cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.5jt25
title: Data from: The mammalian complement system as an epitome of host–pathogen genetic conflicts

description: The complement system is an innate immunity effector mechanism; its action
 is antagonized by a wide array of pathogens and complement evasion
 determines the virulence of several infections. We investigated the
 evolutionary history of the complement system and of bacterial-encoded
 complement-interacting proteins. Complement components targeted by several
 pathogens evolved under strong selective pressure in primates, with
 selection acting on residues at the contact interface with microbial/viral
 proteins. Positively selected sites in CFH and C4BPA account for the human
 specificity of gonococcal infection. Bacterial interactors, evolved
 adaptively as well, with selected sites located at interaction surfaces
 with primate complement proteins. These results epitomize the expectation
 under a genetic conflict scenario whereby the host's and the
 pathogen's genes evolve within binding avoidance-binding seeking
 dynamics. In silico mutagenesis and protein–protein docking analyses
 supported this by showing that positively selected sites, both in the
 host's and in the pathogen's interacting partner, modulate
 binding.
description: Complement_gene_alignmentsPrimates Multispecies alignments used in the evolutionary analysesomegaMap_alignmentscomplement bacterial-encoded interactors alignment filesgammaMap_inputinput files for the human lineage gammaMap analysis
DOI: 10.5061/dryad.mb7qk
title: Data from: Safari science: assessing the reliability of citizen science data for wildlife surveys

description: 1. Protected areas are the cornerstone of global conservation, yet
 financial support for basic monitoring infrastructure is lacking in 60% of
 them. Citizen science holds potential to address these shortcomings in
 wildlife monitoring, particularly for resource-limited conservation
 initiatives in developing countries - if we can account for the
 reliability of data produced by volunteer citizen scientists (VCS) . 2.
 This study tests the reliability of VCS data vs. data produced by trained
 ecologists, presenting a hierarchical framework for integrating diverse
 datasets to assess extra variability from VCS data. 3. Our results show
 that, while VCS data are likely to be overdispersed for our system, the
 overdispersion varies widely by species. We contend that citizen science
 methods, within the context of East African drylands, may be more
 appropriate for species with large body sizes, which are relatively rare,
 or those that form small herds. VCS perceptions of the charisma of a
 species may also influence their enthusiasm for recording it. 4. Tailored
 program design (such as incentives for VCS) may mitigate the biases in
 citizen science data and improve overall participation. However, the cost
 of designing and implementing high quality citizen science programs may be
 prohibitive for the small protected areas that would most benefit from
 these approaches. 5. Synthesis and applications. As citizen science
 methods continue to gain momentum, it is critical that managers remain
 cautious in their implementation of these programs while working to ensure
 methods match data purpose. Context-specific tests of citizen science data
 quality can improve program implementation, and separate data models
 should be used when VCS variability differs from trained ecologists’ data.
 Partnerships across protected areas and between protected areas and other
 conservation institutions could defray the costs of citizen science
 program design and implementation.03-Apr-2017
description: data_JAPPL201601169Species counts were collected using ecological transects (Traditional Sampling, TS =1) and citizen scientists on game drives (Safari Science, SS =1) from June - August 2013. Dist_Livestock was created using points from livestock locations collected during the TS fieldwork, and distance to those points was calculated in ArcGIS. TWI was calculated in ArcGIS using slope and elevation from a 30m DEM. Dist_river was calculated using stream data produced from the same DEM. The wildlife location data were separated into groups ("Groups" column) spanning 16 days, which were centered on each of the Landsat scenes, and the NDVI values were extracted to those locations.
DOI: 10.5061/dryad.v02t3
title: Data from: Terrace aware data structure for phylogenomic inference from supermatrices

description: In phylogenomics the analysis of concatenated gene alignments, the
 so-called supermatrix, is commonly accompanied by the assumption of
 partition models. Under such models each gene, or more generally
 partition, is allowed to evolve under its own evolutionary model. Though
 partition models provide a more comprehensive analysis of supermatrices,
 missing data may hamper the tree search algorithms due to the existence of
 phylogenetic (partial) terraces. Here we introduce the phylogenetic
 terrace aware (PTA) data structure for the efficient analysis under
 partition models. In the presence of missing data PTA exploits (partial)
 terraces and induced partition trees to save computation time. We show
 that an implementation of PTA in IQ-TREE leads to a substantial speedup of
 up to 4.5 and 8 times compared with the standard IQ-TREE and RAxML
 implementations, respectively. PTA is generally applicable to all types of
 partition models and common topological rearrangements thus can be
 employed by all phylogenomic inference software.
description: Online-Appendix-Chernomor_et_al
DOI: 10.5061/dryad.g9v24
title: Data from: Capturing goats: documenting two hundred years of mitochondrial DNA diversity among goat populations from Britain and Ireland

description: The domestic goat (Capra hircus) plays a key role in global agriculture,
 being especially prized in regions of marginal pasture. However, the
 advent of industrialized breeding has seen a dramatic reduction in genetic
 diversity within commercial populations, while high extinction rates among
 feral herds have further depleted the reservoir of genetic variation
 available. Here, we present the first survey of whole mitochondrial
 genomic variation among the modern and historical goat populations of
 Britain and Ireland using a combination of mtDNA enrichment and high
 throughput sequencing. Fifteen historical taxidermy samples, representing
 the indigenous ‘Old Goat’ populations of the islands, were sequenced
 alongside five modern Irish dairy goats and four feral samples from
 endangered populations in western Ireland. Phylogenetic and network
 analyses of European mitochondrial variation revealed distinct groupings
 dominated by historical British and Irish samples, which demonstrate a
 degree of maternal genetic structure between the goats of insular and
 continental Europe. Several Irish modern feral samples also fall within
 these clusters, suggesting continuity between these dwindling populations
 and the ancestral ‘Old Goats’ of Ireland and Britain.
description: Whole mitochondrion
 consensus sequencesFasta consensus
 sequences for 24 goat mitochondria published in the
 study.goat_mtDNA_consensus_sequences.fasta
DOI: 10.5061/dryad.4rd62
title: Data from: On the perplexingly low rate of transport of IgG2 across the human placenta

description: The neonatal receptor, FcRn, mediates both serum half–life extension as
 well as active transport of maternal IgG to the fetus during pregnancy.
 Therefore, transport efficiency and half-life go hand-in-hand. However,
 while the half-life of the human IgG2 subclass is comparable to IgG1, the
 placental transport of IgG2 is not, with the neonatal IgG1 levels
 generally exceeding maternal levels at birth, but not for IgG2. We
 hypothesized that the unique short-hinged structure of IgG2, which enables
 its κ-, but not λ-isotype to form at least three different structural
 isoforms, might be a contributing factor to these differences. To
 investigate whether there was any preference for either light chain, we
 measured placental transport of IgG subclasses as well as κ/λ-light chain
 isotypes of IgG1 and IgG2 in 27 matched mother-child pairs. We also
 studied the half-life of IgG1 and IgG2 light chain isotypes in mice, as
 well as that of synthesized IgG2 structural isotypes κA and κB. In order
 to investigate serum clearance of IgG1 and IgG2 light-chain isotypes in
 humans, we quantified the relative proportions of IgG1 and IgG2 light
 chains in hypogammaglobulinemia patients four weeks after IVIg infusion
 and compared to the original IVIg isotype composition. None of our results
 indicate any light chain preference in either of the FcRn mediated
 mechanisms; half-life extension or maternal transport.
description: Data behind all
 figures.This file contains all
 data points for all figures in the associated PLOS ONE
 manuscriptFigures
 resubmission.xlsx
DOI: 10.5061/dryad.rf551
title: Data from: Using a forest dynamics model to link community assembly processes and traits structure

description: 1. Trait-based approaches have been increasingly used to understand the
 role of environmental and biotic filters on species assembly. However, our
 understanding of the relationships between traits and community assembly
 processes remain limited. Indeed, various assembly processes may lead to
 similar functional patterns, and the effects of a given process may vary
 with the considered traits. Especially, competition can result in trait
 divergence or convergence depending on whether the trait is related to
 niche differences or to species’ competitive abilities. 2. In this study,
 we used a process-based forest gap-model to explore the effect of
 environmental and biotic assembly processes on the functional diversity of
 tree communities along a productivity gradient of 11 sites across central
 Europe. In a simulation experiment, we (i) disentangled the effects of
 environmental and biotic filtering on community structure, and (ii) tested
 whether competition resulted in trait divergence or convergence. 3. Our
 results confirmed the expected decrease in species richness with
 decreasing site fertility. We detected environmental filtering for traits
 related to both species environmental requirements and species competitive
 ability, highlighting that environmental trait filtering can affect all
 aspects of tree life-history strategies. 4. We observed convergence of
 traits related to growth and light capture resulting from competition for
 light, suggesting that tree species assembly is mainly driven by
 differences in competitive abilities. Additionally, the observed trait
 convergence was stronger in more productive sites than in less fertile
 ones, reflecting the impact of environmental conditions on competitive
 interactions. 5. Synthesis. Our study shows that process-based forest
 models can help to test whether functional traits composition reveal the
 signature of community assembly processes. This process-based approach
 challenges the classical view on the links between traits and mechanisms
 driving community assembly.
description: Biomass of species in
 mixed-forest simulationsThis file contains the
 biomass (t.ha-1.yr-1) of each species (in mixed-forest) after 2000 years
 of forest dynamic simulation with ForClim. Species biomass are given for
 each site of the study (column "Site") and for each mixed-forest
 simulation (column "Simulation number").Final_Matrix_allsites.xlsxBiomass of species in monoculturesThis file contains the biomass (t.ha-1.yr-1) of each species (in monoculture) after 2000 years of forest dynamic simulation with ForClim. Species biomass are given for each site of the study (column "Site") and for each monoculture simulation (column "Simulation number").Potential_Matrix_allsites.xlsxTrait matrixThis file contains parameters (considered as traits in our study) of species modelled in ForClim. We used these parameters to explore community assembly processes.Trait_Matrix.txt
DOI: 10.15468/dl.3kqdnk
title: Occurrence Download

description: A dataset containing 420045 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is The fossil collection (F) of the Muséum national d'Histoire naturelle (MNHN - Paris)"
 ]
}

 The dataset includes 420045 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000588-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.7cc7s
title: Data from: Tiny niches and translocations: the challenge of identifying suitable recipient sites for small and immobile species

description: Assisted colonisation, one form of species translocation, has been
 proposed as a tool for helping species to track suitable conditions in a
 changing climate. There are considerable practical challenges associated
 with it, including predicting where to place translocated individuals.
 This problem may be particularly big for small and immobile species, where
 small-scale micro-environmental conditions de-couple them from
 environmental conditions as projected in large-scale climate models. To
 investigate this problem we developed a survey-based model to predict the
 occurrence of our target species, the fruticose terricolous arctic-alpine
 lichen, Flavocetraria nivalis, within the Cairngorm Mountains. We then
 undertook an experimental translocation of this species. A second model,
 using variables that were significant in the survey-based model, was only
 fair at predicting the initial pattern of survival at the recipient site.
 However, model fit of the translocation survival model improved over time
 as the distribution of surviving individuals more accurately reflected the
 distribution of suitable environmental conditions. In addition, model
 predictive power increased with the addition of data on micro-climatic
 conditions at recipient plots. Synthesis and applications. Our results
 demonstrate that, for species which respond strongly to local
 environmental conditions, are immobile and, to some extent, decoupled from
 larger-scale climates, it may be difficult to build a priori accurate
 predictive models of habitat suitability. In these cases, a combination of
 modelling and expert judgement, along with the movement of substantial
 numbers of transplants, may be the appropriate options for maximising the
 success of assisted colonisation.
description: Wider vegetation survey
 dataData from a survey of
 habitats of the lichen Flavocetraria nivalis in the Cairngorm Mountains,
 Scotland. These data were used to produce the survey-based occurrence
 model described in our paper.Translocation survival
 dataThese data were used to
 produce the Translocation Survival Models 1 and 2 as described in our
 paper. They include records of lichen survival in 2011 and 2015, as well
 as values for the explanatory variables within the
 models.
DOI: 10.5061/dryad.v2q3v
title: Data from: Resource limitation prevents the emergence of drug resistance by intensifying within-host competition

description: Slowing the evolution of antimicrobial resistance is essential if we are
 to continue to successfully treat infectious diseases. Whether a
 drug-resistant mutant grows to high densities, and so sickens the patient
 and spreads to new hosts, is determined by the competitive interactions it
 has with drug-susceptible pathogens within the host. Competitive
 interactions thus represent a good target for resistance management
 strategies. Using an in vivo model of malaria infection, we show that
 limiting a resource that is disproportionately required by resistant
 parasites retards the evolution of drug resistance by intensifying
 competitive interactions between susceptible and resistant parasites.
 Resource limitation prevented resistance emergence regardless of whether
 resistant mutants arose de novo or were experimentally added before drug
 treatment. Our work provides proof of principle that chemotherapy paired
 with an “ecological” intervention can slow the evolution of resistance to
 antimicrobial drugs, even when resistant pathogens are present at high
 frequencies. It also suggests that a broad range of previously untapped
 compounds could be used for treating infectious diseases.
description: Data from Experiment 1
 of Wale et al. 2017, PNAS.Excel file containing
 (sheet 1) raw data from Experiment 1 & (sheet 2) information
 describing the contents.Experiment1.xlsxData from Experiment 2 of Wale et al. 2017, PNAS.Excel file containing (sheet 1) raw data from Experiment 2 & (sheet 2) information describing the contents.Experiment2.xlsxData from Experiment 3 of Wale et al. 2017, PNAS.Excel file containing (sheet 1) raw data from Experiment 3 & (sheet 2) information describing the contents.Experiment3.xlsxData from Experiment 4 of Wale et al. 2017, PNAS.Excel file containing (sheet 1) raw data from Experiment 4 & (sheet 2) information describing the contents.Experiment4.xlsx
DOI: 10.5061/dryad.253h0
title: Data from: The genetic contribution to sex determination and number of sex chromosomes vary among populations of common frogs (Rana temporaria)

description: The patterns of sex determination and sex differentiation have been shown
 to differ among geographic populations of common frogs. Notably, the
 association between phenotypic sex and linkage group 2 (LG2) has been
 found to be perfect in a northern Swedish population, but weak and
 variable among families in a southern one. By analyzing these populations
 with markers from other linkage groups, we bring two new insights: (1) the
 variance in phenotypic sex not accounted for by LG2 in the southern
 population could not be assigned to genetic factors on other linkage
 groups, suggesting an epigenetic component to sex determination; (2) a
 second linkage group (LG7) was found to co-segregate with sex and LG2 in
 the northern population. Given the very short timeframe since post-glacial
 colonization (in the order of 1000 generations) and its seemingly
 localized distribution, this neo-sex chromosome system might be the
 youngest one described so far. It does not result from a fusion, but more
 likely from a reciprocal translocation between the original Y chromosome
 (LG2) and an autosome (LG7), causing their co-segregation during male
 meiosis. By generating a strict linkage between several important genes
 from the sex-determination cascade (Dmrt1, Amh and Amhr2), this neo-sex
 chromosome possibly contributes to the 'differentiated sex race'
 syndrome (strictly genetic sex determination and early gonadal
 development) that characterizes this northern population.
description: Table
 S3Raw
 genotypes of 12 families for 62 microsatellite lociLG7 Table S3
 genotypes.xlsx
DOI: 10.5061/dryad.8108
title: Data from: Discovery and characterization of single nucleotide polymorphisms in Chinook salmon, Oncorhynchus tshawytscha

description: Molecular population genetics of non-model organisms has been dominated by
 the use of microsatellite loci over the last two decades. The availability
 of extensive genomic resources for many species is contributing to a
 transition to the use of single nucleotide polymorphisms (SNPs) for the
 study of many natural populations. Here we describe the discovery of a
 large number of SNPs in Chinook salmon, one of the world’s most important
 fishery species, through large-scale Sanger sequencing of expressed
 sequence tag (EST) regions. More than 3MB of sequence was collected in a
 survey of variation in more than 131KB of unique genic regions, from more
 than 225 separate ESTs, in a diverse ascertainment panel of 24 salmon.
 This survey yielded 117 TaqMan (5’ nuclease) assays, almost all from
 separate EST regions, which were validated in population samples from 5
 major stocks of salmon from the three largest basins on the Pacific coast
 of the coterminous United States: the Sacramento, Klamath and Columbia
 Rivers. The proportion of these loci that was variable in each of these
 stocks ranged from 86.3 to 90.6% and the mean minor allele frequency
 ranged from 0.194 to 0.236. There was substantial differentiation between
 populations with these markers, with a mean FST estimate of 0.107, and
 values for individual loci ranging from 0 to 0.592. This substantial
 polymorphism and population-specific differentiation indicates that these
 markers will be broadly useful, including for both pedigree reconstruction
 and genetic stock identification applications.
description: Genotype data for
 Chinook salmon from California and OregonThe file contains
 genotype data at 117 SNP loci for 337 Chinook salmon from the following
 Chinook salmon populations: Feather River spring-run (FRHsp, N=94); Butte
 Creek spring-run (ButteSp, N=54); Central Valley fall-run (MokBattle,
 N=94); Klamath/Trinity River fall-run (N=48); Lower Columbia River
 spring-run (KalCow, N=47). Data is in a text file in the Genepop 2-digit
 format.PrimerNote_PooledPops_117loci_GP2.txt
DOI: 10.5061/dryad.3g02j
title: Data from: Insights into the genetic relationships and breeding patterns of the African tea germplasm based on nSSR markers and cpDNA sequences

description: Africa is one of the key centers of global tea production. Understanding
 the genetic diversity and relationships of cultivars of African tea is
 important for future targeted breeding efforts for new crop cultivars,
 specialty tea processing, and to guide germplasm conservation efforts.
 Despite the economic importance of tea in Africa, no research work has
 been done so far on its genetic diversity at a continental scale.
 Twenty-three nSSRs and three plastid DNA regions were used to investigate
 the genetic diversity, relationships, and breeding patterns of tea
 accessions collected from eight countries of Africa. A total of 280
 African tea accessions generated 297 alleles with a mean of 12.91 alleles
 per locus and a genetic diversity (HS) estimate of 0.652. A STRUCTURE
 analysis suggested two main genetic groups of African tea accessions which
 corresponded well with the two tea types Camellia sinensis var. sinensis
 and C. sinensis var. assamica, respectively, as well as an admixed
 “mosaic” group whose individuals were defined as hybrids of F2 and BC
 generation with a high proportion of C. sinensis var. assamica being
 maternal parents. Accessions known to be C. sinensis var. assamica further
 separated into two groups representing the two major tea breeding centers
 corresponding to southern Africa (Tea Research Foundation of Central
 Africa, TRFCA), and East Africa (Tea Research Foundation of Kenya, TRFK).
 Tea accessions were shared among countries. African tea has relatively
 lower genetic diversity. C. sinensis var. assamica is the main tea type
 under cultivation and contributes more in tea breeding improvements in
 Africa. International germplasm exchange and movement among countries
 within Africa was confirmed. The clustering into two main breeding
 centers, TRFCA, and TRFK, suggested that some traits of C. sinensis var.
 assamica and their associated genes possibly underwent selection during
 geographic differentiation or local breeding preferences. This study
 represents the first step toward effective utilization of differently
 inherited molecular markers for exploring the breeding status of African
 tea. The findings here will be important for planning the exploration,
 utilization, and conservation of tea germplasm for future breeding efforts
 in Africa.
description: SSR alleles at 23 loci
 for 280 tea accessions from 8 countries in Africa. Missing data points are
 denoted by a zero ("0")The Excel file has 49
 columns; the first three columns show the serial number, sample ID, and
 country of origin respectively while the rest 46 columns depict the 23 SSR
 loci. Missing data points are denoted by "0".SSR
 data.xls