cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1340q4t
title: Data from: Assessment of lung function in successfully treated Tuberculosis reveals high burden of ventilatory defects and COPD

description: Background: Burden, phenotype and risk-factors of lung function defects in
 successfully treated tuberculosis cases are unclear. Methods: We performed
 spirometry with bronchodilators in new drug-sensitive adult (&gt;18
 years) pulmonary tuberculosis cases during the 12 months following
 successful treatment in India. Airflow obstruction was defined as
 pre-bronchodilator FEV1/FVC&lt;5th percentile of Global Lung
 Initiative mixed-ethnicity reference (lower limit of normal [LLN]).
 Chronic obstructive pulmonary disease (COPD) was defined as
 post-bronchodilator FEV1/FVC Methods: We performed spirometry with
 bronchodilators in new drug-sensitive adult (≥18 years) pulmonary
 tuberculosis cases during the 12 months following successful treatment in
 India. Airflow obstruction was defined as pre-bronchodilator
 FEV1/FVC&lt;5th percentile of Global Lung Initiative mixed-ethnicity
 reference (lower limit of normal [LLN]). Chronic obstructive pulmonary
 disease (COPD) was defined as post-bronchodilator FEV1/FVC&lt;LLN
 among participants with obstruction. Restrictive spirometry pattern was
 defined as FVC&lt;LLN among participants without obstruction.
 Multivariable logistic and linear regression was used to identify
 risk-factors for obstruction, restriction and low lung function despite
 successful treatment. Results: Of the 172 participants included in the
 analysis, 82 (48%) were female, 22 (13%) had diabetes and 34 (20%)
 ever-smoked with a median (IQR) exposure of 3.5 (0.2–9.9) pack-years.
 Median (IQR) age and body-mass index (BMI) at enrollment was 32 (23–39)
 years and 18.1 (16.0–20.5) kg/m2 respectively. Airflow obstruction was
 detected in 42 (24%) participants; of whom 9 (21%) responded to
 short-acting bronchodilators and 25 (56%) had COPD; and was associated
 with duration of illness prior to treatment (aOR = 1.32 per 30-days, 95%CI
 1.04–1.68, p = 0.02). A restrictive spirometry pattern was detected in 89
 (52%) participants and was associated with female sex (aOR = 3.73, 95%CI
 1.51–9.17, p = 0.004) and diabetes (aOR = 4.06, 95%CI 1.14–14.42, p =
 0.03). Higher HbA1c at treatment initiation was associated with greater
 odds of a restrictive spirometry pattern (aOR = 1.29 per unit higher
 HbA1c, 95%CI 1.04 to 1.60, p = 0.02). We found a high burden of lung
 function defects and COPD in tuberculosis cases who successfully completed
 treatment. Screening for chronic lung diseases following treatment and
 linkage to respiratory health clinics should be included in the routine
 management plan of all tuberculosis cases in India, regardless of
 conventional COPD risk-factors such as older age and smoking.
description: Paper2_PlosOne_Dyrad
DOI: 10.5061/dryad.rq3dg01
title: Data from: Resource partitioning and interspecific interactions among sympatric rain forest arboreal mammals of the Western Ghats, India

description: Resource partitioning in a community of diurnal arboreal mammals
 consisting of the lion-tailed macaque Macaca silenus, bonnet macaque (BM)
 Macaca radiata, Nilgiri langur Semnopithecus johnii, and the Indian giant
 squirrel Ratufa indica of the Western Ghats, southern India, was studied.
 Differences in their diet, vertical stratification, food resource niche
 breadth, niche overlap, and behavioral interactions were examined.
 Resource partitioning was through differential habitat use, resource use,
 and vertical stratification. Of the four species, the BM was not a
 resident species and made frequent forays into evergreen forest from the
 adjacent deciduous forest during the flowering season of Cullenia
 exarillata and fruiting season of Ficus microcarpa. The macaques had
 narrower niches, and the langur and the squirrel had wider niches. Niche
 overlap was highest between the two macaques. Overlap among the study
 species was particularly pronounced during the flowering of C. exarillata.
 There was significant correlation between niche overlap and intolerance
 among the study species. Certain species pairs showed little or no mutual
 intolerance despite high overlap. Cooperative interactions such as alarm
 calls occurred more frequently among the resident species. Interaction
 matrices revealed an underlying pattern of interspecific dominance
 hierarchy, with the BM dominating over the other three species. Our study
 suggests that the BM do not coexist with the other three because of high
 overlap with its congener and low occurrence of cooperative interactions.
DOI: 10.5061/dryad.9118
title: Data from: Purifying selection and molecular adaptation in the genome of Verminephrobacter, the heritable symbiotic bacteria of earthworms

description: While genomic erosion is common among intracellular symbionts, patterns of
 genome evolution in heritable extracellular endosymbionts remain elusive.
 We study vertically transmitted extracellular endosymbionts
 (Verminephrobacter, Betaproteobacteria) that form a beneficial,
 species-specific, and evolutionarily old (60-130 MYA) association with
 earthworms. We assembled a draft genome of Verminephrobacter aporrectodeae
 and compared it to the genomes of Verminephrobacter eiseniae and two
 non-symbiotic close relatives (Acidovorax). Similar to V. eiseniae, the V.
 aporrectodeae genome was not markedly reduced in size and showed no A-T
 bias. We characterized the strength of purifying selection (dN/dS) and
 codon usage bias in 876 orthologous genes. Symbiont genomes exhibited
 strong purifying selection (dN/dS = 0.09 ± 0.07), although transition to
 symbiosis entailed relaxation of purifying selection as evidenced by 50%
 higher values and less codon usage bias in symbiont compared to reference
 genomes. Relaxation was not evenly distributed among functional gene
 categories but was overrepresented in genes involved in signal
 transduction and cell envelope biogenesis. The same gene categories also
 harbored instances of positive selection in the Verminephrobacter clade.
 In total, positive selection was detected in 89 genes, including also
 genes involved in DNA metabolism, tRNA modification, and TonB-dependent
 iron uptake, potentially highlighting functions important in symbiosis.
 Our results suggest that the transition to symbiosis was accompanied by
 molecular adaptation, while purifying selection was only moderately
 relaxed, despite the evolutionary age and stability of the
 host-association. We hypothesize that bi-parental transmission of
 symbionts and rare genetic mixing during transmission can prevent genome
 erosion in heritable symbionts.
description: orthologs_nuc_ali_JAN12Zip Archive containing 4-species alignments for a set of 1038 orthologs. Nucleotide alignments are in FASTA format. Locus tags for each sequence match those reported in the supplementary material of our GBE publication.
DOI: 10.5061/dryad.bd2b1r1
title: Data from: Sporadic genetic connectivity among small insular populations of the rare geoendemic plant Caulanthus amplexicaulis var. barbarae (Santa Barbara Jewelflower)

description: Globally, a small number of plants have adapted to terrestrial
 outcroppings of serpentine geology, which are characterized by soils with
 low levels of essential mineral nutrients (N, P, K, Ca, Mo) and toxic
 levels of heavy metals (Ni, Cr, Co). Paradoxically, many of these plants
 are restricted to this harsh environment. Caulanthus ampexlicaulis var.
 barbarae (Brassicaceae) is a rare annual plant that is strictly endemic to
 a small set of isolated serpentine outcrops in the coastal mountains of
 central California. The goals of the work presented here were to 1)
 determine the patterns of genetic connectivity among all known populations
 of Caulanthus ampexlicaulis var. barbarae, and 2) estimate contemporary
 effective population sizes (Ne), in order to inform ongoing genomic
 analyses of the evolutionary history of this taxon, and to provide a
 foundation upon which to model its future evolutionary potential and
 long-term viability in a changing environment. Eleven populations of this
 taxon were sampled, and population-genetic parameters were estimated using
 11 nuclear microsatellite markers. Contemporary effective population sizes
 were estimated using multiple methods and found to be strikingly small
 (typically Ne &lt; 10). Further, our data showed that a substantial
 component of genetic connectivity of this taxon is not at equilibrium, and
 instead showed sporadic gene flow. Several lines of evidence indicate that
 gene flow between isolated populations is maintained through long-distance
 seed dispersal (e.g. &gt; 1 km), possibly via zoochory.
description: Burrell_et_al_2019_dryad_txt
DOI: 10.5061/dryad.8d4r3vd
title: Divergence, gene flow and the origin of leapfrog geographic distributions: the history of color pattern variation in Phyllobates poison-dart frogs

description: The geographic distribution of phenotypic variation among closely related
 populations is a valuable source of information about the evolutionary
 processes that generate and maintain biodiversity. Leapfrog distributions,
 in which phenotypically similar populations are disjunctly distributed and
 separated by one or more phenotypically distinct populations, represent
 geographic replicates for the existence of a phenotype, and are therefore
 especially informative. Phyllobates poison frogs. We found evidence for
 high levels of gene flow between neighboring populations but not over long
 distances, indicating that gene flow between populations exhibiting the
 central phenotype may have a homogenizing effect that maintains their
 similarity, and that introgression between “leapfroging” taxa has not
 played a prominent role as a driver of phenotypic diversity in
 Phyllobates. Although phylogenetic analyses suggest that the leapfrog
 distribution was formed through independent evolution of the peripheral
 (i.e. leapfrogging) populations, the elevated levels of gene flow between
 geographically close populations poise alternative scenarios, such as the
 history of phenotypic change becoming decoupled from genome-averaged
 patterns of divergence, which we cannot rule out. These results highlight
 the importance of incorporating gene flow between populations into the
 study of geographic variation in phenotypes, both as a driver of
 phenotypic diversity and as a confounding factor of phylogeographic
 inferences.
description: This repository contains 10 folders, each corresponding to a
 different section of the paper's analyses. Within each folder is a
 text file detailing the how each analysis was performed.
DOI: 10.5061/dryad.82n006f
title: Data from: Transparency improves concealement in cryptically coloured moths

description: Predation is a ubiquitous and strong selective pressure on living
 organisms. Transparency is a predation defence widespread in water but
 rare on land. Some Lepidoptera display transparent patches combined with
 already cryptic opaque patches. A recent study showed that transparency
 reduced detectability of aposematic prey with conspicuous patches.
 However, whether transparency has any effect at reducing detectability of
 already cryptic prey is still unknown. We conducted field predation
 experiments with free avian predators where we monitored and compared
 survival of a fully opaque grey artificial form (cryptic), a form
 including transparent windows and a wingless artificial butterfly body.
 Survival of the transparent forms was similar to that of wingless bodies
 and higher than that of fully opaque forms, suggesting a reduction of
 detectability conferred by transparency. This is the first evidence that
 transparency decreases detectability in cryptic terrestrial prey. Future
 studies should explore the organization of transparent and opaque patches
 in animals and their interplay on survival, as well as the costs and other
 potential benefits associated with transparency on land.
description: DataRouviereZoo
DOI: 10.5061/dryad.m2d1h37
title: Data from: From forest to city: Urbanization modulates relative abundance of anti-predator coloration

description: Increased urbanization has resulted in community changes including
 alteration of predator communities. Little is known, however, about how
 such changes affect morphological anti-predator traits. Given the
 importance of coloration in predator avoidance, this trait in particular
 is expected to be susceptible to novel selective environments in urban
 areas. Here we investigate the coloration pattern of a Neotropical anuran
 species, the túngara frog (Engystomops pustulosus), along an urbanization
 gradient. Túngara frogs have two distinct color patterns (unstriped and
 striped) which we found to occur at different frequencies along an
 urbanization gradient. Striped individuals increased in frequency with
 urbanization. To assess the strength of selection imposed by predators on
 the two color morphs, we deployed clay models of túngara frogs in forest
 and semi-urban populations. In addition, we examined microhabitat
 selection by individuals of the different morphs. We found higher
 predation rates associated with urbanization than forested areas. In
 particular, frogs from forested habitats had lower number of attacks by
 avian predators. Contrary to our predictions, however, predation rates
 were similar for both color morphs independent of urbanization. Also,
 coloration of the frogs did not affect their microhabitat preference.
 Overall, túngara frogs are more likely to have a striped coloration
 pattern in semi-urban areas where predation by birds is higher than in the
 forest. Our findings suggest that factors other than predation pressure
 shape the coloration pattern of urban frogs and emphasize the complex
 nature of effects that anthropogenic changes in habitat and predator
 communities may have on prey morphology.
description: Background Preference
 Experiment DataData collected from the
 background preference experiment.Sampled Morph Frequency
 DataThat sampling data
 collected for the two different color morphs of the túngara
 frog.Sampled Morph
 Frequency.xlsxSelection Predation
 ExperimentThe data collected from
 the clay model experiment.Anderson et al_Attack
 Data(1).xlsxTungara vs Clay
 ReflectanceThe reflectance data
 collected on the clay models and túngara frogs.
DOI: 10.5061/dryad.h48d445
title: Data from: Socio-ecological conditions and female infidelity in the Seychelles warbler

description: Within socially monogamous breeding systems, levels of extra-pair
 paternity can vary not only between species, populations and individuals,
 but also across time. Uncovering how different extrinsic conditions
 (ecological, demographic and social) influence this behavior will help
 shed light on the factors driving its evolution. Here, we simultaneously
 address multiple socio-ecological conditions potentially influencing
 female infidelity in a natural population of the cooperatively breeding
 Seychelles warbler, Acrocephalus sechellensis. Our contained study
 population has been monitored for over 25 years, enabling us to capture
 variation in socio-ecological conditions between individuals and across
 time and to accurately assign parentage. We test hypotheses predicting the
 influence of territory quality, breeding density and synchrony, group size
 and composition (number and sex of subordinates), and inbreeding avoidance
 on female infidelity. We find that a larger group size promotes the
 likelihood of extra-pair paternity in offspring from both dominant and
 subordinate females, but this paternity is almost always gained by
 dominant males from outside the group (not by subordinate males within the
 group). Higher relatedness between a mother and the dominant male in her
 group also results in more extra-pair paternity — but only for subordinate
 females — and this does not prevent inbreeding occurring in this
 population. Our findings highlight the role of social conditions favoring
 infidelity and contribute towards understanding the evolution of this
 enigmatic behavior.
description: Socio-ecological
 conditions associated with the natal territory of each
 offspringData was gathered from
 the long-term Seychelles warbler database and the pedigree available for
 the Seychelles warbler population on Cousin Island, Seychelles. The
 data-set consists of offspring, their parentage and the socio-ecological
 variables associated with each offspring's natal group during the
 individual's hatching season. It includes 990 offspring born in major
 breeding seasons (June-September) between 1997 and 2014 on Cousin Island.
 The column 'ExtraGroup' describes whether an offspring was sired
 by a male outside of its natal group (1) or by a within-group male (0).
 Columns with a name starting with 'Presence' indicate whether
 one or more male/female subordinates/helpers were present (1) or absent
 (0) in the offspring's natal group. Columns 'MumStatus' and
 'DadStatus' describe the status of the offspring's parents,
 which can be either dominant ('Dom') or subordinate
 ('Sub').Socio-ecologicalConditions&InfidelityInTheSeychellesWarbler_FullDataset.csv
DOI: 10.5061/dryad.18931zcrq
title: RAD-seq reveals patterns of diversification, hybridization, and the accumulation of reproductive isolation in a clade of partially sympatric, tropical island trees

description: A common pattern observed in temperate tree clades is that species are
 often morphologically distinct and partially interfertile but maintain
 species cohesion despite ongoing hybridization where ranges overlap.
 Although closely related species commonly occur in sympatry in tropical
 ecosystems, little is known about patterns of hybridization within a clade
 over time, and the implications of this hybridization for the maintenance
 of species boundaries. In this study, we focused on a clade of sympatric
 trees in the genus Diospyros in the Mascarene islands and investigated
 whether species are genetically distinct, whether they hybridize, and how
 patterns of hybridization are related to the time since divergence among
 species. We sampled multiple populations from each of 12 Mascarene
 Diospyros species, generated genome-wide SNP data using 2bRADseq, and
 conducted population genomic and phylogenomic analyses. We found that
 Mascarene Diospyros species diverged millions of years ago and are largely
 genetically distinct from one another. Although hybridization was observed
 between closely related species belonging to the same subclade, more
 distantly related species showed little evidence of interspecific
 hybridization. Phylogenomic analyses also suggested that introgression
 occurred during the evolutionary history of the clade. This suggests that,
 as diversification progressed, interspecific hybridization also occurred
 among species, but became infrequent as lineages diverged from one another
 and evolved reproductive barriers. Species now co-exist in partial
 sympatry, and experience limited hybridization between close relatives.
 Additional research is needed to better understand the role introgression
 may have played in adaptation and diversification of Mascarene Diospyros,
 and its relevance for conservation.
description: Fresh leaf material was collected in field and immediately stored
 in silica gel to be later extracted using CTAB method.
 Extracted DNA was then used to create 2bRAD libraries according
 to Mikhail Matz lab 2015 protocol.
 2b-RAD: Wang S., Meyer E., McKay JK., Matz
 MV. (2012) 2b-RAD: a simple and flexible method for genome-wide
 genotyping. Nat Methods 9:808-10 Exact
 protocol used can be found at:
 https://github.com/Kenizzer/2bRAD-Edwards-Lab
description: dryad-data-upload_pt1n-5n.tar.gz - raw demultiplxed fastq
 files ipyrad-parameter-files.zip - contains ipyrad
 parameters used for each dataset specified in table 3
 ipyrad-summary-files.zip - contains summary files of assembled
 loci generated by ipyrad phylip-files.zip - contains
 various phylip files for dataset min10 62 taxa (see table 3) used in
 RaxML, tetrad, and D-statistic analyses vcf-files.zip -
 contains vcf files representing datasets summarized in table 3
DOI: 10.5061/dryad.j6q573n7v
title: Modeling human migration across spatial scales in Colombia

description: Human mobility, both short and long term, are important considerations in
 the study of numerous systems. Economic and technological advances have
 led to a more interconnected global community, further increasing the need
 for considerations of human mobility. While data on human mobility are
 better recorded in many developed countries, availability of such data
 remains limited in many low- and middle-income countries around the world,
 particularly at the fine temporal and spatial scales required by many
 applications. In this study, we used 5-year census-based internal
 migration microdata for 32 departments in Colombia (i.e., Admin-1 level)
 to develop a novel spatial interaction modeling approach for estimating
 migration, at a finer spatial scale, among the 1,122 municipalities in the
 country (i.e., Admin-2 level). Our modeling approach bridges a significant
 gap in the availability of migration data at administrative unit levels
 finer than those at which migration data are typically recorded. Due to
 the widespread availability of census-based migration microdata at the
 Admin-1 level, our modeling approach opens up for the possibilities of
 modeling migration patterns at Admin-2 and Admin-3 levels across many
 other countries where such data are currently lacking. 
description: We developed a novel spatial interaction modeling approach for
 Colombia using previously identified economic, socio-demographic and
 geographic factors including the regional equivalent of the gross domestic
 product, relative population size, proportion of urban population and
 geographic contiguity of locations, in addition to the absolute population
 size and distance between locations to fit a municipality level (i.e.,
 Admin-2 level) model to observed census-based department level (i.e.,
 Admin-1 level) migration data.   
  
description: The dataset contains estimated migration between 2000 and 2005
 between 1122 municipalities in Columbia.  The first three columns identify
 the municipalities. While the remainder are estimated figures of migrant
 numbers from the munucipality identified by the row to the minicipality
 identified by the column.  All rows and columns are sorted the same
 way.