UL30 gene sequences to further elucidate the evolutionary
 history of this virus. Surprisingly, genome-wide recombination analyses
 showed that all HSV-2 genomes sequenced to date contain HSV-1 fragments.
 Using phylogenomic analyses, we could also show that two main HSV-2
 lineages exist. One lineage is mostly restricted to subSaharan Africa
 whereas the other has reached a global distribution. Interestingly, only
 the worldwide lineage is characterized by ancient recombination events
 with HSV-1. Our findings highlight the complexity of HSV-2 evolution, a
 virus of putative zoonotic origin which later recombined with its
 human-adapted relative. They also suggest that coinfections with HSV-1 and
 2 may have genomic and potentially functional consequences and should
 therefore be monitored more closely.
description: Annotated HSV-2v
 genomesPutative coding
 sequences were annotated with Geneious 10.0.5 using a conservative
 similarity threshold of 60% to coding sequences annotated in the HSV-2
 reference genome (NC_001798). GFF3 format.annotated_genomes.zipMutliple sequence alignments including HSV-2v sequencesThis archive contains the following alignments: Whole genome 1, 2 and 3; Whole genome de novo 2 and 3; Non recombinant 1 to 10; UL15 non recombinant and recombinant, UL29 non recombinant and recombinant, UL30 non recombinant and recombinant, UL39 non recombinant and recombinant. Whole genome 2 and 3 and Whole genome de novo 2 and 3 are provided as NEXUS files and include site masks pinpointing the recombinant regions (Whole genome 2 and Whole genome de novo 2 and 3) and large non recombinant fragments (Whole genome 3). All other alignments are provided as FASTA files.alignments.zip
DOI: 10.5061/dryad.fn53k
title: Data from: Genetic identification of source and likely vector of a widespread marine invader

description: The identification of native sources and vectors of introduced
 species informs its ecological and evolutionary history and may
 guide policies that seek to prevent future introductions. Population
 genetics represents a powerful set of tools to identify origins and
 vectors, but can mislead when the native range is poorly sampled or few
 molecular markers are used. Here, we traced the introduction
 of the Asian seaweed Gracilaria vermiculophylla
 (Rhodophyta) into estuaries in coastal western North
 America, the eastern United States, Europe and
 northwestern Africa by genotyping more than 2500 thalli from 37
 native and 53 non-native sites at both mitochondrial and nuclear loci.
 Overall, greater than 90% of introduced thalli have a genetic signature
 similar to thalli sampled from the coastline of northeastern Japan,
 strongly indicating this region served as the principal source of the
 invasion. Notably, northeastern Japan exported the vast majority of the
 oyster Crassostrea gigas during the 20th Century. The preponderance of
 evidence suggests G. vermiculophylla may have been inadvertently
 introduced with C. gigas shipments and that northeastern Japan is a common
 source region for estuarine invaders. Each invaded Northern Hemisphere
 coastline reflects a complex mix of direct introductions from Japan and
 secondary introductions from each invaded coastlines. The spread of G.
 vermiculophylla along each coastline was likely facilitated by
 aquaculture, fishing and boating activities. Our ability to document a
 source region was enabled by a robust sampling of locations and loci that
 previous studies lacked and strong phylogeographic structure along native
 coastlines.
description: KruegerHadfieldetal_EcolEvol_ploidyPloidy designation of each thallus used in this studyKruegerHadfieldetal_EcolEvol_diploidstotalGenAlEx file with all diploid thalli (before Psex calculation)KruegerHadfieldetal_EcolEvol_haploidstotalGenAlEx file with all haploid thalli (before Psex calculation)KruegerHadfieldetal_EcolEvol_diploidspsexGenAlEx file with diploid thalli where Psex &gt; 0.05KruegerHadfieldetal_EcolEvol_cox1_haplotypescox1 Haplotypes from Kim et al. (2010) and our studyKruegerHadfieldetal_EcolEvol_gvseqsG. vermiculophylla sequences from this study and haplotypes from Kim et al. (2010) and our studyKruegerHadfieldetal_EcolEvol_cox1SNPcox1 SNP (C or T) for each thallus
DOI: 10.5061/dryad.n0n60
title: Data from: Genetic structure and invasion history of the house mouse (Mus musculus domesticus) in Senegal, West Africa: a legacy of colonial and contemporary times

description: Knowledge of the genetic make-up and demographic history of invasive
 populations is critical to understand invasion mechanisms. Commensal
 rodents are ideal models to study whether complex invasion histories are
 typical of introductions involving human activities. The house mouse Mus
 musculus domesticus is a major invasive synanthropic rodent originating
 from South-West Asia. It has been largely studied in Europe and on several
 remote islands, but the genetic structure and invasion history of this
 taxon have been little investigated in several continental areas,
 including West Africa. In this study, we focussed on invasive populations
 of M. m. domesticus in Senegal. In this focal area for European settlers,
 the distribution area and invasion spread of the house mouse is documented
 by decades of data on commensal rodent communities. Genetic variation at
 one mitochondrial locus and 16 nuclear microsatellite markers was analysed
 from individuals sampled in 36 sites distributed across the country. A
 combination of phylogeographic and population genetics methods showed that
 there was a single introduction event on the northern coast of Senegal,
 from an exogenous (probably West European) source, followed by a secondary
 introduction from northern Senegal into a coastal site further south. The
 geographic locations of these introduction sites were consistent with the
 colonial history of Senegal. Overall, the marked microsatellite genetic
 structure observed in Senegal, even between sites located close together,
 revealed a complex interplay of different demographic processes occurring
 during house mouse spatial expansion, including sequential founder effects
 and stratified dispersal due to human transport along major roads.
description: MusPop36_2014_sanscoordMicrosatellite data (16 loci) for Mus musculus domesticus sampled in 36 localities of Senegal, West Africa; Genepop format fileLippens_FinalAlignmentSequence alignment (1793 sequences, 889 bp) of the D-loop control region and flanking tRNA genes, Mus musculus domesticus: 1313 sequences published in Bonhomme et al. (2011), 361 sequences obtained from other studies (Prager et al., 1996, 1998; Gündüz et al., 2000, 2001, 2005; Ihle et al., 2006; Searle et al., 2009a, b; Jones et al., 2010; Linnenbrinck et al., 2013 ; Suzuki et al., 2013; Gabriel et al., 2015; Jones and Searle, 2015), and 119 sequences from house mice sampled in Senegal (this study)
DOI: 10.5061/dryad.2vt31
title: Data from: Moving beyond linear food chains: trait-mediated indirect interactions in a rocky intertidal food web

description: In simple, linear food chains, top predators can have positive indirect
 effects on basal resources by causing changes in the traits (e.g.
 behaviour, feeding rates) of intermediate consumers. Although less is
 known about trait-mediated indirect interactions (TMIIs) in more complex
 food webs, it has been suggested that such complexity dampens trophic
 cascades. We examined TMIIs between a predatory crab (Carcinus maenas) and
 two ecologically important basal resources, fucoid algae (Ascophyllum
 nodosum) and barnacles (Semibalanus balanoides), which are consumed by
 herbivorous (Littorina littorea) and carnivorous (Nucella lapillus)
 snails, respectively. Because crab predation risk suppresses snail feeding
 rates, we hypothesized that crabs would also shape direct and indirect
 interactions among the multiple consumers and resources. We found that the
 magnitude of TMIIs between the crab and each resource depended on the
 suite of intermediate consumers present in the food web. Carnivorous
 snails (Nucella) transmitted TMIIs between crabs and barnacles. However,
 crab–algae TMIIs were transmitted by both herbivorous (Littorina) and
 carnivorous (Nucella) snails, and these TMIIs were additive. By causing
 Nucella to consume fewer barnacles, crab predation risk allowed fucoids
 that had settled on or between barnacles to remain in the community.
 Hence, positive interactions between barnacles and algae caused crab–algae
 TMIIs to be strongest when both consumers were present. Studies of TMIIs
 in more realistic, reticulate food webs will be necessary for a more
 complete understanding of how predation risk shapes community dynamics.
description: 1-initialshellsData on initial shell lengths of Nucella and Littorina used in the experiment.2-nucellaFinal shell lengths of Nucella measured at the end of the experiment.3-littorinaFinal shell length and shell thickness of Littorina measured at the end of the experiment.4-resourcesInitial and final densities of barnacles (Semibalanus balanoides) and fucoid algae (Ascophyllum nodosum) on experimental tiles.5-tmiiIndirect effect magnitudes (TMIIs) of green crabs (Carcinus maenas) on barnacles (Semibalanus balanoides) and fucoids (Ascophyllum nodosum).
DOI: 10.5061/dryad.vj853
title: Data from: Biological factors contributing to bark and ambrosia beetle species diversification

description: The study of species diversification can identify the processes that shape
 patterns of species richness across the tree of life. Here we perform
 comparative analyses of species diversification using a large dataset of
 bark beetles. Three examined covariates – permanent inbreeding (sibling
 mating), fungus farming, and major host type – represent a range of
 factors that may be important for speciation. We studied the association
 of these covariates with species diversification while controlling for
 evolutionary lag on adaptation. All three covariates were significantly
 associated with diversification, but fungus farming showed conflicting
 patterns between different analyses. Genera that exhibited interspecific
 variation in host type had higher rates of species diversification, which
 may suggest that host switching is a driver of species diversification or
 that certain host types or forest compositions facilitate colonization and
 thus allopatric speciation. Because permanent inbreeding is thought to
 facilitate dispersal, the positive association of permanent inbreeding on
 diversification rates suggests that dispersal ability may contribute to
 species richness. Bark beetles are ecologically unique; however, our
 results indicate that their impressive species diversity is largely driven
 by mechanisms shown to be important for many organism groups.
description: R scripts and input
 filesFile contents: 1: Two
 BEAST input files for phylogenetic reconstructions; 2: input file,
 settings file and sample prob. file for BAMM analysis; 3: R script for
 downloading COI sequences from genbank; 4: R script for processing the 305
 species tree (data extraction and pruning to genus tree); 5: R script for
 prepping 602 spp tree for BAMM and analyses of BAMM output files; 6: R
 scripts for SLOUCH analyses
DOI: 10.5061/dryad.vr3hk
title: Data from: Virus resistance is not costly in a marine alga evolving under multiple environmental stressors

description: Viruses are important evolutionary drivers of host ecology and evolution.
 The marine picoplankton Ostreococcus tauri has three known resistance
 types that arise in response to infection with the Phycodnavirus OtV5:
 susceptible cells (S) that lyse following viral entry and replication;
 resistant cells (R) that are refractory to viral entry; and resistant
 producers (RP) that do not all lyse but maintain some viruses within the
 population. To test for evolutionary costs of maintaining antiviral
 resistance, we examined whether O. tauri populations composed of each
 resistance type differed in their evolutionary responses to several
 environmental drivers (lower light, lower salt, lower phosphate and a
 changing environment) in the absence of viruses for approximately 200
 generations. We did not detect a cost of resistance as measured by
 life-history traits (population growth rate, cell size and cell
 chlorophyll content) and competitive ability. Specifically, all R and RP
 populations remained resistant to OtV5 lysis for the entire 200-generation
 experiment, whereas lysis occurred in all S populations, suggesting that
 resistance is not costly to maintain even when direct selection for
 resistance was removed, or that there could be a genetic constraint
 preventing return to a susceptible resistance type. Following evolution,
 all S population densities dropped when inoculated with OtV5, but not to
 zero, indicating that lysis was incomplete, and that some cells may have
 gained a resistance mutation over the evolution experiment. These findings
 suggest that maintaining resistance in the absence of viruses was not
 costly.
description: SelectionExperimentRcodeVirusVirusRaw3dSelectionExperimentRcodeGrowthCellCountsRawCellCountsRaw1Differences3daysSusceptibleChange
DOI: 10.5061/dryad.ps009
title: Data from: Flightin maintains myofilament lattice organization required for optimal flight power and courtship song quality in Drosophila

description: The indirect flight muscles (IFMs) of Drosophila and other insects with
 asynchronous flight muscles are characterized by a crystalline myofilament
 lattice structure. The high-order lattice regularity is considered an
 adaptation for enhanced power output, but supporting evidence for this
 claim is lacking. We show that IFMs from transgenic flies expressing
 flightin with a deletion of its poorly conserved N-terminal domain
 (flnΔN62) have reduced inter-thick filament spacing and a less regular
 lattice. This resulted in a decrease in flight ability by 33% and in
 skinned fibre oscillatory power output by 57%, but had no effect on
 wingbeat frequency or frequency of maximum power output, suggesting that
 the underlying actomyosin kinetics is not affected and that the flight
 impairment arises from deficits in force transmission. Moreover, we show
 that flnΔN62 males produced an abnormal courtship song characterized by a
 higher sine song frequency and a pulse song with longer pulses and longer
 inter-pulse intervals (IPIs), the latter implicated in male reproductive
 success. When presented with a choice, wild-type females chose control
 males over mutant males in 92% of the competition events. These results
 demonstrate that flightin N-terminal domain is required for optimal
 myofilament lattice regularity and IFM activity, enabling powered flight
 and courtship song production. As the courtship song is subject to female
 choice, we propose that the low amino acid sequence conservation of the
 N-terminal domain reflects its role in fine-tuning species-specific
 courtship songs.
description: Supplemental
 FiguresAudio
 S2Audio
 S1Video
 S1Video
 S2Video
 S3Electronic Supplementary
 Material_FINALSupplementary
 experimental procedures
DOI: 10.5061/dryad.74b2c
title: Data from: Fire-regime variability impacts forest carbon dynamics for centuries to millennia

description: Wildfire is a dominant disturbance agent in forest ecosystems, shaping
 important biogeochemical processes including net carbon (C) balance.
 Long-term monitoring and chronosequence studies highlight a resilience of
 biogeochemical properties to large, stand-replacing, high-severity fire
 events. In contrast, the consequences of repeated fires or temporal
 variability in a fire regime (e.g., the characteristic timing or severity
 of fire) are largely unknown, yet theory suggests that such variability
 could strongly influence forest C trajectories (i.e., future states or
 directions) for millennia. Here we combine a 4500-year paleoecological
 record of fire activity with ecosystem modeling to investigate how
 fire-regime variability impacts soil C and net ecosystem carbon balance.
 We found that C trajectories in a paleo-informed scenario differed
 significantly from an equilibrium scenario (with a constant fire return
 interval), largely due to variability in the timing and severity of past
 fires. Paleo-informed scenarios contained multi-century periods of
 positive and negative net ecosystem C balance, with magnitudes
 significantly larger than observed under the equilibrium scenario.
 Further, this variability created legacies in soil C trajectories that
 lasted for millennia. Our results imply that fire-regime variability is a
 major driver of C trajectories in stand-replacing fire regimes. Predicting
 carbon balance in these systems, therefore, will depend strongly on the
 ability of ecosystem models to represent a realistic range of fire-regime
 variability over the past several centuries to millennia.
description: Ds01_supportingdataset_firehistoryrecordFire history record used as input for fire occurrence in DayCentModel Outputoutput used to create figures and computationsDs02_modeloutput.csvModel Climate InputClimate forcing data for DayCentds03_climate.csvDayCent .100 filesParameterization/Input files for DayCent simulationsDs04_100files.pdf
DOI: 10.5061/dryad.17s0s
title: Data from: Contribution of lianas to community-level canopy transpiration in a warm-temperate forest

description: 1. Lianas (woody climbers) have a greater amount of leaves relative to
 basal area or standing biomass than trees, and very wide vessels that
 permit efficient water transport. These features suggest that lianas
 possibly consume proportionally more water through transpiration than
 trees. Despite their potential importance, researchers have made only
 limited attempts to evaluate effects of lianas on forest water dynamics.
 2. We conducted sap flow measurements for 1 year using a
 thermal-dissipation method for four species each of lianas and trees in a
 liana-rich, warm-temperate forest in Japan and estimated the contribution
 of lianas to stand canopy transpiration. 3. Based on a calibration
 measuring water uptake rates from cut-stem ends, the actual sap flux (Fd)
 in liana stems was several times greater than those estimated from the
 original calibration provided for the method. In the field, lianas showed
 an average of 2–4 times greater Fd than trees throughout the year. Except
 for this difference, diurnal and seasonal patterns of relative changes of
 Fd were similar in both groups. The whole-plant transpiration (Qt) of
 sample plants were exponentially related to basal diameter for both lianas
 and trees; Qt of lianas increased more steeply with basal diameter than
 that of trees. By extrapolating the relationships between Qt and basal
 diameter to the inventory data of the study plot, we estimated that lianas
 contributed 12.8% to the annual stand canopy transpiration while
 comprising 2.3% of stand basal area, which probably reflected the
 top-heavy architecture of lianas.4. Our results indicate that the
 contribution of lianas to forest water dynamics may be several times
 greater than their contribution to forest basal area. This implies that a
 slight increase of liana abundance might have greater effects on water
 dynamics and, through competitions with trees for limited water, the
 carbon sequestration capacity of forests than expected from the increase
 in basal area. This study underlines the necessity of evaluating the
 relative importance of lianas to forest water dynamics in forests
 worldwide.
description: sap flux and census
 dataThis file includes
 30-min and daily data of sap flux for 11 lianas and 10 trees, as well as
 meteorological variables (precipitation, temperature, vapour pressure
 deficit and solar radiation) over 1 year period. This also contains census
 data for lianas and trees rooted in our study plot.sapflux and census
 data.xlsx