cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.60t0f
title: Data from: Inference of adaptive shifts for multivariate correlated traits

description: To study the evolution of several quantitative traits, the classical
 phylogenetic comparative framework consists of a multivariate random
 process running along the branches of a phylogenetic tree. The
 Ornstein-Uhlenbeck (OU) process is sometimes preferred to the simple
 Brownian Motion (BM) as it models stabilizing selection toward an optimum.
 The optimum for each trait is likely to be changing over the long periods
 of time spanned by large modern phylogenies. Our goal is to automatically
 detect the position of these shifts on a phylogenetic tree, while
 accounting for correlations between traits, which might exist because of
 structural or evolutionary constraints. We show that, in the presence
 shifts, phylogenetic Principal Component Analysis (pPCA) fails to
 decorrelate traits efficiently, so that any method aiming at finding shift
 needs to deal with correlation simultaneously. We introduce here a
 simplification of the full multivariate OU model, named scalar OU (scOU),
 which allows for noncausal correlations and is still computationally
 tractable. We extend the equivalence between the OU and a BM on a
 re-scaled tree to our multivariate framework. We describe an Expectation
 Maximization algorithm that allows for a maximum likelihood estimation of
 the shift positions, associated with a new model selection criterion,
 accounting for the identifiability issues for the shift localization on
 the tree. The method, freely available as an R-package (PhylogeneticEM) is
 fast, and can deal with missing values. We demonstrate its efficiency and
 accuracy compared to another state-of-the-art method (l1ou) on a wide
 range of simulated scenarios, and use this new framework to re-analyze
 recently gathered datasets on New World Monkeys and Anolis lizards.
description: Online Appendices for:
 Inference of Adaptive Shifts for Multivariate Correlated
 TraitsThis document contains
 three online appendices.appendices_online.pdf
DOI: 10.5061/dryad.7kr85
title: Data from: A transmission-virulence evolutionary trade-off explains attenuation of HIV-1 in Uganda

description: Evolutionary theory hypothesizes that intermediate virulence maximizes
 pathogen fitness as a result of a trade-off between virulence and
 transmission, but empirical evidence remains scarce. We bridge this gap
 using data from a large and long-standing HIV-1 prospective cohort, in
 Uganda. We use an epidemiological-evolutionary model parameterised with
 this data to derive evolutionary predictions based on analysis and
 detailed individual-based simulations. We robustly predict stabilising
 selection towards a low level of virulence, and rapid attenuation of the
 virus. Accordingly, set-point viral load, the most common measure of
 virulence, has declined in the last 20 years. Our model also predicts that
 subtype A is slowly outcompeting subtype D, with both subtypes becoming
 less virulent, as observed in the data. Reduction of set-point viral loads
 should have resulted in a 20% reduction in incidence, and a three years
 extension of untreated asymptomatic infection, increas ing opportunities
 for timely treatment of infected individuals.
description: data analysis and
 simulationssee read me
 fileto_share.zip
DOI: 10.15468/dl.e4aa3p
title: Occurrence Download

description: A dataset containing 6123 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Harungana madagascariensis"
 ]
}

 The dataset includes 6123 records from 166 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000590-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.89qb406
title: Data from: Population genetic analysis of Chadian Guinea worms reveals that human and non-human hosts share common parasite populations

description: Following almost 10 years of no reported cases, Guinea worm disease (GWD
 or dracunculiasis) reemerged in Chad in 2010 with peculiar epidemiological
 patterns and unprecedented prevalence of infection among non-human hosts,
 particularly domestic dogs. Since 2014, animal infections with Guinea
 worms have also been observed in the other three countries with endemic
 transmission (Ethiopia, Mali, and South Sudan), causing concern and
 generating interest in the parasites’ true taxonomic identity and
 population genetics. We present the first extensive population genetic
 data for Guinea worm, investigating mitochondrial and microsatellite
 variation in adult female worms from both human and non-human hosts in the
 four endemic countries to elucidate the origins of Chad’s current outbreak
 and possible host-specific differences between parasites. Genetic
 diversity of Chadian Guinea worms was considerably higher than that of the
 other three countries, even after controlling for sample size through
 rarefaction, and demographic analyses are consistent with a large, stable
 parasite population. Genealogical analyses eliminate the other three
 countries as possible sources of parasite reintroduction into Chad, and
 sequence divergence and distribution of genetic variation provide no
 evidence that parasites in human and non-human hosts are separate species
 or maintain isolated transmission cycles. Both among and within countries,
 geographic origin appears to have more influence on parasite population
 structure than host species. Guinea worm infection in non-human hosts has
 been occasionally reported throughout the history of the disease,
 particularly when elimination programs appear to be reaching their end
 goals. However, no previous reports have evaluated molecular support of
 the parasite species identity. Our data confirm that Guinea worms
 collected from non-human hosts in the remaining endemic countries of
 Africa are Dracunculus medinensis and that the same population of worms
 infects both humans and dogs in Chad. Our genetic data and the
 epidemiological evidence suggest that transmission in the Chadian context
 is currently being maintained by canine hosts.
description: Raw microsatellite
 allelic data_DmedinensisRaw_microsatellite_allele_calls.txtDerived maternal genotypes_DmedinensisDerived_maternal_genotypes.txt
DOI: 10.5061/dryad.3vc1b
title: Data from: Fine scale genetic correlates to condition and migration in a wild Cervid

description: The relationship between genetic variation and phenotypic traits is
 fundamental to the study and management of natural populations. Such
 relationships often are investigated by assessing correlations between
 phenotypic traits and heterozygosity or genetic differentiation. Using an
 extensive data set compiled from free-ranging mule deer (Odocoileus
 hemionus), we combined genetic and ecological data to (i) examine
 correlations between genetic differentiation and migration timing, (ii)
 screen for mitochondrial haplotypes associated with migration timing, and
 (iii) test whether nuclear heterozygosity was associated with condition.
 Migration was related to genetic differentiation (more closely related
 individuals migrated closer in time) and mitochondrial haplogroup. Body
 fat was related to heterozygosity at two nuclear loci (with antagonistic
 patterns), one of which is situated near a known fat metabolism gene in
 mammals. Despite being focused on a widespread panmictic species, these
 findings revealed a link between genetic variation and important
 phenotypes at a fine scale. We hypothesize that these correlations are
 either the result of mixing refugial lineages or differential
 mitochondrial haplotypes influencing energetics. The maintenance of
 phenotypic diversity will be critical to enable the potential tracking of
 changing climatic conditions, and these correlates highlight the need to
 consider evolutionary mechanisms in management, even in widely distributed
 panmictic species.
description: 4_areasDeer genotypes for 17 microsatellite loci. The first two letters in the sample name denote the locations used in the analysis.
DOI: 10.5061/dryad.7d3s9
title: Data from: Evolutionary dynamics of interlinked public goods traits: an experimental study of siderophore production in Pseudomonas aeruginosa

description: Public goods cooperation is common in microbes, and there is much interest
 in understanding how such traits evolve. Research in recent years has
 identified several important factors that shape the evolutionary dynamics
 of such systems, yet few studies have investigated scenarios involving
 interactions between multiple public goods. Here we offer general
 predictions about the evolutionary trajectories of two public goods traits
 having positive, negative or neutral regulatory influence on one
 another's expression, and we report on a test of some of our
 predictions in the context of Pseudomonas aeruginosa's production of
 two interlinked iron-scavenging siderophores. First, we confirmed that
 both pyoverdine and pyochelin siderophores do operate as public goods
 under appropriate environmental conditions. We then tracked their
 production in lines experimentally evolved under different iron-limitation
 regimes known to favour different siderophore expression profiles. Under
 strong iron limitation, where pyoverdine represses pyochelin, we saw a
 decline in pyoverdine and a concomitant increase in pyochelin – consistent
 with expansion of pyoverdine-defective cheats derepressed for pyochelin.
 Under moderate iron limitation, pyochelin declined – again consistent with
 an expected cheat invasion scenario – but there was no concomitant shift
 in pyoverdine because cross-suppression between the traits is
 unidirectional only. Alternating exposure to strong and moderate
 iron-limitation caused qualitatively similar though lesser shifts compared
 to the constant-environment regimes. Our results confirm that the
 regulatory inter-connections between public goods traits can significantly
 modulate the course of evolution, yet also suggest how we can start to
 predict the impacts such complexities will have on phenotypic divergence
 and community stability.
description: Data from all
 experiments described in the studyThe data in this file
 feature in the paper "Evolutionary dynamics of interlinked public
 goods traits: an experimental study of siderophore production in
 Pseudomonas aeruginosa", by Adin Ross-Gillespie, Zoé Dumas and Rolf
 Kümmerli. The paper has been accepted for publication in the Journal of
 Evolutionary Biology (as of November 2014) The xls file comprises two
 sheets, namely 'SelectionExperiment' and
 'CompetitionExperiment', comprising data from figures 3 and 4;
 and figures 2 and S1, respectively. Further information, including
 description of the variables, is provided in each
 spreadsheet.Ross-Gillespie_et_al_JEB12559_Data_for_Dryad.xlsx
DOI: 10.5061/dryad.qb36g
title: Data from: DNA barcoding of tuberous Orchidoideae: a resource for identification of orchids used in Salep

description: Tubers of terrestrial orchids are harvested and traded from the eastern
 Mediterranean to the Caspian Sea for the traditional product Salep.
 Overexploitation of wild populations and increased middle-class prosperity
 have escalated prices for Salep, causing overharvesting, depletion of
 native populations and providing an incentive to expand harvesting to
 untapped areas in Iran. Limited morphological distinctiveness among traded
 Salep tubers renders species identification impossible, making it
 difficult to establish which species are targeted and affected the most.
 In this study, a reference database of 490 nrITS, trnL-F spacer and matK
 sequences of 133 taxa was used to identify 150 individual tubers from 31
 batches purchased in 12 cities in Iran to assess species diversity in
 commerce. The sequence reference database consisted of 211 nrITS, 158
 trnL-F and 121 matK sequences, including 238 new sequences from
 collections made for this study. The markers enabled unambiguous species
 identification with tree-based methods for nrITS in 67% of the tested
 tubers, 58% for trnL-F and 59% for matK. Species in the genera Orchis
 (34%), Anacamptis (27%) and Dactylorhiza (19%) were the most common in
 Salep. Our study shows that all tuberous orchid species in this area are
 threatened by this trade, and further stresses the urgency of controlling
 illegal harvesting and cross-border trade of Salep tubers.
description: Supplements
 1-12Supplemental Data
 Supplement 1. Reference sequences derived from vouchers collected for this
 study. Supplement 2. Reference sequences derived from external NCBI
 GenBank accessions. Supplement 3. GenBank accession numbers of the Salep
 tubers. Supplement 4. RAxML maximum likelihood phylogenetic tree for
 nrITS. Supplement 5. RAxML maximum likelihood phylogenetic tree for trnL-F
 spacer. Supplement 6. RAxML maximum likelihood phylogenetic tree for matK.
 Supplement 7. RAxML maximum likelihood phylogenetic tree for the
 concatenated matrix. Supplement 8. MrBayes bayesian phylogenetic tree for
 nrITS. Supplement 9. MrBayes bayesian phylogenetic tree for trnL-F spacer.
 Supplement 10. MrBayes bayesian phylogenetic tree for matK. Supplement 11.
 MrBayes bayesian phylogenetic tree for the concatenated matrix. Supplement
 12. Molecular identifications of tubers based on similarity- and
 tree-based approaches.Sequence alignment
 filesAlignment matrices in
 FASTA format per individual marker and concatenated matrix for RAxML and
 MrBayes phylogenetic analyses. Matrices are labelled with the
 corresponding tree supplement name and number.
DOI: 10.5061/dryad.44g1b
title: Data from: Specialization to extremely low-nutrient soils limits the nutritional adaptability of plant lineages

description: Specialization to extreme selective situations promotes the acquisition of
 traits whose coadaptive integration may compromise evolutionary
 flexibility and adaptability. We test this idea in the context of the
 foliar stoichiometry of plants native to the South African Cape. Whereas
 foliar concentrations of nitrogen, phosphorus (P), potassium (K), calcium,
 magnesium, and sodium showed strong phylogenetic signal, as did the foliar
 ratios of these nutrients to P, the same was not true of the corresponding
 soil values. In addition, although foliar traits were often related to
 soil values, the coefficients of determination were consistently low.
 These results identify foliar stoichiometry as having a strong genetic
 component, with variation in foliar nutrient concentrations, especially
 [P] and [K], being identified as potentially adaptive. Comparison of
 stoichiometric variation across 11 similarly aged clades revealed
 consistently low foliar nutrient concentrations in lineages showing
 specialization to extremely low-nutrient fynbos heathlands. These lineages
 also display lower rates of evolution of these traits as well as a reduced
 tendency for foliar [P] to track soil [P]. Reduced evolutionary lability
 and adaptability in the nutritional traits of fynbos-specialist lineages
 may explain the floristic distinctness of the fynbos flora and implies a
 reduced scope for edaphically driven ecological speciation.
description: TableS1Spreadsheet containing raw data for all of the foliar and soil variables studied. Each accession is furnished with a species identity, a voucher number and a collection locality. All nutrient concentration (soil and foliar) are expressed in units of g kg-1, while nutrient ratios were determined on a mass-basis.TableS2Spreadsheet scoring (present = 1, absent = 0) the vegetation (columns 5-9) and geological (columns 10-14) associations of study species. The final two columns indicate the total number of vegetation types and geologies occupied by each species.beast_revisedBEAST xml file used to generate the phylogenetic tree for comparative analyses.beast_revised_mcc_newickBEAST maximum clade credibility tree used for comparative analyses.R filesZip archive containing the R code and associated input files used for the main analyses.
DOI: 10.5061/dryad.0f8p4c5
title: Data from: Native lagomorphs suppress grass establishment in a shrub‐encroached, semiarid grassland

description: Shrub encroachment into arid grasslands has been associated with reduced
 grass abundance, increased soil erosion, and local declines in
 biodiversity. Livestock overgrazing and the associated reduction of fine
 fuels has been a primary driver of shrub encroachment in the southwestern
 United States, but shrublands continue to persist despite livestock
 removal and grassland restoration efforts. We hypothesized that herbivory
 feedbacks from native mammals may contribute to continued suppression of
 grasses after the removal of livestock. Our herbivore exclusion experiment
 in southeastern Arizona included five treatment levels and allowed access
 to native mammals based on their relative body size, separating the
 effects of rodents, lagomorphs, and mule deer. We included two control
 treatments and replicated each treatment 10 times (n = 50). We introduced
 uniform divisions of lawn sod (Cynodon dactylon) into each exclosure for
 24-hour periods prior to (n = 2) and following (n = 2) the monsoon rains
 and used motion-activated cameras to document herbivore visitations. In
 the pre-monsoon trials, treatments that allowed lagomorph access had less
 sod biomass relative to other treatments (p &lt; 0.001), averaging 44%
 ( 36%) and 29% ( 45%) remaining biomass after the 24-hour trial periods.
 Following the onset of monsoons, differences in remaining biomass among
 treatments disappeared. Desert cottontails (Sylvilagus audubonii) were
 detected more frequently than any of the other 11 herbivore species
 present at the site, accounting for 83% of detections during the
 pre-monsoon trials. Significantly more (p &lt; 0.001) desert
 cottontails were detected during the pre-monsoon trials (2,077) compared
 to the post-monsoon trials (174), which coincided with biomass removal
 from lagomorph accessible treatments. We conclude that desert cottontails
 are significant consumers of herbaceous vegetation in shrub-encroached
 arid grasslands and they, along with other native herbivores, may act as a
 biotic feedback contributing to the competitive advantage and persistence
 of shrubs.
description: Herbivore_DetectionsHerbivore detections captured with trail cameras during sod trialsSod_DataSod data results from experimental herbivore exclosuresSeed_Addition_Cover_EstimatesGrass cover in experimental herbivore exclosures from direct seeding experiment
DOI: 10.5061/dryad.2dv7r
title: Data from: Trends in malaria in Odisha, India—an analysis of the 2003-2013 time-series data from the National Vector Borne Disease Control Program

description: Background: Although Odisha is the largest contributor to the malaria
 burden in India, no systematic study has examined its malaria trends.
 Hence, the spatio-temporal trends in malaria in Odisha were assessed
 against the backdrop of the various anti-malaria strategies implemented in
 the state. Methods: Using the district-wise malaria incidence and blood
 examination data (2003-2013) from the National Vector Borne Disease
 Control Program, blood examination-adjusted time-trends in malaria
 incidence were estimated and predicted for 2003-2013 and 2014-2016,
 respectively. An interrupted time series analysis using segmented
 regression was conducted to compare the disease trends between the pre
 (2003-2007) and post-intensification (2009-2013) periods. Key-informant
 interviews of state stakeholders were used to collect the information on
 the various anti-malaria strategies adopted in the state. Results: The
 state annual malaria incidence declined from 10.82/1000 to 5.28/1000
 during 2003-2013 (adjusted annual decline: -0.54/1000, 95% CI: -0.78 to
 -0.30). However, the annual blood examination rate remained almost
 unchanged from 11.25% to 11.77%. The key-informants revealed that
 intensification of anti-malaria activities in 2008 led to a more rapid
 decline in malaria incidence during 2009-2013 as compared to that in
 2003-2007 [adjusted decline: -0.83 (-1.30 to -0.37) and -0.27 (-0.41 to
 -0.13), respectively]. There was a significant difference in the two
 temporal slopes, i.e., -0.054 (-0.10 to -0.002, p=0.04) per 1000
 population per month, between these two periods, indicating almost a 200%
 greater decline in the post-intensification period. Although, the seven
 southern high-burden districts registered the highest decline, they
 continued to remain in that zone, thereby, making the achievement of
 malaria elimination (incidence &lt;1/1000) unlikely by 2017.
 Conclusion: The anti-malaria strategies in Odisha, especially their
 intensification since 2008, have helped improve its malaria situation in
 recent years. These successful measures need to be sustained and perhaps
 intensified further for eliminating malaria from Odisha.
description: Total blood slides
 examined for malaria vs total slide positives during
 2003-2013,Odisha(India)Malaria_2003-2013_Odisha.zip
DOI: 10.5061/dryad.1713
title: Data from: Host associated genetic differentiation in a seed parasitic weevil Rhinusa antirrhini (Coleptera: Curculionidae) revealed by mitochondrial and nuclear sequence data

description: Plant feeding insects and the plants they feed upon represent an
 ecological association that is thought to be a key factor for the
 diversification of many plant feeding insects, through differential
 adaptation to different plant selective pressures. While a number of
 studies have investigated diversification of plant feeding insects above
 the species level, relatively less attention has been given to patterns of
 diversification within species, particularly those that also require
 plants for oviposition and subsequent larval development. In the case of
 plant feeding insects that also require plant tissues for the completion
 of their reproductive cycle through larval development, the divergent
 selective pressure not only acts on adults, but on the full life history
 of the insect. Here we focus attention on Rhinusa antirrhini
 (Curculionidae), a species of weevil broadly distributed across Europe
 that both feeds on, and oviposits and develops within, species of the
 plant genus Linaria (Plantaginaceae). Using a combination of mtDNA (COII)
 and nuclear DNA (EF1-α) sequencing and copulation experiments we assess
 evidence for host associated genetic differentiation within R. antirrhini.
 We find substantial genetic variation within this species that is best
 explained by ecological specialisation on different host plant taxa. This
 genetic differentiation is most pronounced in the mtDNA marker, with
 patterns of genetic variation at the nuclear marker suggesting incomplete
 lineage sorting and/or gene flow between different host plant forms of R.
 antirrhini, whose origin is estimated to date to the mid-Pliocene (3.77
 mya; 2.91-4.80 mya).
description: R.antirrhiniCOII-AlignmentNexus.txtNexus file of COII sequencesR.antirrhiniEF1-AlignmentNexus.txtNexus file of Elongation Factor sequencesAccessionsList-R.antirrhini.xlsxthe list of samples analyses in the paper with relevant accession codes