cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7p1c5
title: Data from: Diet- and genetically-induced obesity differentially affect the fecal microbiome and metabolome in Apc1638N mice

description: Obesity is a risk factor for colorectal cancer (CRC), and alterations in
 the colonic microbiome and metabolome may be mechanistically involved in
 this relationship. The relative contribution of diet and obesity per se
 are unclear. We compared the effect of diet- and genetically-induced
 obesity on the intestinal microbiome and metabolome in a mouse model of
 CRC. Apc1638N mice were made obese by either high fat (HF) feeding or the
 presence of the Leprdb/db (DbDb) mutation. Intestinal tumors were
 quantified and stool microbiome and metabolome were profiled. Genetic
 obesity, and to a lesser extent HF feeding, promoted intestinal
 tumorigenesis. Each induced distinct microbial patterns: taxa enriched in
 HF were mostly Firmicutes (6 of 8) while those enriched in DbDb were split
 between Firmicutes (7 of 12) and Proteobacteria (5 of 12). Parabecteroides
 distasonis was lower in tumor-bearing mice and its abundance was inversely
 associated with colonic Il1b production (p&lt;0.05). HF and genetic
 obesity altered the abundance of 49 and 40 fecal metabolites respectively,
 with 5 in common. Of these 5, adenosine was also lower in obese and in
 tumor-bearing mice (p&lt;0.05) and its concentration was inversely
 associated with colonic Il1b and Tnf production (p&lt;0.05). HF and
 genetic obesity differentially alter the intestinal microbiome and
 metabolome. A depletion of adenosine and P.distasonis in tumor-bearing
 mice could play a mechanistic role in tumor formation. Adenosine and P.
 distasonis have previously been shown to be anti-inflammatory in the colon
 and we postulate their reduction could promote tumorigenesis by
 de-repressing inflammation.
description: Meta and tumor
 dataFile includes genotype
 and treatment data as well as tumor, weight, MRI, glucose, insulin and
 colonic cytokine dataOTU
 tableQIIIME output showing
 relative abundance of bacterial taxa in stool from each
 mouseStool
 metabolitesScaled and imputed
 metabolomics data for stool samples
DOI: 10.5061/dryad.p2c6r
title: Data from: Drivers of diversification in individual life courses

description: Heterogeneity in life courses among individuals of a population influences
 the speed of adaptive evolutionary processes, but it is less clear how
 biotic and abiotic environmental fluctuations influence such
 heterogeneity. We investigate principal drivers of variability in sequence
 of stages during an individual's life in a stage-structured
 population. We quantify heterogeneity by measuring population entropy of a
 Markov chain, which computes the rate of diversification of individual
 life courses. Using individual data of a primate population, we show that
 density regulates the stage composition of the population, but its entropy
 and the generating moments of heterogeneity are independent of density.
 This lack of influence of density on heterogeneity is neither due to low
 year-to-year variation in entropy nor due to differences in survival among
 stages, but due to differences in stage transitions. Our analysis thus
 shows that well-known classical ecological selective forces, such as
 density regulation, are not linked to potential selective forces governing
 heterogeneity through underlying stage dynamics. Despite evolution acting
 heavily on individual variability in fitness components, our understanding
 is poor whether observed heterogeneity is adaptive and how it evolves and
 is maintained. Our analysis illustrates how entropy represents a more
 integrated measure of diversity compared to the population structural
 composition, giving us new insights about the underlying drivers of
 individual heterogeneity within populations and potential evolutionary
 mechanisms.
description: Demographic data of Cayo
 Santiago female rhesusDemographic data of Cayo
 Santiago female rhesus macaques. The data set includes a reference ID,
 date of birth, date of death and/or date of removal from Cayo Santiago,
 mom reference ID, and age at delivery of females alive during the period
 from 1973 to 2013. Original IDs were replaced by dummy codes. The data was
 collected by staff of the Caribbean Primate Research Center, University of
 Puerto Rico, and shared to the authors.Cayo_Santiago_female rhesus
 macaque data.xlsxAnnual projection
 matrices RAbsorbing annual
 matrices *R* of Cayo Santiago female rhesus macaques. Annual matrices were
 parameterized with demographic data of female rhesus macaques from 1973 to
 2013.Annual
 Projection Matrices R.xlsxAnnual projection
 matrices PAbsorbing annual
 matrices *P* of Cayo Santiago female rhesus macaques. Annual matrices were
 parameterized with demographic data of female rhesus macaques from 1973 to
 2013.Annual
 Projection Matrices P.xlsxAnnual number of adult
 rhesus macaquesAnnual number of Cayo
 Santiago adult rhesus macaques from 1973 to 2013.Annual number of
 adults.xlsx
DOI: 10.5061/dryad.q3s66
title: Data from: Not as ubiquitous as we thought: taxonomic crypsis, hidden diversity and cryptic speciation in the cosmopolitan fungus Thelonectria discophora (Nectriaceae, Hypocreales, Ascomycota)

description: The distribution of microbial species, including fungi, has long been
 considered cosmopolitan. Recently, this perception has been challenged by
 molecular studies in historical biogeography, phylogeny and population
 genetics. Here we explore this issue using the fungal morphological
 species Thelonectria discophora, one of the most common species of fungi
 in the family Nectriaceae, encountered in almost all geographic regions
 and considered as a cosmopolitan taxon. In order to determine if T.
 discophora is a single cosmopolitan species or an assemblage of sibling
 species, we conducted various phylogenetic analyses, including standard
 gene concatenation, Bayesian concordance methods, and coalescent-based
 species tree reconstruction on isolates collected from a wide geographic
 range. Results show that diversity among isolates referred as T.
 discophora is greatly underestimated and that it represents a species
 complex. Within this complex, sixteen distinct highly supported lineages
 were recovered, each of which has a restricted geographic distribution and
 ecology. The taxonomic status of isolates regarded as T. discophora is
 reconsidered, and the assumed cosmopolitan distribution of this species is
 rejected. We discuss how assumptions about geographically widespread
 species have implications regarding their taxonomy, true diversity,
 biological diversity conservation, and ecological functions.
description: Salgado-Salazar-PlosOne-2013Fused alignment of 6 loci used in this study.
DOI: 10.5281/zenodo.11866487
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Paul A.J.B. Van der Veken, http://www.wikidata.org/entity/Q19002860. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q19002860
DOI: 10.5281/zenodo.18381965
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Paul A.J.B. Van der Veken, http://www.wikidata.org/entity/Q19002860. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q19002860
DOI: 10.5061/dryad.907cv
title: Data from: Predicting evolutionary responses to selection on polyandry in the wild: additive genetic covariances with female extra-pair reproduction

description: The evolutionary forces that underlie polyandry, including extra-pair
 reproduction (EPR) by socially monogamous females, remain unclear.
 Selection on EPR and resulting evolution have rarely been explicitly
 estimated or predicted in wild populations, and evolutionary predictions
 are vulnerable to bias due to environmental covariances and correlated
 selection through unmeasured traits. However, evolutionary responses to
 (correlated) selection on any trait can be directly predicted as additive
 genetic covariances (covA) with appropriate components of relative
 fitness. I used comprehensive life-history, paternity and pedigree data
 from song sparrows (Melospiza melodia) to estimate covA between a female’s
 liability to produce extra-pair offspring and two specific fitness
 components: relative annual reproductive success (ARS) and survival to
 recruitment. All three traits showed non-zero additive genetic variance.
 Estimates of covA were positive, predicting evolution towards increased
 EPR, but 95% credible intervals overlapped zero. There was therefore no
 conclusive prediction of evolutionary change in EPR due to (correlated)
 selection through female ARS or recruitment. Negative environmental
 covariance between EPR and ARS would have impeded evolutionary prediction
 from phenotypic selection differentials. These analyses demonstrate an
 explicit quantitative genetic approach to predicting evolutionary
 responses to components of (correlated) selection on EPR that should be
 unbiased by environmental covariances and unmeasured traits.
description: fem.phen.data.finalPhenotypic data for analysis of female annual reproductive success and extra-pair reproductionfem.invA.finalInverted A matrix data for animal model analysis of female annual reproductive success and extra-pair reproductionfem.surv.phen.data.finalPhenotypic data for analysis of female extra-pair reproduction and survival to recruitmentfem.surv.invA.finalInverted A matrix data for animal model analysis of female extra-pair reproduction and survival to recruitment.
DOI: 10.5281/zenodo.18381967
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Carlo Luigi Giuseppe Bertero, http://www.wikidata.org/entity/Q522467. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q522467
DOI: 10.5281/zenodo.8360502
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Carlo Luigi Giuseppe Bertero, http://www.wikidata.org/entity/Q522467. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q522467
DOI: 10.5061/dryad.39pt5fg
title: Data from: Tuberculosis in people newly diagnosed with HIV at a large HIV care and treatment center in Northwest Cameroon: burden, comparative screening and diagnostic yields, and patient outcomes

description: Background Diagnosis of tuberculosis in people living with HIV is
 challenging due to non-specific clinical presentations and inadequately
 sensitive diagnostic tests. The WHO recommends screening using a clinical
 algorithm followed by rapid diagnosis using the Xpert MTB/RIF assay, and
 more information is needed to evaluate these recommendations in different
 settings. Methods From August 2012 to September 2013, consecutive adults
 newly diagnosed with HIV in Bamenda, Cameroon, were screened for TB
 regardless of symptoms by smear microscopy and culture; the Xpert MTB/RIF
 assay was performed retrospectively. Time to treatment and patient
 outcomes were obtained from routine registers. Results Among 1,149 people
 enrolled, 940 (82%) produced sputum for lab testing; of these, 68% were
 women, the median age was 35 years (IQR, 28-42 years), the median CD4
 count was 291cells/µL (IQR, 116-496 cells/µL), and 86% had one or more of
 current cough, fever, night sweats, or weight loss. In total, 131 people
 (14%, 95% CI, 12-16%) had sputum culture-positive TB. The WHO symptom
 screening algorithm had a sensitivity of 92% (95%CI, 86-96%) and
 specificity of 15% (95%CI, 12-17%) in this population. Compared to TB
 culture, the sensitivity of direct smear microscopy was 25% (95% CI,
 18-34%), and the sensitivity of Xpert was 68% (95% CI, 58-76); the
 sensitivity of both was higher for people reporting more symptoms. Only
 one of 69 people with smear-negative/culture-positive TB was started on TB
 treatment prior to culture positivity. Of 71 people with
 bacteriologically-confirmed TB and known outcome after 6 months, 13 (17%)
 had died, including 11 people with smear-negative TB and 6 people with
 both smear and Xpert-negative TB. Conclusions Use of the most sensitive
 rapid diagnostic test available is critical in people newly diagnosed with
 HIV in this setting to maximize the detection of
 bacteriologically-confirmed TB. However, this intervention is not
 sufficient alone and should be combined with more comprehensive clinical
 diagnosis of TB to improve outcomes.
description: 2018-TBinPLHIV-Bamenda-PONE-fin
DOI: 10.5061/dryad.b6d75
title: Data from: Bet hedging via multiple mating: a meta-analysis

description: Polyandry has been hypothesized to allow females to “bet hedge” against
 mating only with unsuitable mates, reducing variance in offspring fitness
 between members of a polyandrous lineage relative to a single-mating one.
 Theoretically, this reduction in fitness variance could select for
 polyandrous genotypes even when polyandry carries a direct cost,
 especially in small populations. However, this hypothesis is controversial
 and difficult to test empirically. Here, I apply a novel simulation model
 to 49 published empirical datasets, and quantify the potential selective
 advantage of multiple mating via reduced offspring fitness variance. For a
 wide range of assumptions, including those that most favor the evolution
 of bet hedging, I show that any fitness gains are meager. The variance in
 offspring quality caused by mate identity does not appear to be high
 enough for bet hedging to drive the evolution of polyandry.
description: readmeDescribes the contents
 of the other filesHolman bet hedging -
 open this one to run the analysisThe main R script to run
 the simulation and produce figures from the simulation results I have
 archived. It is heavily annotated.Holman bet hedging -
 functionsAn R script containing
 custom functions used in the simulation.Dataset
 infoA
 .csv file containing information about each of the 49 primary datasets
 appearing in the study. Contains information necessary for making the
 Figures in the main R script.Results of simulation -
 for various Ne valuesA zip archive,
 containing many .csv files, containing the results of a full run of the
 simulation (one for each dataset-parameter space combination). The output
 is calculated assuming there is no cost of multiple mating (p=0), and Ne
 has been specified. See readme for further info.Varying N
 analyses.zipResults of simulation -
 for various p valuesA zip archive,
 containing many .csv files, containing the results of a full run of the
 simulation (one for each dataset-parameter space combination). The output
 is calculated assuming the cost of multiple mating (p) has been specified,
 and the critical value of N needs to be calculated. See readme for further
 info.Varying p
 analyses.zip
DOI: 10.5061/dryad.491
title: Data from: More characters or more taxa for a robust phylogeny — case study from the coffee family (Rubiaceae)

description: Using different data sets mainly from the plant family Rubiaceae, but in
 parts also from the Apocynaceae, Asteraceae, Lardizabalaceae,
 Saxifragaceae, and Solanaceae, we have investigated the effect of number
 of characters, number of taxa, and kind of data on bootstrap values within
 phylogenetic trees. The percentage of supported nodes within a tree is
 positively correlated with the number of characters, and negatively
 correlated with the number of taxa. The morphological analyses are based
 on few characters and weakly supported trees are expected. The percentage
 of supported nodes is also dependent on the kind of data analyzed. In
 analyses of Rubiaceae based on the same number of characters, RFLP data
 give trees with higher percentage of supported nodes than rbcL and
 morphological data. We also discuss the support values for particular
 nodes at the familial and subfamilial levels. Two new data sets of ndhF
 and rbcL sequences of Rubiaceae are analyzed and together with earlier
 studies of the family we can conclude that the monophyly of the Rubiaceae
 is supported and within the family there are three well supported, but not
 easily characterized, large subfamilies, Rubioideae, Cinchonoideae s.s.
 and Ixoroideae s.l. There are also a few genera (Luculia and Coptosapelta)
 unclassified to subfamily.
description: Bremer et al Data
 SetBremer.txt
DOI: 10.5061/dryad.0463n
title: Data from: Mechanosensation is evolutionarily tuned to locomotor mechanics

description: The biomechanics of animal limbs has evolved to meet the functional
 demands for movement associated with different behaviors and environments.
 Effective movement relies not only on limb mechanics but also on
 appropriate mechanosensory feedback. By comparing sensory ability and
 mechanics within a phylogenetic framework, we show that peripheral
 mechanosensation has evolved with limb biomechanics, evolutionarily tuning
 the neuromechanical system to its functional demands. We examined sensory
 physiology and mechanics of the pectoral fins, forelimb homologs, in the
 fish family Labridae. Labrid fishes exhibit extraordinary morphological
 and behavioral diversity and employ pectoral fin-based propulsion with
 fins ranging in shape from high aspect ratio (AR) wing-like fins to low AR
 paddle-like fins. Phylogenetic character analysis demonstrates that high
 AR fins evolved independently multiple times in this group. Four pairs of
 species were examined; each included a pleseiomorphic low AR and a high AR
 species. Within each species pair, the high AR species demonstrated
 significantly stiffer fin rays in comparison to the low AR species.
 Afferent sensory nerve activity was recorded during fin ray bending. In
 all cases, afferents of stiffer fins were more sensitive at lower
 displacement amplitudes demonstrating mechanosensory tuning to fin
 mechanics, and a consistent pattern of correlated evolution. We suggest
 that this is a clear example of parallel evolution in a complex
 neuromechanical system, with a strong link between multiple phenotypic
 characters: pectoral fin shape, swimming behavior, fin ray stiffness, and
 mechanosensory sensitivity.
description: Dataset S1: GenBank
 database gene accession numbersGenBank database gene
 accession numbers for the genes used to create the
 phylogeny.Dataset
 S1.xlsxDataset 2: Aspect ratio
 sources and dataFish image sources and
 corresponding pectoral fin aspect ratio data. Cat=additional image
 identification. SL, TL (cm) = the standard length and total length,
 respectively. In most cases, both SL and TL are given. In cases where only
 length is given, the number is identified as either SL or TL. AR = Aspect
 Ratio. L/M/H = low, medium, and high, respectively.Dataset
 S2.xlsxDataset
 S3Pectoral fin ray (ray 3)
 flexural stiffness data for each species at different fin ray lengths
 (16.67, 50, and 83.33 % fin ray length).Dataset S4:
 electrophysiology dataThis file contains the
 electrophysiology data associated with the publication. On the left: the
 duration of the initial burst associated with fin ray movement in response
 to a step-and-hold stimulus for each species. On the right: the spike rate
 associated with the hold portion of each step-and-hold stimulus. Each
 stimulus set was randomly presented and repeated four times per
 individual.Dataset
 S4.xlsxPhylogeny Nexus
 fileThe Nexus (.nex) file
 associated with the published phylogeny.Labrid340PNAS.nexPhylogeny tree file(.phy) tree file.Labrid340PNAS.phy
DOI: 10.5061/dryad.6p6568r
title: Data from: Pleiotropic jaw morphology links the evolution of mechanical modularity and functional feeding convergence in Lake Malawi Cichlids

description: Complexity in how mechanistic variation translates into ecological novelty
 could be critical to organismal diversification. For instance, when
 multiple distinct morphologies can generate the same mechanical or
 functional phenotype this could mitigate tradeoffs and/or provide
 alternative ways to meet the same ecological challenge. To investigate how
 this type of complexity shapes diversity in a classic adaptive radiation,
 we tested several evolutionary consequences of the anterior jaw four-bar
 linkage for Lake Malawi cichlid trophic diversification. Using a novel
 phylogenetic framework, we demonstrated that different mechanical outputs
 of the same four jaw elements are evolutionarily associated with both jaw
 protrusion distance and jaw protrusion angle. However, these two
 functional aspects of jaw protrusion have evolved independently.
 Additionally, although four-bar morphology showed little evidence for
 attraction to optima, there was substantial evidence of adaptive peaks for
 emergent four-bar linkage mechanics and jaw protrusion abilities among
 Malawi feeding guilds. Finally, we highlighted a clear case of
 "cryptic convergence" in which two cichlid species that have
 independently evolved to graze algae in less than two million years, have
 converged on similar jaw protrusion abilities as well as four-bar linkage
 mechanics, but have evolved these similarities via non-convergent four-bar
 morphologies.
description: 100treesSNPhyloThe 100 random post burn-in trees from the SNPhylo analyses.4barmodjawreducedConvData table containing phenotypes for comparative analyses
DOI: 10.5061/dryad.gs352
title: Data from: Patterns of domestication in the Ethiopian oil-seed crop Noug (Guizotia abyssinica)

description: Noug (Guizotia abyssinica) is a semi-domesticated oil-seed crop, which is
 primarily cultivated in Ethiopia. Unlike its closest crop relative,
 sunflower, noug has small seeds, small flowering heads, many branches,
 many flowering heads, indeterminate flowering, and it shatters in the
 field. Here we conducted common garden studies and microsatellite analyses
 of genetic variation to test whether high levels of crop-wild gene flow
 and/or unfavorable phenotypic correlations have hindered noug
 domestication. With the exception of one population, analyses of
 microsatellite variation failed to detect substantial recent admixture
 between noug and its wild progenitor. Likewise, only very weak
 correlations were found between seed mass and the number or size of
 flowering heads. Thus, noug's ‘atypical’ domestication syndrome does
 not seem to be a consequence of recent introgression or unfavorable
 phenotypic correlations. Nonetheless, our data do reveal evidence of local
 adaptation of noug cultivars to different precipitation regimes, as well
 as high levels of phenotypic plasticity, which may permit reasonable
 yields under diverse environmental conditions. Why noug has not been fully
 domesticated remains a mystery, but perhaps early farmers selected for
 resilience to episodic drought or untended environments rather than larger
 seeds. Domestication may also have been slowed by noug's outcrossing
 mating system.
description: Noug microsatellite
 dataThis file contains
 microsatellite scores (allele fragment lengths) for 16 loci and 639
 individuals, representing 33 populations of noug (Guizotia abyssinica) and
 it's wild relative (Guizotia scabra ssp.
 schimperii).noug_microsatellitest.txtNoug phenotypic dataThis file contains phenotypic data collected on the level of individuals (sheet: Noug_Individual_Data), accessions (sheet: Noug_Pooled_Data) and environmental data of the collecting sites (sheet: Environmental_Data).noug_pheno_data.xlsx