cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.c316t
title: Data from: Niche differentiation and colonization of a novel environment by an asexual parasitic wasp.

description: How do asexual taxa become adapted to a diversity of environments, and how
 do they persist despite changing environmental conditions? These questions
 are linked by their mutual focus on the relationship between genetic
 variation, which is often limited in asexuals, and the ability to respond
 to environmental variation. Asexual taxa originating from a single
 ancestor present a unique opportunity to assess rates of phenotypic and
 genetic change when access to new genetic variation is limited to
 mutation. Diachasma muliebre is an asexual Hymenopteran wasp that is
 geographically and genetically isolated from all sexual relatives. D.
 muliebre attack larvae of the western cherry fruit fly (Rhagoletis
 indifferens), which in turn feed inside bitter cherry fruit (Prunus
 emarginata) in August and September. R. indifferens has recently colonized
 a new host plant with an earlier fruiting phenology (June/July),
 domesticated sweet cherries (P. avium), and D. muliebre has followed its
 host into this temporally earlier niche. We tested three hypotheses: 1)
 that all D. muliebre lineages originate from a single asexual ancestor; 2)
 that different D. muliebre lineages (as defined by unique mtDNA
 haplotypes) have differentiated on their ancestral host in an important
 life-history trait, eclosion timing; and 3) that early-eclosing lineages
 have preferentially colonized the new sweet cherry niche. We find that
 mitochondrial COI and microsatellite data provide strong support for a
 single ancestral origin for all lineages. Furthermore, COI sequencing
 revealed five mitochondrial haplotypes among D. muliebre, and individual
 wasps possessing one distinctive mitochondrial haplotype (haplotype II)
 eclosed as reproductive adults significantly earlier than wasps with all
 other haplotypes. In addition, this early-eclosing lineage of D. muliebre
 is one of two lineages that have colonized the P. avium habitat,
 consistent with the preferential colonization hypothesis. These data
 suggest that D. muliebre has evolved adaptive phenotypic variation despite
 limited genetic variation, and that this variation has subsequently
 allowed an expansion of some wasps into a novel habitat. The D. muliebre
 system may allow for in-depth study of adaptation and long-term
 persistence of asexual taxa.
description: Dryad 1 - Emergence
 dates and haplotypesContains eclosion dates
 of all D. muliebre wasps in the study, alongside scored haplotypes
 (numbered 1-5 and corresponding with sequences on
 GenBank).Dryad 2 -
 microsatellites - DmuliebreD. muliebre
 microsatellite allele scoresDryad 3 -
 microsatellites - DferrugineumMicrosatellite allele
 scores for D. ferrugineum
DOI: 10.5061/dryad.ng4b0
title: Data from: There’s no place like home: the contribution of direct and extended phenotypes on the expression of spider aggressiveness

description: Architectural constructions allow animals to modify their environment in
 order to improve their reproductive success. Constructions also modulate
 the expression of individual behavior, ultimately affecting the presence
 and importance of animal personality within populations. The exact impact
 of constructions on personality is seldom investigated. We quantified
 experimentally the impact of web characteristics on individual foraging
 behavior in the Western black widow spider (Latrodectus hesperus). We
 assayed aggressiveness toward a prey cue, and boldness while individuals
 resided on their own web versus after being translocated onto webs built
 by con-specifics. We quantified the importance of individual differences
 in aggressiveness and boldness while accounting for differences in web
 characteristics. We tested for relationships between web building,
 aggressiveness, and boldness. Web characteristics affected spider
 aggressiveness and interacted with individual web-building behavior to
 explain up to a fifth of the variation in foraging aggression, but did not
 affect spider boldness. Even after accounting for web characteristics,
 individuals still exhibited important differences in aggressiveness. We
 detected no relationship between an individual’s aggressiveness behavioral
 type and the characteristics of the web it built. Surprisingly, web
 characteristics impacted aggressiveness differently from one individual to
 the next. Hence the effect of web characteristics on foraging behavior
 might depend on condition or past experience. Webs contributed mostly to
 the variation in aggressiveness within-individuals. Variation in web
 building behavior might affect the amount of consistent differences in
 foraging, mating, and anti-predator behavior among individuals and needs
 to be accounted for when quantifying individual variation in behavior in
 spiders.
description: metadataDescribes all the variables in the csv file data.black.widow.spiderdata.black.widow.spidersDataset used for the study. Variables are explained in the file metadata.new.script.anotatedscript allowing to redo all the analyses presented in the data and to produce the figures.
DOI: 10.5061/dryad.n581t
title: Data from: Deliberation favours social efficiency by making people disregard their relative shares: evidence from USA and India

description: Groups make decisions on both the production and the distribution of
 resources. These decisions typically involve a tension between increasing
 the total level of group resources (i.e. social efficiency) and
 distributing these resources among group members (i.e. individuals'
 relative shares). This is the case because the redistribution process may
 destroy part of the resources, thus resulting in socially inefficient
 allocations. Here we apply a dual-process approach to understand the
 cognitive underpinnings of this fundamental tension. We conducted a set of
 experiments to examine the extent to which different allocation decisions
 respond to intuition or deliberation. In a newly developed approach, we
 assess intuition and deliberation at both the trait level (using the
 Cognitive Reflection Test, henceforth CRT) and the state level (through
 the experimental manipulation of response times). To test for robustness,
 experiments were conducted in two countries: the USA and India. Despite
 absolute-level differences across countries, in both locations we show
 that: (i) time pressure and low CRT scores are associated with
 individuals' concerns for their relative shares and (ii) time delay
 and high CRT scores are associated with individuals' concerns for
 social efficiency. These findings demonstrate that deliberation favours
 social efficiency by overriding individuals' intuitive tendency to
 focus on relative shares.
description: DataThis file contains the
 data of our experiment
DOI: 10.5061/dryad.7n344
title: Data from: Origin, acquisition and diversification of heritable bacterial endosymbionts in louse flies and bat flies

description: The γ-proteobacterium Arsenophonus and its close relatives (Arsenophonus
 and like organisms, ALOs) are emerging as a novel clade of endosymbionts,
 which are exceptionally widespread in insects. The biology of ALOs is,
 however, in most cases entirely unknown, and it is unclear how these
 endosymbionts spread across insect populations. Here, we investigate this
 aspect through the examination of the presence, the diversity and the
 evolutionary history of ALOs in 25 related species of blood-feeding flies:
 tsetse flies (Glossinidae), louse flies (Hippoboscidae) and bat flies
 (Nycteribiidae and Streblidae). While these endosymbionts were not found
 in tsetse flies, we identify louse flies and bat flies as harbouring the
 highest diversity of ALO strains reported to date, including a novel ALO
 clade, as well as Arsenophonus and the recently described Candidatus
 Aschnera chinzeii clade. We further show that the origin of ALO
 endosymbiosies extends deep into the evolutionary past of louse flies and
 bat flies, and that it likely played a major role in the ecological
 specialization of their hosts. The evolutionary history of ALOs is notably
 complex and was shaped by both vertical transmission and horizontal
 transfers with frequent host turnover and apparent symbiont replacement in
 host lineages. In particular, ALOs have evolved repeatedly and
 independently close relationships with diverse groups of louse flies and
 bat flies, as well as phylogenetically more distant insect families,
 suggesting that ALO endosymbioses are exceptionally dynamic systems.
description: aligned_ALO_groel_fasta_sequencesBacterial GroEL aligned sequencesALO_fbaA_tree_fileBacterial fbaA ML tree filealigned_ALO_fbaA_fasta_sequencesBacterial fbaA aligned fasta sequencesALO_GroEL_tree_fileBacterial GroEL ML tree filealigned_ALO_ftsK_fasta_sequencesBacterial ftsK aligned fasta sequencesALO_ftsK_tree_fileBacterial FtsK ML tree filealigned_ALO_yaeT_fasta_sequencesBacterial yaeT aligned fasta sequencesALO_yaeT_tree_fileBacterial yaeT ML tree file
DOI: 10.5061/dryad.sk2pg32
title: Data from: Optimizing prevention of HIV mother to child transmission: duration of antiretroviral therapy and viral suppression at delivery among pregnant Malawian women

description: Background: Effective antiretroviral therapy during pregnancy minimizes
 the risk of vertical HIV transmission. Some women present late in their
 pregnancy for first antenatal visit; whether these women achieve viral
 suppression by delivery and how suppression varies with time on ART is
 unclear. Methods: We conducted a prospective cohort study of HIV-infected
 pregnant women initiating antiretroviral therapy for the first time from
 June 2015 to November 2016. Multivariable Poisson models with robust
 variance estimators were used to estimate risk ratios (RR) and 95%
 confidence intervals (CI) of the association between duration of ART and
 both viral load (VL) ≥1000 copies/ml and VL ≥40 copies/ml at delivery.
 Results: Of the 252 women who had viral load testing at delivery, 40 (16%)
 and 78 (31%) had VL ≥1000 copies/ml and VL ≥40 copies/ml, respectively.
 The proportion of women with poor adherence to ART was higher among women
 who were on ART for ≤12 weeks (9/50 = 18.0%) than among those who were on
 ART for 13-35 weeks (18/194 = 9.3%). Compared to women who were on ART for
 ≤12 weeks, women who were on ART for 13-20 weeks (RR = 0.52; 95% CI:
 0.36-0.74) or 21-35 weeks (RR = 0.26; 95% CI: 0.14-0.48) had a lower risk
 of VL ≥40 copies/ml at delivery. Similar comparisons for VL ≥1000
 copies/ml at delivery showed decrease in risk although not significant for
 those on ART 13-20 weeks. Conclusion: Longer duration of ART during
 pregnancy was associated with suppressed viral load at delivery. Early ANC
 attendance in pregnancy to facilitate prompt ART initiation for
 HIV-positive women is essential in the effort to eliminate HIV vertical
 transmission.
description: Viral
 suppressionViral suppression for
 HIV-infected pregnant women initiating ART for the first
 time.
DOI: 10.5061/dryad.rb06j
title: Data from: The cryptic and the apparent reversed: lack of genetic differentiation within the morphologically diverse plexus of the planktonic foraminifer Globigerinoides sacculifer

description: Previous genetic studies of extant planktonic foraminifera have provided
 evidence that the traditional, strictly morphological definition of
 species in these organisms underestimates their biodiversity. Here, we
 report the first case where this pattern is reversed. The modern
 (sub)tropical species plexus Globigerinoides sacculifer is characterized
 by large morphological variability, which has led to the proliferation of
 taxonomic names attributed to morphological end-members within the plexus.
 In order to clarify the taxonomic status of its morphotypes and to
 investigate the genetic connectivity among its currently partly disjunct
 (sub)tropical populations, we carried out a global survey of two ribosomal
 RNA regions (SSU and ITS-1) in all recent morphotypes of the plexus
 collected throughout (sub)tropical surface waters of the global ocean.
 Unexpectedly, we find an extremely reduced genetic variation within the
 plexus and no correlation between genetic and morphological divergence,
 suggesting taxonomical overinterpretation. The genetic homogeneity within
 the morphospecies is unexpected, considering its partly disjunct range in
 the (sub)tropical Atlantic and Indo-Pacific and its old age (early
 Miocene). A sequence variant in the rapidly evolving ITS-1 region
 indicates the existence of an exclusively Atlantic haplotype, which
 suggests an episode of relatively recent (last glacial) isolation,
 followed by subsequent resumption of unidirectional gene flow from the
 Indo-Pacific into the Atlantic. This is the first example in planktonic
 foraminifera where the morphological variability in a morphospecies
 exceeds its rDNA genetic variability. Such evidence for inconsistent
 scaling of morphological and genetic diversity in planktonic foraminifera
 could complicate the interpretation of evolutionary patterns in their
 fossil record.
description: Supplement Table1_ANDRE
 ET AL_2013Supplementary
 information on individuals of the Globigerinoides sacculifer plexus
 sequenced in the work by André et al. (2013)
DOI: 10.5061/dryad.12g6g
title: Data from: Rates and predictors of attrition among children on antiretroviral therapy in Ethiopia: a prospective cohort study

description: Introduction: Attrition from antiretroviral therapy (ART) programmes is a
 critical challenge among children receiving care in resource-limited
 settings. Our objective was to determine the rates and predictors of
 attrition among children on ART in Ethiopia. Methods: Between December
 2014 and September 2016, we conducted a prospective cohort study in eight
 health facilities in Ethiopia. Eligibility criteria included age 3
 months-14 years; being on ART for not more than a month. Outcome was
 attrition due to death and/or loss to follow-up. Predictor variables were
 child clinical and socio-demographic characteristics, and caregiver
 socio-demographic characteristics. We used Cox Regression analyses to
 examine the association between predictors and outcome. Results: Of 309
 children, 304 were included, 52% were male. Their median age was 9 years
 (Inter-quartile range, IQR, 6-12). At ART initiation, their median CD4 was
 362 cells/mm3 (IQR 231-499); and 74.3% had WHO stage 1 or 2 disease.
 During 287.7 person-years of observation (PYO), 24 attritions were
 recorded, yielding an attrition rate of 8.3 per 100 PYO (95% CI 5.4-12.1).
 Of these, six children were reported dead, leading to a mortality rate of
 2.1 per 100 PYO (95% CI 0.8-4.3). Eighteen were lost to follow-up (LTFU)
 leading to LTFU rate of 6.26 per 100 PYO (95% CI: 3.83-9.70). The
 majority, 14 (58%) of attrition occurred during the first six months of
 treatment. Age below three years [aHR]= 5.14 (95% CI: 2.07-12.96), rural
 residence (aHR = 3.97, 95% CI: 1.34-11.78) and baseline Hgb in g/dl
 &lt; 10 g/dl [aHR]= 5.68 (95% CI: 2.03-6.23) predicted higher risk of
 attrition. Baseline Hgb &lt; 10 g/dl (aHR= 16.63, 95% CI: 1.64-168.4)
 and WHO stage III or IV (aHR= 12.25, 95% CI: 1.26-119.05) predicted the
 death of the child. Higher attrition was documented among children of both
 biological parents alive and biologically related close family caregivers.
 Conclusion: Younger children, those from rural areas, and children with
 anaemia were at higher risk of attrition, especially during the early
 months of treatment, and therefore should be prioritized during treatment
 follow-up. Further studies should examine underlying reasons for higher
 attrition
description: Supporting information
 filesData file includes the
 analysis outputs of tables, chart and graphs to support the accepted
 research article.
DOI: 10.5061/dryad.8590
title: Data from: Between-year variation in population sex ratio increases with complexity of the breeding system in Hymenoptera

description: While adaptive adjustment of sex ratio in function of colony kin structure
 and food availability commonly occurs in social Hymenoptera, long-term
 studies have revealed substantial unexplained between-year variation in
 sex ratio at the population level. In order to identify factors that
 contribute to increased between-year variation in population sex ratio, we
 conducted a comparative analysis across 47 Hymenoptera species differing
 in their breeding system. We found that between-year variation in
 population sex ratio steadily increased as one moves from solitary
 species, to primitively eusocial species, to single-queen eusocial
 species, to multiple-queen eusocial species. Specifically, between-year
 variation in population sex ratio was low (6.6% of total possible
 variation) in solitary species, which is consistent with the view that in
 solitary species sex ratio can only vary in response to fluctuations in
 ecological factors such as food availability. In contrast, we found
 significantly higher (19.5%) between-year variation in population sex
 ratio in multiple-queen eusocial species, which supports the view that in
 these species sex ratio can also fluctuate in response to temporal changes
 in social factors such as queen number, queen-worker control over sex
 ratio, and factors influencing caste determination. The simultaneous
 adjustment of sex ratio in response to temporal fluctuations in ecological
 and social factors seems to preclude the existence of a single sex ratio
 optimum. The absence of such an optimum may reflect an additional cost
 associated with the evolution of complex breeding systems in Hymenoptera
 societies.
description: RK_LK_sexratio_rawdata_AmNatThis file contains the raw estimates of sex ratio for the 81 populations and 47 species used in this comparative analysis. It also includes the nexus code for the inferred phylogeny used in this paper.
DOI: 10.5061/dryad.bc4gk
title: Data from: The use of a mercury biosensor to evaluate the bioavailability of mercury-thiol complexes and mechanisms of mercury uptake in bacteria

description: As mercury (Hg) biosensors are sensitive to only intracellular Hg, they
 are useful in the investigation of Hg uptake mechanisms and the effects of
 speciation on Hg bioavailability to microbes. In this study, bacterial
 biosensors were used to evaluate the roles that several transporters such
 as the glutathione, cystine/cysteine, and Mer transporters play in the
 uptake of Hg from Hg-thiol complexes by comparing uptake rates in strains
 with functioning transport systems to strains where these transporters had
 been knocked out by deletion of key genes. The Hg uptake into the
 biosensors was quantified based on the intracellular conversion of
 inorganic mercury (Hg(II)) to elemental mercury (Hg(0)) by the enzyme
 MerA. It was found that uptake of Hg from Hg-cysteine (Hg(CYS)2) and
 Hg-glutathione (Hg(GSH)2) complexes occurred at the same rate as that of
 inorganic complexes of Hg(II) into Escherichia coli strains with and
 without intact Mer transport systems. However, higher rates of Hg uptake
 were observed in the strain with a functioning Mer transport system. These
 results demonstrate that thiol-bound Hg is bioavailable to E. coli and
 that this bioavailability is higher in Hg-resistant bacteria with a
 complete Mer system than in non-resistant strains. No difference in the
 uptake rate of Hg from Hg(GSH)2 was observed in E. coli strains with or
 without functioning glutathione transport systems. There was also no
 difference in uptake rates between a wildtype Bacillus subtilis strain
 with a functioning cystine/cysteine transport system, and a mutant strain
 where this transport system had been knocked out. These results cast doubt
 on the viability of the hypothesis that the entire Hg-thiol complex is
 taken up into the cell by a thiol transporter. It is more likely that the
 Hg in the Hg-thiol complex is transferred to a transport protein on the
 cell membrane and is subsequently internalized.
description: Data for Biosensor
 Paper-aData for Biosensor
 Paper-c
DOI: 10.5061/dryad.3nf8b
title: Data from: Exploiting mycorrhizas in broad daylight: partial mycoheterotrophy is a common nutritional strategy in meadow orchids.

description: Partial mycoheterotrophy (PMH) is a nutritional mode in which plants
 utilize organic matter, i.e. carbon, both from photosynthesis and a fungal
 source. The latter reverses the direction of plant-to-fungus carbon flow
 as usually assumed in mycorrhizal mutualisms. Based on significant
 enrichment in the heavy isotope 13C, a growing number of PMH orchid
 species have been identified. These PMH orchids are mostly associated with
 fungi simultaneously forming ectomycorrhizas with forest trees. In
 contrast, the much more common orchids that associate with rhizoctonia
 fungi, which are decomposers, have stable isotope profiles most often
 characterized by high 15N enrichment and high nitrogen concentrations but
 either an insignificant 13C enrichment or depletion relative to
 autotrophic plants. Using hydrogen stable isotope abundances recent
 investigations showed PMH in rhizoctonia-associated orchids growing under
 light-limited conditions. Hydrogen isotope abundances can be used as
 substitute for carbon isotope abundances in cases where autotrophic and
 heterotrophic carbon sources are insufficiently distinctive to indicate
 PMH. To determine whether rhizoctonia-associated orchids growing in
 habitats with high irradiance feature PMH as a nutritional mode, we
 sampled 13 orchid species growing in montane meadows, four forest orchid
 species and 34 autotrophic reference species. We analysed δ2H, δ13C, δ15N
 and δ18O and determined nitrogen concentrations. Orchid mycorrhizal fungi
 were identified by DNA sequencing. As expected, we found high enrichments
 in 2H, 13C, 15N and nitrogen concentrations in the
 ectomycorrhiza-associated forest orchids, and the rhizoctonia-associated
 Neottia cordata from a forest site was identified as PMH. Most orchids
 inhabiting sunny meadows lacked 13C enrichment or were even significantly
 depleted in 13C relative to autotrophic references. However, we infer PMH
 for the majority of these meadow orchids due to both significant 2H and
 15N enrichment and high nitrogen concentrations. Pseudorchis albida was
 the sole autotrophic orchid in this study as it exhibited neither
 enrichment in any isotope nor a distinctive leaf nitrogen concentration.
 Synthesis. Our findings demonstrate that partial mycoheterotrophy is a
 trophic continuum between the extreme endpoints of autotrophy and full
 mycoheterotrophy, ranging from marginal to pronounced. In
 rhizoctonia-associated orchids, partial mycoheterotrophy plays a far
 greater role than previously assumed, even in full light conditions.
description: Stable isotope and
 nitrogen concentration dataSingle and mean δ15N,
 δ13C, δ2H, δ18O values, enrichment factors ε15N, ε13C, ε2H, ε18O and total
 nitrogen concentration data of 17 Orchidaceae species and 34 autotrophic
 reference species.JEcol-2017-0083_data.xlsx