cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.9188nq3
title: Data from: Na+/K+‐ATPase gene duplications in clitellate annelids are associated with freshwater colonization

description: Major habitat transitions, such as those from marine to freshwater
 habitats or from aquatic to terrestrial habitats, have occurred
 infrequently in animal evolution and may represent a barrier to
 diversification. Identifying genomic events associated with these
 transitions can help us better understand mechanisms that allow animals to
 cross these barriers and diversify in new habitats. Study of the Capitella
 telata and Helobdella robusta genomes allows examination of one such
 habitat transition (marine to freshwater) in Annelida. Initial examination
 of these genomes indicated that the freshwater leech H. robusta contains
 many more copies (12) of the sodium-potassium pump alpha subunit
 (Na+/K+-ATPase) gene than does the marine polychaete C. telata (2). The
 sodium-potassium pump plays a key role in maintenance of cellular ionic
 balance and osmoregulation, and Na+/K+-ATPase duplications may have helped
 annelids invade and diversify in freshwater habitats. To assess whether
 the timing of Na+/K+-ATPase duplications coincided with the
 marine-to-freshwater transition in Clitellata we used transcriptomic data
 from 18 annelid taxa, along with the two genomes, to infer a species
 phylogeny and identified Na+/K+-ATPase gene transcripts in order to infer
 the timing of gene duplication events using tree-based methods. The
 inferred timing of Na+/K+-ATPase duplication events is consistent with the
 timing of the initial marine-to-freshwater transition early in the history
 of clitellate annelids, supporting the hypothesis that gene duplications
 may have played a role in the annelid diversification into freshwater
 habitats.
description: molluskoutgroup_species_min10_concatData matrix for maximum likelihood phylogenetic analysis with mollusk outgroups.annelidonly_species_min10_filtered_concatData matrix for maximum likelihood phylogenetic analysis without mollusk outgroupsmolluskoutgroup_min10_raxml_partitionRAxML partition file for data matrix with mollusk outgroupsannelidonly_filtered_raxml_partitionRAxML partition file for data matrix without mollusk outgroupsLB_PD_filterR script to filter loci based on branch length heterogeneity of the gene trees.node_collapsePython script to collapse species-specific nodes into one sequence
DOI: 10.5061/dryad.2kf78h8
title: Data from: Is dietary or microhabitat specialization associated with environmental heterogeneity in horned lizards (Phrynosoma)?

description: Niche breadth is predicted to correlate with environmental heterogeneity,
 such that generalists will evolve in heterogeneous environments and
 specialists will evolve in environments that vary less over space and
 time. We tested the hypothesis that lizards in a heterogeneous environment
 were generalists compared to lizards in a homogeneous environment. We
 compared niche breadths of greater short-horned lizards by quantifying
 resource selection in terms of two different niche axes, diet (prey items
 and trophic level) and microhabitat (ground cover and shade cover),
 between two populations occurring at different elevations. We assessed the
 heterogeneity of dietary and microhabitat resources within each
 population’s environment by quantifying the availability of prey items,
 ground cover, and shade cover in each environment. Overall, our results
 demonstrate that despite differences in resource heterogeneity between
 elevations, resource selection did not consistently differ between
 populations. Moreover, environmental heterogeneity was not associated with
 generalization of resource use. The low-elevation site had a broader range
 of available prey items, yet lizards at the high-elevation site
 demonstrated more generalization in diet. In contrast, the high-elevation
 site had a broader range of available microhabitats, but the lizard
 populations at both sites were similarly generalized for shade cover
 selection, and were similarly specialized for ground cover selection. Our
 results demonstrate that environmental heterogeneity of a particular
 resource does not necessarily predict the degree to which organisms
 specialize on that resource.
description: dietary and microhabitat
 data, used and availableDiet data, 1: stable
 isotope analysis of lizard fecal samples and primary producers at high and
 low elevation sites. Diet data, 2: used prey items (from stomach samples)
 and available prey items (from pitfall traps) at high and low elevation
 sites. Microhabitat data: ground cover types and shade cover amounts at
 sites used by lizards, and paired unused but available sites (random
 sites), at high and low elevation.lizard diet and microhabitat
 data.xlsx
DOI: 10.5061/dryad.639k103
title: Data from: Individual factors associated with time to non-adherence to ART pick-up within HIV care and treatment services in three health facilities of Zambézia Province, Mozambique

description: Introduction: Mozambique has made significant gains in addressing its HIV
 epidemic, yet adherence to visit schedules remains a challenge. HIV
 programmatic gains to date could be impaired if adherence and retention to
 ART remains low. We investigate individual factors associated with
 non-adherence to ART pick-up in Mozambique. Methods: This was a
 retrospective cohort of patients initiating ART between January 2013 and
 June 2014. Non-adherence to ART pick-up was defined as a delay in pick-up
 ? 15 days. Descriptive statistics were used to calculate socio-demographic
 and clinical characteristics. Adherence to ART pick-up was assessed using
 Kaplan Meier estimates. Cox proportional hazards model was used to
 determine factors associated with non-adherence. Results: 1,413
 participants were included (77% female). Median age was 30.4 years. 19% of
 patients remained adherent to ART pick-up during the evaluation period,
 while 81% of patients were non-adherent to ART pick-up. Probability of
 being non-adherent to ART pick-up by 166 days following initiation was
 50%. In univariate analysis, being widowed was associated with higher
 adherence to ART pick-up than other marital status groups (p=0.01). After
 adjusting, being ?35 years (aHR: 0.843, 95% CI: 0.738-0.964, p=0.012);
 receiving efavirenz (aHR: 0.932, 95% CI: 0.875-0.992, p=0.026); and being
 urban (aHR: 0.754, 95% CI: 0.661-0.861, p&lt;0.0001) were associated
 with improved adherence. Non-participation in a Community ART Support
 Group (CASG) was associated with a 43% increased hazard of non-adherence
 to ART pick-up (aHR 1.431, 1.192-1.717, p&lt;0.0001) . Conclusions:
 Interventions should focus on the first 6 months following ARV initiation
 for improvements. Younger persons and widows are two target groups for
 better understanding facilitators and barriers to visit schedule
 adherence. Future strategies should explore the benefits of joining CASGs
 earlier in one´s treatment course. Finally, greater efforts should be made
 to accelerate the scale-up of viral load capacity and HIV resistance
 monitoring.
description: dataset_Indiv factors
 assoc with non-adh to ART pick-upthis is a dataset of
 deidentified data of patients enrolled in the HIV care and treatment
 program of Zambezia Province, Mozambique
DOI: 10.5061/dryad.3fh816m
title: Data from: Latitudinal variation and coevolutionary diversification of sexually dimorphic traits in the false blister beetle Oedemera sexualis

description: Sexual traits are subject to evolutionary forces that maximize
 reproductive benefits and minimize survival costs, both of which can
 depend on environmental conditions. Latitude explains substantial
 variation in environmental conditions. However, little is known about the
 relationship between sexual trait variation and latitude, although body
 size often correlates with latitude. We examined latitudinal variation in
 male and female sexual traits in 22 populations of the false blister
 beetle Oedemera sexualis in the Japanese Archipelago. Males possess
 massive hind legs that function as a female‐grasping apparatus, while
 females possess slender hind legs that are used to dislodge mounting
 males. Morphometric analyses revealed that male and female body size
 (elytron length), length and width of the hind femur and tibia, and
 allometric slopes of these four hind leg dimensions differed significantly
 among populations. Of these, three traits showed latitudinal variation,
 namely, male hind femur was stouter; female hind tibia was slenderer, and
 female body was smaller at lower latitudes than at higher latitudes. Hind
 leg sizes and shapes, as measured by principal component analysis of these
 four hind leg dimensions in each sex, covaried significantly between
 sexes, suggesting coevolutionary diversification in sexual traits.
 Covariation between sexes was weaker when variation in these traits with
 latitude was removed. These results suggest that coevolutionary
 diversification between male and female sexual traits is mediated by
 environmental conditions that vary with latitude.
description: Morphological
 measurements of Oedemera sexualis, in JapanOedemera sexualis
 (Coleoptera: Oedemeridae) is endemic to the Japanese Archipelago and
 distributed from the southern end of the Ryukyu Islands to the western
 part of Honshu mainland. Individuals were collected from 22 localities in
 Japan from 2002 to 2016.measurement.data.xls
DOI: 10.5061/dryad.7kk71d0
title: Data from: Using GPS collars to investigate the frequency and behavioural outcomes of intraspecific interactions among carnivores: a case study of male cheetahs in the Maasai Mara, Kenya

description: Intraspecific interactions between individuals or groups of individuals of
 the same species are an important component of population dynamics.
 Interactions can be static, such as spatial overlap, or dynamic based on
 the interactions of movements, and can be mediated through communication,
 such as the deployment of scent marks. Interactions and their behavioural
 outcomes can be difficult to determine, especially for species that live
 at low densities. With the use of GPS collars we quantify both static and
 dynamic interactions between male cheetahs (Acinonyx jubatus) and the
 behavioural outcomes. The 99% home-ranges of males overlapped
 significantly while there was little overlap of the 50% home-ranges.
 Despite this overlap, male cheetahs rarely came into close proximity of
 one another, possibly because presence was communicated through frequent
 visits to marking posts. The minimum distance between individuals in a
 dyad ranged from 89m to 196m but the average proximity between individuals
 ranged from 17,145 ± 6,865m to 26,367 ± 11,288m. Possible interactions
 took place more frequently at night than by day and occurred mostly in the
 50% home-range of one individual of a dyad or where cores of both
 individuals overlapped. After a possible encounter male cheetahs stayed in
 close proximity to each other for up to 6 hours, which could be the result
 of a territory defence strategy or the presence of a receptive female. We
 believe that one of the encounters between a singleton and a 5-male
 coalition resulted in the death of the singleton. Our results give new
 insights into cheetah interactions, which could help our understanding of
 ecological processes such as disease transmission.
description: Cheetah marking post
 locationsThe locations of cheetah
 marking posts that were found based on a cluster analysis using data from
 the GPS collars and opportunistically when conducting
 fieldwork.Cheetah marking
 posts.csvCheetah location
 dataGPS locations for each
 cheetah within each dyad i.e. pair of cheetahs.
DOI: 10.5061/dryad.b0j2td6
title: Data from: Floral regulators FLC and SOC1 directly regulate expression of the B3-type transcription factor TARGET OF FLC AND SVP 1 at the Arabidopsis shoot apex via antagonistic chromatin modifications

description: Integration of environmental and endogenous cues at plant shoot meristems
 determines the timing of flowering and reproductive development. The MADS
 box transcription factor FLOWERING LOCUS C (FLC) of Arabidopsis thaliana
 is an important repressor of floral transition, which blocks flowering
 until plants are exposed to winter cold. However, the target genes of FLC
 have not been thoroughly described, and our understanding of the
 mechanisms by which FLC represses transcription of these targets and how
 this repression is overcome during floral transition is still fragmentary.
 Here, we identify and characterize TARGET OF FLC AND SVP1 (TFS1), a novel
 target gene of FLC and its interacting protein SHORT VEGETATIVE PHASE
 (SVP). TFS1 encodes a B3-type transcription factor, and we show that tfs1
 mutants are later flowering than wild-type, particularly under short days.
 FLC and SVP repress TFS1 transcription leading to deposition of
 trimethylation of Iysine 27 of histone 3 (H3K27me3) by the Polycomb
 Repressive Complex 2 at the TFS1 locus. During floral transition, after
 downregulation of FLC by cold, TFS1 transcription is promoted by
 SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1), a MADS box protein
 encoded by another target of FLC/SVP . SOC1 opposes PRC function at TFS1
 through recruitment of the histone demethylase RELATIVE OF EARLY FLOWERING
 6 (REF6) and the SWI/SNF chromatin remodeler ATPase BRAHMA (BRM). This
 recruitment of BRM is also strictly required for SQUAMOSA PROMOTER BINDING
 PROTEIN-LIKE 9 (SPL9) binding at TFS1 to coordinate RNAPII recruitment
 through the Mediator complex. Thus, we show that antagonistic chromatin
 modifications mediated by different MADS box transcription factor
 complexes play a crucial role in defining the temporal and spatial
 patterns of transcription of genes within a network of interactions
 downstream of FLC/SVP during floral transition.
description: Richter2019PLoSG data
 folderOriginal source of
 information for ChIP-qPCR, RT-qPCR and MNase-qPCR analysis was collected
 from a Roche Light Cycler 480 Instrument (Roche) and BioRad CFX384 Touch
 Real-Time Detection System (BioRad). Data was analysed with Microsoft
 Excel Version 15 (Microsoft). Immunoblots were performed and analysed with
 LAS-4000 Mini Image Analyzer (FujiFilm). Confocal images were taken with
 confocal laser scanning microscopy (Zeiss LSM780). Images were processed
 with and figure construction was performed with Adobe Photoshop CS6
 (Adobe). Flowering time data was obtained from plants that were grown on
 soil at 22°C under long-day or short-day conditions. Data was analysed
 with Microsoft Excel Version version 15.27 (Microsoft). Mechanistic sketch
 of modus operandi for the regulation of TFS1 was generated with Microsoft
 PowerPoint version 15.27 (Microsoft).
DOI: 10.5061/dryad.3v3r2h8
title: Data from: Does thermal plasticity align with local adaptation? – An interspecific comparison of wing morphology in sepsid flies

description: Although genetic and plastic responses are sometimes considered as
 unrelated processes, their phenotypic effects may often align because
 genetic adaptation is expected to mirror phenotypic plasticity if
 adaptive, but run counter to it when maladaptive. The magnitude and
 direction of this alignment has further consequences for both the tempo
 and mode of adaptation. To better understand the interplay between
 phenotypic plasticity and genetic change in mediating adaptive phenotypic
 variation to climate variability, we here quantified genetic latitudinal
 variation and thermal plasticity in wing loading and wing shape in two
 closely related and widespread sepsid flies. Common garden rearing of 16
 geographical populations reared across multiple temperatures revealed that
 wing loading decreases with latitude in both species. This pattern could
 be driven by selection for increased dispersal capacity in the cold.
 However, although allometry, sexual dimorphism, thermal plasticity and
 latitudinal differentiation in wing shape all show similar patterns in the
 two species, the relationship between the plastic and genetic response
 differed between them. While latitudinal differentiation (south to north)
 mirrored thermal plasticity (hot to cold) in Sepsis punctum, there was no
 relationship in Sepsis fulgens. While this suggests that thermal
 plasticity may have helped to mediate local adaptation in S. punctum, it
 also demonstrates that genetic wing shape differentiation and its relation
 to thermal plasticity may be complex and idiosyncratic, even among
 ecologically similar and closely related species. Hence, genetic responses
 can, but do not necessarily, align with phenotypic plasticity induced by
 changing environmental selection pressures.
description: wing coordinates (15
 landmarks)Raw landmark coordinates
 describing wing morphology in two species of sepsid flies (Sepsis punctum
 and Sepsis fulgens). Several iso-female lines per population were reared
 under a common garden regime with different temperature treatments
 (=rearing temperature). These landmark data are untransformed and are in
 unit pixel. The “resolution” column can be used to transform distances in
 unit pixel to distances in unit millimetre [mm]. See the original
 publication for further information on population sampling, laboratory
 rearing, digitization and analytic procedures. Additional, more detailed
 information on analysis and data collection available upon
 request.DRYAD.xlsx
DOI: 10.5061/dryad.bf144m6
title: Data from: Shifts along parasite-mutualist continuum are opposed by fundamental trade-offs

description: Theory suggests that symbionts can readily evolve more parasitic or
 mutualistic strategies with respect to hosts. However, many symbionts have
 stable interactions with hosts that improve nutrient assimilation or
 confer protection from pathogens. We explored the potential for evolution
 of increased parasitism or decreased parasitism and mutualism in a natural
 gut symbiosis between larvae of Plutella xylostella and the microbe
 Enterobacter cloacae. We focused on interactions with the pathogen,
 Bacillus thuringiensis: selecting for parasitism in terms of facilitating
 pathogen infection, or increased mutualism in terms of host protection.
 Selection for parasitism led to symbionts increasing pathogen-induced
 mortality, but reduced their competitive ability with pathogens and their
 in vitro growth rates. Symbionts did not evolve to confer protection from
 pathogens. However, several lineages evolved reduced parasitism, primarily
 in terms of moderating impacts on host growth, potentially because
 prudence pays dividends through increased host size. Overall, evolution of
 increased parasitism was achievable but was opposed by trade-offs likely
 to reduce fitness. The evolution of protection may not have occurred
 because suppressing growth of B. thuringiensis in the gut might provide
 only weak protection or because evolution towards protective interactions
 was opposed by loss of competitive fitness in symbionts.
description: Enterobacter cloacae
 reproduction during experimental evolutiontab delimited text
 filereproduction_during_passage_expt.txtEffect of rearing conditions on parastism of Ectab delimited textEb_commensal_parasite.txtLineage variation in gut colonizationtab delimited text filegut_colonization_lineages_data.txtEnterobacter cloacae characterization effects on host fitnesstab delimited text fileEb_commensal_parasite.txtpassage12__bioassay_ datatab delimited text filepassage12__survivorship_data.txtCompetition experiment between Bt and E. cloacaetab delimited text- bacterial plate countsEc_ Bt_injection.txtCompetiion between E cloacae ancestor and evolved lineages via injectiontab delimited text - bacterial plate countsrel_fitness_injection_data.txtExponential growth of evolved & ancestor E. cloacae in vitrotab delimited textVmax_data.txtImpact of evolved E cloacae lineages on host growth & survivaltab delimited text filegrowth_virulence_data.txt
DOI: 10.5061/dryad.jb677gv
title: Data from: Differential effects of soil chemistry on the foliar resorption of nitrogen and phosphorus across altitudinal gradients

description: 1.Nutrient resorption from senescing leaves prior to litterfall is a
 strategy for nutrient conservation in vascular plants. However, the
 mechanisms through which soil fertility and/or foliar nutrient status
 affect nutrient resorption are not yet fully known. 2.We used two 1000
 m‐wide altitudinal gradients on two different bedrock types (carbonate and
 silicate) for analysing the interactive effects of temperature and soil
 chemistry on the resorption efficiency of two major nutrients, nitrogen
 (N) and phosphorus (P). Our objective was to assess how nutrient
 resorption varied across the gradients through the adaptation of
 individual species to changing environmental conditions rather than
 through changes in species composition. 3.Both N and P resorption
 efficiency increased across the altitudinal gradients independent of
 bedrock type. The main process regulating nutrient resorption was a
 negative feedback to nutrient availability in the soil. The negative
 feedback of nutrient resorption efficiency to soil nutrient status was
 unrelated to total soil nutrient contents but depended on concentrations
 of organic N forms for nitrogen resorption efficiency (NRE) and on
 inorganic P forms for phosphorus resorption efficiency (PRE),
 respectively. 4.While we hypothesized that the resorption of P, as a
 principally rock‐derived nutrient, depended on physical‐chemical processes
 affected by soil chemistry, our results showed that microbial P
 mineralization was the main source of inorganic P supply to the plants.
 Both NRE and PRE were effective to improve the growth potential of plants
 but there was no evidence of stoichiometric adaptations of N:P RE to
 nutrient ratio in the soil.
description: Leaf, litter and soil
 chemistry
DOI: 10.5061/dryad.9nk3757
title: Data from: Genetics and evidence for balancing selection of a sex-linked colour polymorphism in a songbird

description: Colour polymorphisms play a key role in sexual selection and speciation,
 yet the mechanisms that generate and maintain them are not fully
 understood. Here, we use genomic and transcriptomic tools to identify the
 precise genetic architecture and evolutionary history of a sex-linked
 colour polymorphism in the Gouldian finch Erythrura gouldiae that is also
 accompanied by remarkable differences in behaviour and physiology. We find
 that differences in colour are associated with an ~72-kbp region of the Z
 chromosome in a putative regulatory region for follistatin, an antagonist
 of the TGF-β superfamily genes. The region is highly differentiated
 between morphs, unlike the rest of the genome, yet we find no evidence
 that an inversion is involved in maintaining the distinct haplotypes.
 Coalescent simulations confirm that there is elevated nucleotide diversity
 and an excess of intermediate frequency alleles at this locus. We conclude
 that this pleiotropic colour polymorphism is most probably maintained by
 balancing selection.
description: Kim et al
 2019Source data files used
 to produce Figures in Kim et al. 2019