cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7dp3126p
title: Data from: When phenotypes do not match genotypes – unexpected phenotypic diversity and potential environmental constraints in Icelandic stickleback

description: Divergent lateral plate phenotypes in stickleback represent one of only a
 few cases known where a single gene underlies the phenotype under
 divergent selection between different habitats. However, the selection
 pressures leading to the repeated loss of lateral plates in freshwater are
 still not well understood. By genotyping 838 individuals from nine
 independently colonized lakes and one marine population in Iceland, we
 found i) that only in some lakes are phenotypes associated with the
 expected genotype and ii) that the independent repeated occurrence of a
 rarely described plate phenotype is expressed in the absence of an allele
 that is usually associated with this phenotype. This suggests that either
 other genes such as modifiers might be under divergent selection between
 lakes or that lateral plate expression in these populations is restricted
 due to environmental constraints.
description: Lateral plate counts and
 EDA STN382 allel numberIndividual based data
 providing the name of the lake sampled (Lake), an identifier for each
 individual (Individual), the number of later plates counted on the left
 side on the keel (Keel), the number of STN382 C alleles (STNallele), the
 total number of lateral plates counted on the left side (Total_Plates) and
 the assigned phenotypic morph (Morph). Plate morph abbreviations are as
 follow: LP - low plated with 10 or less anterior plates, LPK - as LP but
 with plates on the keel, PPNK - partial plated, i.e. having &gt; 10 plates
 but no plates on the keel, PPK - as PPNK but with plates on the keel, FP -
 fully plated with plates continuously along the left
 sidedryad.txt
DOI: 10.57745/4er1c7
title: DEPA14_MG1655_lambda_pLTet_dam_5aTC.fastq.gz

description: Sequencing of lambda induced in MG1655_dam-_Tn10::tetR-tetA_pLTet_dam at 5mM aTC
DOI: 10.5061/dryad.13p8g30
title: Data from: Bidirectionality of hormone-behavior relationships and satellite-caller dynamics in green treefrogs

description: Whether hormonal differences among males that conditionally alternate
 between mating tactics are a cause or consequence of behavioral expression
 is central to understanding the mechanisms regulating alternative mating
 tactics. This issue is rooted in the bidirectionality of hormone-behavior
 relationships and is particularly relevant to alternative mating tactics
 in anuran amphibians because the social-acoustic environment can mediate
 changes in both tactic expression and hormone levels. Hence, it is not
 clear whether males adopt different mating tactics in response to rival
 male signals, changes in hormone levels, or both. Here, we address this
 problem in male green treefrogs, Hyla cinerea, using vocal playback
 experiments combined with measures of circulating hormone levels, vocal
 attractiveness, body size, body condition, and plasma glucose levels.
 Calling males in natural choruses that adopted non-calling satellite
 behavior in response to broadcast advertisement calls produced less
 attractive calls, were smaller and in poorer body condition than males
 that continued to call, but did not differ in circulating levels of the
 stress hormone corticosterone (CORT), androgens, or glucose. These results
 were unexpected because satellite males in natural choruses possess higher
 CORT levels and lower androgen levels than calling males and CORT
 administration increases the probability of satellite tactic expression in
 this species. Our results suggest that there may be no clear cause versus
 consequence dichotomy associated with hormonal disparities among males
 practicing different mating tactics because multiple intrinsic and
 extrinsic factors can influence tactic expression.
description: Crocker-Buta and Leary
 (2018)Data on the relationship
 between hormone level, body size and condition, call characteristics and
 the adoption of alternative mating tactics in the green
 treefrog.
DOI: 10.57745/d7gxkr
title: DEPA3_MG1655_Z1.fastq.gz

description: Sequencing of lambda infecting MG1655 WT
DOI: 10.57745/tawbck
title: DEPA8_MG1655_Z1_pLTet_dam_5aTC.fastq.gz

description: Sequencing of lambda infecting MG1655_Z1_pLTet_dam at 5mM aTc
DOI: 10.57745/8hql1d
title: DEPA11_MG1655_Z1_pLTet_dam_50aTC.fastq.gz

description: Sequencing of lambda infecting MG1655_Z1_pLTet_dam at 50mM aTC (replicate)
DOI: 10.57745/zpz2np
title: DEPA1_MG1655.fastq.gz

description: Sequencing of lambda induced in MG1655 WT
DOI: 10.5061/dryad.612g8
title: Data from: Genetic drift and collective dispersal can result in chaotic genetic patchiness

description: Chaotic genetic patchiness denotes unexpected patterns of genetic
 differentiation that are observed at a fine scale and are not stable in
 time. These patterns have been described in marine species with
 free-living larvae, but are unexpected because they occur at a scale below
 the dispersal range of pelagic larvae. At the scale where most larvae are
 immigrants, theory predicts spatially homogeneous, temporally stable
 genetic variation. Empirical studies have suggested that genetic drift
 interacts with complex dispersal patterns to create chaotic genetic
 patchiness. Here we use a coancestry model and individual-based
 simulations to test this idea. We found that chaotic genetic patterns
 (qualified by global FST and spatio-temporal variation in FST's
 between pairs of samples) arise from the combined effects of (1) genetic
 drift created by the small local effective population sizes of the sessile
 phase and variance in contribution among breeding groups and (2)
 collective dispersal of related individuals in the larval phase.
 Simulations show that patchiness levels qualitatively comparable to
 empirical results can be produced by a combination of strong variance in
 reproductive success and mild collective dispersal. These results call for
 empirical studies of the effective number of breeders producing larval
 cohorts, and population genetics at the larval stage.
description: Parameter files for
 simulationschaos.zip
DOI: 10.57745/kewmei
title: DEPA4_MG1655_Z1.fastq.gz

description: Sequencing of lambda infecting MG1655 WT (replicate)
DOI: 10.57745/yvexss
title: DEPA2_MG1655.fastq.gz

description: Sequencing of lambda induced in MG1655 WT (replicate)
DOI: 10.57745/lktcsr
title: DEPA7_MG1655_Z1_pLTet_dam_0aTC.fastq.gz

description: Sequencing of lambda infecting MG1655_Z1_pLTet_dam at 0 aTc (replicate)
DOI: 10.57745/zwybxm
title: DEPA6_MG1655_Z1_pLTet_dam_0aTC.fastq.gz

description: Sequencing of lambda infecting MG1655_Z1_pLTet_dam at 0 aTc
DOI: 10.5061/dryad.8jf67k4
title: Data from: Missed opportunities for HIV testing among patients newly presenting for HIV care at a Swiss university hospital: a retrospective analysis

description: Objectives: To determine the frequency of missed opportunities (MOs) among
 patients newly-diagnosed with HIV, risk factors for presenting MOs, and
 the association between MOs and late presentation to care. Design:
 Retrospective analysis Setting: HIV outpatient clinic at a Swiss tertiary
 hospital Participants: Patients aged ≥18 years old newly presenting for
 HIV care between 2010 and 2015 Measures: Number of medical visits, up to
 five years preceding HIV diagnosis, at which HIV testing had been
 indicated, according to Swiss HIV testing recommendations. A visit at
 which testing was indicated but not performed was considered a MO for HIV
 testing. Results: Complete records were available for all 201 new patients
 of whom 51% were male and 33% from sub-Saharan Africa. Thirty patients
 (15%) presented with acute HIV infection while 119 patients (59%) were
 late presenters (LPs) (CD4 counts &lt;350 cells/mm3 at diagnosis).
 Ninety-four patients (47%) had presented at least one MO, of whom 44 (47%)
 had multiple MOs. MOs were more frequent among individuals from
 sub-Saharan Africa, men who have sex with men, and patients under
 follow-up for chronic disease. MOs were less frequent in LPs than non-LPs
 (42.5% versus 57.5%, P = 0.03). Conclusions: At our centre, 47% of
 patients presented at least one MO. Whilst our late presentation rate is
 higher than the national figure of 49.8%, LPs were less likely to
 experience MOs, suggesting that these patients were diagnosed late through
 presenting late, rather than through being failed by our hospital. We
 conclude that, in addition to optimising physician-initiated testing,
 access to testing must be improved among patients unaware they are at HIV
 risk and who do not seek health care.
description: Data file for the missed
 opportunities for HIV diagnosis studymissed_opportunities.csv
DOI: 10.57745/lu7wws
title: DEPA13_MG1655_lambda_pLTet_dam_0aTC.fastq.gz

description: Sequencing of lambda induced in MG1655_dam-_Tn10::tetR-tetA_pLTet_dam at 0 aTC (replicate
DOI: 10.57745/qez0xe
title: DEPA5_MG1655_delta_dam.fastq.gz

description: Sequencing of lambda infecting MG1655_dam-
DOI: 10.57745/rh1lzo
title: DEPA12_MG1655_lambda_pLTet_dam_0aTC.fastq.gz

description: Sequencing of lambda induced in MG1655_dam-_Tn10::tetR-tetA_pLTet_dam at 0 aTC
DOI: 10.57745/ufeoq9
title: DEPA10_MG1655_Z1_pLTet_dam_50aTC.fastq.gz

description: Sequencing of lambda infecting MG1655_Z1_pLTet_dam at 50mM aTC
DOI: 10.5061/dryad.qj367
title: Data from: The impact of rate heterogeneity on inference of phylogenetic models of trait evolution

description: Rates of trait evolution are known to vary across phylogenies; however,
 standard evolutionary models assume a homogeneous process of trait change.
 These simple methods are widely applied in small-scale phylogenetic
 studies, whereas models of rate heterogeneity are not, so the prevalence
 and patterns of potential rate variation in groups up to hundreds of
 species remain unclear. The extent to which trait evolution is modelled
 accurately on a given phylogeny is also largely unknown because studies
 typically lack absolute model fit tests. We investigated these issues by
 applying both rate-static and variable-rates methods on (i) body mass data
 for 88 avian clades of 10–318 species, and (ii) data simulated under a
 range of rate-heterogeneity scenarios. Our results show that rate
 heterogeneity is present across small-scaled avian clades, and
 consequently applying only standard single-process models prompts
 inaccurate inferences about the generating evolutionary process.
 Specifically, these approaches underestimate rate variation, and
 systematically mislabel temporal trends in trait evolution. Conversely,
 variable-rates approaches have superior relative fit (they are the best
 model) and absolute fit (they describe the data well). We show that rate
 changes such as single internal branch variations, rate decreases and
 early bursts are hard to detect, even by variable-rates models. We also
 use recently developed absolute adequacy tests to highlight misleading
 conclusions based on relative fit alone (e.g. a consistent preference for
 constrained evolution when isolated terminal branch rate increases are
 present). This work highlights the potential for robust inferences about
 trait evolution when fitting flexible models in conjunction with tests for
 absolute model fit.
description: Simulation
 codeFunctions that simulate
 trees and associated tip-trait data under various scenarios of
 rate-heterogeneity.paper_man_sim_code.RMedian scaled tree (BAMM)Function that outputs the median scaled tree (a tree with branches scaled by the rate of evolution) obtained by fitting BAMM on a tree & the associated tip trait data. The function computes the per-branch median rates across the posterior tree distribution.paper_man_median_BAMM.RRate-heterogeneity prevalence and patternsFunctions that determine the patterns and prevalence of trait rate-heterogeneity across trees, using as input scaled trees obtained after fitting variable-rates models to the phylogeny & associated tip trait data.paper_man_heterogeneity_patterns.R
DOI: 10.57745/qxesez
title: Seq_methylation_bed.zip

description: Methylation frequency determined per position using modkit
DOI: 10.57745/sqyhcb
title: DEPA17_MG1655_lambda_pLTet_dam_50aTC.fastq.gz

description: Sequencing of lambda induced in MG1655_dam-_Tn10::tetR-tetA_pLTet_dam at 50mM aTC (replicate)
DOI: 10.57745/ip8izb
title: DEPA9_MG1655_Z1_pLTet_dam_5aTC.fastq.gz

description: Sequencing of lambda infecting MG1655_Z1_pLTet_dam at 5mM aTc (replicate)
DOI: 10.57745/uwgroj
title: DEPA16_MG1655_lambda_pLTet_dam_50aTC.fastq.gz

description: Sequencing of lambda induced in MG1655_dam-_Tn10::tetR-tetA_pLTet_dam at 50mM aTC
DOI: 10.5061/dryad.c4jp3
title: Data from: Axial allometry in a neutrally buoyant environment: effects of the terrestrial-aquatic transition on vertebral scaling

description: Ecological diversification into new environments presents new mechanical
 challenges for locomotion. An extreme example of this is the transition
 from a terrestrial to an aquatic lifestyle. Here, we examine the
 implications of life in a neutrally buoyant environment on adaptations of
 the axial skeleton to evolutionary increases in body size. On land,
 mammals must use their thoracolumbar vertebral column for body support
 against gravity and thus exhibit increasing stabilization of the trunk as
 body size increases. Conversely, in water, the role of the axial skeleton
 in body support is reduced, and, in aquatic mammals, the vertebral column
 functions primarily in locomotion. Therefore, we hypothesize that the
 allometric stabilization associated with increasing body size in
 terrestrial mammals will be minimized in secondarily aquatic mammals. We
 test this by comparing the scaling exponent (slope) of vertebral measures
 from 57 terrestrial species (23 felids, 34 bovids) to 23 semi-aquatic
 species (pinnipeds), using phylogenetically corrected regressions.
 Terrestrial taxa meet predictions of allometric stabilization, with
 posterior vertebral column (lumbar region) shortening, increased vertebral
 height compared to width, and shorter, more disc-shaped centra. In
 contrast, pinniped vertebral proportions (e.g. length, width, height)
 scale with isometry, and in some cases, centra even become more
 spool-shaped with increasing size, suggesting increased flexibility. Our
 results demonstrate that evolution of a secondarily aquatic lifestyle has
 modified the mechanical constraints associated with evolutionary increases
 in body size, relative to terrestrial taxa.
description: Vertebral
 measuresLinear measures from the
 vertebral columns of Felidae, Bovidae and Pinnipedia. Data from Jones
 (2015) and Pierce et al. (2011)RAW
 DATA.xlsx
DOI: 10.57745/vtqxqg
title: DEPA15_MG1655_lambda_pLTet_dam_5aTC.fastq.gz

description: Sequencing of lambda induced in MG1655_dam-_Tn10::tetR-tetA_pLTet_dam at 5mM aTC (replicate)
DOI: 10.57745/bzqy6j
title: NC_001416_lambda.gb

description: Reference genome and annotation of lambda
DOI: 10.57745/hiqf2n
title: GATC methylation level in bacteriophage lambda

description: Determination of Adenine Methylation at GATC Sites in lambda DNA. Dam protein was overexpressed, in E. coli cells expressing TetR constitutively (MG1655 Z1X strain, overexpressing tetR, lacI and araC), by addition of the plasmid pLTetO1-dam and growing the cells on LB + 10 mM MgSO4 + 0.2% Maltose + a gradient of concentration of anhydrotetracycline (aTc). TetO/tetR system allows a strong repression of the locus controlled by TetO, allowed by TetR; aTc is a strong competitor for TetR binding, allowing expression of the locus. lambda phage was multiplied on liquid cultures of MD301 strain with varying levels of aTc concentration (0,5 or 50 µM), starting from a hundred phages (to be sure not to have a loss of function cII mutant in the inoculum) and 4 x105 bacteria. Phage and bacteria were initially mixed in 10 µL of LB supplemented with MgSO4 10 mM and maltose at 0.2% and incubated for one hour at 37°C. After one hour, 1 ml of LB at 37°C was added, and the phage/ bacteria mixture was incubated for another two hours at 37°C with agitation, after what it was diluted in 9 ml of LB and incubated with agitation until lysis occurred (monitored by a drop of optical density). Culture was centrifuged at 4500 g for 10 minutes and the supernatant filtered with a 0.2 µm size pore filter, and kept at 4°C until use. Phage DNA was extracted from 5 ml of lysate. The lysates were centrifugated 20 min at 4500g, filtered with a 0.2 μm filter, treated with Turbo DNase™ (Invitrogen™, US) and RNase I to remove the host contaminant DNA and RNA and precipitated with polyethylene glycol 10% and NaCl 0.5 M for 6 hours. The lysates were centrifuged and the pellets were resuspended in SM buffer, treated with proteinase K, and the phage DNA was purified using a standard phenol:chloroform procedure. DNA purity and concentration were checked with the NanoDrop™ 2000 spectrophotometer (Thermo Scientific™, US) and the Qubit4™ fluorometer (Invitrogen™, US), respectively. DNA integrity was checked by 1% agarose gel electrophoresis. DNA was sent for sequencing at the I2BC sequencing facility. DNA was sequenced with a GridION X5 (Oxford Nanopore Technologies, UK) and long-reads were analysed with modkit v0.3.1 (https://github.com/nanoporetech/modkit) using per default parameters. The results of the comparative mode were used, using DNA from a dam knockout condition (MVEC232) as reference (methylation level fixed at 0). An additional control was added, lambda phage grown on WT MG1655 were prepared by induction of lambda at 42°C for 10 min, followed by 1h incubation at 37°C. As a positive control, we used lysogenic cells for lambda, deleted for dam, harbouring pLTetO1-dam and Tn10-tetR-tetA (lambda plTet-dam). This genotype results in an overexpression of dam independently of the aTc concentration.
DOI: 10.57745/w8zhpp
title: ReadMe.txt

description: :unav
DOI: 10.5061/dryad.tp14201
title: Data from: Responses of aerial insectivorous bats to local and landscape-level features of coffee agroforestry systems in Western Ghats, India

description: Shade coffee has shown great promise in providing crucial habitats for
 biodiversity outside formal protected areas. Insectivorous bats have been
 understudied in coffee, although they may provide pest control services.
 We investigated the influence of local and landscape-level features of
 coffee farms on aerial insectivorous bats in Chikmagalur district in the
 Western Ghats biodiversity hotspot, India. Bats were monitored in 20 farm
 sites using ultrasound detectors, and the response of bat species richness
 and activity to changes in tree density, proportion of built-up area in
 the neighborhood, and distance of farm from forest areas quantified. We
 examined if models built to explain the species richness and activity
 could also predict them in nine additional sites. We detected nine phonic
 types/species in the study area. The quantified predictors had no effect
 on assemblage-level species richness and activity of bats. Responses of
 edge-space and cluttered-space forager guilds mirrored those of the
 overall assemblage, but some species vulnerable to forest conversion like
 *Rhinolophus beddomei* were detected rarely. Best models explained up to
 20% and 15% variation in assemblage-level species richness and activity
 respectively, and were poor predictors of both response variables. We
 conclude that coffee farms in our study area offer an important commuting
 space for insectivorous bats across a gradient of shade management.
 Further research should include species-specific responses to management
 decisions for at-risk species and quantification of ecosystem services
 like natural pest control to inform biodiversity conservation initiatives
 in the Western Ghats coffee landscapes.
description: S1_FileAcoustic presence/absence data of 20 plantation sites sampled in 2015-16 and 2016-17S2_FileAcoustic presence/absence data of 9 plantation sites sampled in 2016-17
DOI: 10.5061/dryad.5bn81
title: Data from: Removal of an apex predator initiates a trophic cascade that extends from herbivores to vegetation and the soil nutrient pool

description: It is widely assumed that organisms at low trophic levels, particularly
 microbes and plants, are essential to basic services in ecosystems, such
 as nutrient cycling. In theory, apex predators' effects on ecosystems
 could extend to nutrient cycling and the soil nutrient pool by influencing
 the intensity and spatial organization of herbivory. Here, we take
 advantage of a long-term manipulation of dingo abundance across
 Australia's dingo-proof fence in the Strzelecki Desert to investigate
 the effects that removal of an apex predator has on herbivore abundance,
 vegetation and the soil nutrient pool. Results showed that kangaroos were
 more abundant where dingoes were rare, and effects of kangaroo exclusion
 on vegetation, and total carbon, total nitrogen and available phosphorus
 in the soil were marked where dingoes were rare, but negligible where
 dingoes were common. By showing that a trophic cascade resulting from an
 apex predator's lethal effects on herbivores extends to the soil
 nutrient pool, we demonstrate a hitherto unappreciated pathway via which
 predators can influence nutrient dynamics. A key implication of our study
 is the vast spatial scale across which apex predators' effects on
 herbivore populations operate and, in turn, effects on the soil nutrient
 pool and ecosystem productivity could become manifest.
description: Morris_Letnic_Data_1_FaunaData on dingo and kangaroo counts collected in the field.Morris_Letnic_Data_2_DietData on content of dingo scats collected in the field.Morris_Letnic_Data_3_VegetationData on vegetation cover collected in the field.Morris_Letnic_Data_4_SoilData on soil nutrients collected in the field and analysed at the Southern Cross University, Environmental Analysis Laboratory.Morris_Letnic_RcodeR code used for data preparation, graphing and statistical analysis.