cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.pj160
title: Data from: Reduction in arterial stiffness and vascular age by naltrexone-induced interruption of opiate agonism

description: Objective: To prospectively assess if opiate antagonist treatment or the
 opiate-free status could reverse opiate-related vasculopathy. Design:
 Longitudinal Open Observational, Serial “N of One”, over 6.5 years under
 various treatment conditions: opiate dependence, naltrexone and
 opiate-free. Setting: Primary care, Australia. Participants: 20 opiate
 dependent patients (16 males: 16 cases of buprenorphine 4.11+1.17mg, two
 of methadone 57.5+12.5mg and two of heroin 0.75+0.25g). Intervention:
 Studies of Central Arterial Stiffness and vascular reference age (RA) were
 performed longitudinally by SphygmoCor Pulse Wave Analysis (AtCor,
 Sydney). Primary Outcomes: Primary outcome was vascular age and arterial
 stiffness accrual under different treatment conditions. Results: The mean
 chronological age (CA) was 33.62+2.03 years. The opiate-free condition was
 associated with a lower apparent vascular age both in itself (males:
 P=0.0402, females: P=0.0360) and in interaction with time (males:
 P=0.0001; females: P=0.0004), and confirmed with other measures of
 arterial stiffness. The mean modelled RA was 38.82, 37.73 and 35.05 years
 in the opiate, naltrexone and opiate-free conditions respectively. The
 opiate-free condition was superior to opiate agonism after full
 multivariate adjustment (P=0.0131), with modelled RA/CA of 1.0173, 0.9563,
 and 0.8985 (reductions of 6.1% and 11.9% respectively). Conclusions: Data
 demonstrate that opiate-free status improves vascular age and arterial
 stiffness in previous chronic opiate users.. The role of opiate antagonist
 treatment in achieving these outcomes requires future clarification and
 offers hope of novel therapeutic remediation.
description: delta4.1.6.5.4.1
 Expcsv file,
 de-identifed
DOI: 10.5061/dryad.q6qn0
title: Data from: High-resolution mapping reveals hundreds of genetic incompatibilities in hybridizing fish species

description: Hybridization is increasingly being recognized as a common process in both
 animal and plant species. Negative epistatic interactions between genes
 with different parental ancestry decrease the fitness of hybrids and can
 limit gene flow between species. However, little is known about the number
 and genome-wide distribution of genetic incompatibilities separating
 species. To detect interacting genes, we perform a detailed genome scan
 for linkage disequilibrium between unlinked genomic regions in naturally
 occurring hybrid populations of swordtail fish. We estimate that hundreds
 of pairs of genomic regions contribute to reproductive isolation between
 these species, despite them being recently diverged. Many of these
 incompatibilities are likely the result of natural or sexual selection on
 hybrids, since intrinsic isolation is known to be weak. Patterns of
 genomic divergence at these regions imply that genetic incompatibilities
 play a significant role in limiting gene flow even in young species.
description: Scripts used for
 analysis of linkage disequilibrium, sequence divergence, ABC simulations,
 hybrid zone age, and coalescent simulationsR, perl and php scripts
 used for data analysisLD_analysis_scripts.zipABC_simulation_drift.RUsage: Rscript ABC_simulation_drift.R #simulates data equally under two possible BDM fitness matrices based on specified parameter ranges
DOI: 10.5061/dryad.vb229
title: Data from: Experimental evidence for the evolution of the mammalian baculum by sexual selection

description: Male genitalia exhibit a taxonomically widespread pattern of rapid and
 divergent evolution. Sexual selection is generally believed to be
 responsible for these patterns of evolutionary divergence, although
 empirical support for the sexual selection hypothesis comes mainly from
 studies of insects. Here we show that sexual selection is responsible for
 an evolutionary divergence in baculum morphology among populations of
 house mice Mus domesticus. We sourced mice from three isolated populations
 known to be subject to differing strengths of postcopulatory sexual
 selection and bred them under common-garden conditions. Mice from
 populations with strong postcopulatory sexual selection had bacula that
 were relatively thicker compared with mice from populations with weak
 selection. We used experimental evolution to determine whether these
 patterns of divergence could be ascribed to postcopulatory sexual
 selection. After 27 generations of experimental evolution, populations of
 mice subjected to postcopulatory sexual selection evolved bacula that were
 relatively thicker than populations subjected to enforced monogamy. Our
 data thereby provide evidence that postcopulatory sexual selection
 underlies an evolutionary divergence in the mammalian baculum and supports
 the hypothesis that sexual selection plays a general role in the evolution
 of male genital morphology across evolutionary diverse taxonomic groups.
description: Simmons & Firman
 2013Excel spreadsheet
 containing data on body weights and male genital measurements from natural
 populations of house mice, and populations undergoing experimental
 evolution.
DOI: 10.5061/dryad.8nr8p
title: Data from: Nutritional state reveals complex consequences of risk in a wild predator–prey community

description: Animal populations are regulated by the combined effects of top-down,
 bottom-up and abiotic processes. Ecologists have struggled to isolate
 these mechanisms because their effects on prey behaviour, nutrition,
 security and fitness are often interrelated. We monitored how forage,
 non-consumptive effects (NCEs), consumptive predation and climatic
 conditions influenced the demography and nutritional state of a wild prey
 population during predator recolonization. Combined measures of nutrition,
 survival and population growth reveal that predators imposed strong
 effects on the prey population through interacting non-consumptive and
 consumptive effects, and forage mechanisms. Predation was directly
 responsible for adult survival, while declining recruitment was attributed
 to predation risk-sensitive foraging, manifested in poor female nutrition
 and juvenile recruitment. Substituting nutritional state into the
 recruitment model through a shared term reveals that predation
 risk-sensitive foraging was nearly twice as influential as summer forage
 conditions. Our findings provide a novel, mechanistic insight into the
 complex means by which predators and forage conditions affect prey
 populations, and point to a need for more ecological studies that
 integrate behaviour, nutrition and demography. This line of inquiry can
 provide further insight into how NCEs interactively contribute to the
 dynamics of terrestrial prey populations; particularly, how predation
 risk-sensitive foraging has the potential to stabilize predator–prey
 coexistence.
description: DeWitt et al - Capture
 HistoryCapture histories of
 porcupines at Sandhill Wildlife Area from 1996 to 2011. Each capture
 includes porcupine identity, date of capture, body mass at capture, the
 mean summer North Atlantic Oscillation (sNAO), the mean winter North
 Atlantic Oscillation (wNAO), the mean North Atlantic Oscillation measured
 between the start of winter and the date an individual was captured (NAO),
 and whether fishers were present within the study area during the capture
 year.DeWitt
 et al - CAPTURE HISTORY - Nutritional state reveals complex consequences
 of risk.csvDeWitt et al - Annual
 RecruitmentAnnual recruitment of
 porcupines at Sandhill Wildlife Area from 1996 to 2011. Each capture year
 includes the number of adult females, number of juveniles, and whether
 fishers were present within the study area during the capture
 year.DeWitt
 et al - RECRUITMENT - Nutritional state reveals complex consequences of
 risk.csv
DOI: 10.5061/dryad.g663p2b
title: Data from: Range‐wide population genetic structure of the Caribbean marine angiosperm Thalassia testudinum

description: Many marine species have widespread geographic ranges derived from their
 evolutionary and ecological history particularly their modes of dispersal.
 Seagrass (marine angiosperm) species have ranges that are unusually
 widespread, which is not unexpected following recent reviews of
 reproductive strategies demonstrating the potential for long distance
 dispersal combined with longevity through clonality. An exemplar of these
 dual biological features is turtlegrass (Thalassia testudinum) which is an
 ecologically important species throughout the tropical Atlantic region.
 Turtlegrass has been documented to have long distance dispersal via
 floating fruits and also extreme clonality and longevity. We hypothesise
 that across its range, Thalassia testudinum will have very limited
 regional population structure due to these characteristics and under
 typical models of population structure would expect to detect high levels
 of genetic connectivity. There are very few studies of range-wide genetic
 connectivity documented for seagrasses or other sessile marine species.
 This study presents a population genetic data set that represents a
 geographic area exceeding 14,000 km2. Population genetic diversity was
 evaluated from 32 Thalassia testudinum populations sampled across the
 Caribbean and Gulf of Mexico. Genotypes were based on nine microsatellites
 and haplotypes were based on chloroplast DNA sequences. Very limited
 phylogeographic signal from cpDNA reduced the potential comparative
 analyses possible. Multiple analytical clustering approaches on population
 genetic data revealed two significant genetic partitions: 1) The
 Caribbean, and 2) The Gulf of Mexico. Genetic diversity was high (HE =
 0.641) and Isolation by Distance was significant, gene flow and migration
 estimates across the entire range were however modest, we suggest that the
 frequency of successful recruitment across the range is uncommon.
 Thalassia testudinum maintains genetic diversity across its entire
 distribution range. The genetic split may be explained by genetic drift
 during recolonsation from refugia following relatively recent reduction in
 available habitat such as the last glacial maxima.
description: Thalassa testudinum
 genet genotypesGenepop infile for
 Thalassia testudinum genet genotypes.ThT_CarGulf.txt
DOI: 10.5061/dryad.nb26b
title: Data from: Identifying litchi (Litchi chinensis Sonn.) cultivars and their genetic relationships using single nucleotide polymorphism (SNP) markers

description: Litchi is an important fruit tree in tropical and subtropical areas of the
 world. However, there is widespread confusion regarding litchi cultivar
 nomenclature and detailed information of genetic relationships among
 litchi germplasm is unclear. In the present study, the potential of single
 nucleotide polymorphism (SNP) for the identification of 96 representative
 litchi accessions and their genetic relationships in China was evaluated
 using 155 SNPs that were evenly spaced across litchi genome. Ninety SNPs
 with minor allele frequencies above 0.05 and a good genotyping success
 rate were used for further analysis. A relatively high level of genetic
 variation was observed among litchi accessions, as quantified by the
 expected heterozygosity (He = 0.305). The SNP based multilocus matching
 identified two synonymous groups, ‘Heiye’ and ‘Wuye’, and ‘Chengtuo’ and
 ‘Baitangli 1’. A subset of 14 SNPs was sufficient to distinguish all the
 non-redundant litchi genotypes, and these SNPs were proven to be highly
 stable by repeated analyses of a selected group of cultivars. Unweighted
 pair-group method of arithmetic averages (UPGMA) cluster analysis divided
 the litchi accessions analyzed into four main groups, which corresponded
 to the traits of extremely early-maturing, early-maturing,
 middle-maturing, and late-maturing, indicating that the fruit maturation
 period should be considered as the primary criterion for litchi taxonomy.
 Two subpopulations were detected among litchi accessions by STRUCTURE
 analysis, and accessions with extremely early- and late-maturing traits
 showed membership coefficients above 0.99 for Cluster 1 and Cluster 2,
 respectively. Accessions with early- and middle-maturing traits were
 identified as admixture forms with varying levels of membership shared
 between the two clusters, indicating their hybrid origin during litchi
 domestication. The results of this study will benefit litchi germplasm
 conservation programs and facilitate maximum genetic gains in litchi
 breeding programs.
description: SNP data for
 litchiThis file contains
 genotype data at 90 SNP loci for 96 litchi accessions sampled in
 China.Litchi
 SNP-dryad.xlsx
DOI: 10.5061/dryad.1f4nj20
title: Data from: Tropical rainforest conversion and land-use intensification reduce understory plant phylogenetic diversity

description: 1. Conversion of rainforest into agricultural land affects multiple facets
 of tropical plant diversity. While the effects of tropical land use change
 and intensification on species diversity are comparatively well studied,
 the effects on phylogenetic diversity and structure of plant communities
 are largely unknown. Furthermore, it is not clear how the loss of native
 species and addition of alien species collectively affect phylogenetic
 diversity and structure. 2. We investigated the phylogenetic diversity and
 structure of understorey plants; a diverse and ecologically important, yet
 poorly studied group. We studied four prominent land use systems (tropical
 lowland rainforest, jungle rubber agroforest, rubber plantations and oil
 palm plantations) in the lowlands of Sumatra (Indonesia), a region
 experiencing dramatic land use changes. 3. Across the four systems, we
 investigated differences in four metrics of phylogenetic community
 structure (phylogenetic diversity, mean pairwise distance, mean nearest
 taxon distance and their abundance-weighted variants). Our analyses were
 based on a comprehensive vegetation survey consisting of 32 plots, 1,197
 species of vascular plants, and 146,599 plant individuals. 4. Our results
 showed that forest conversion into agricultural systems leads to a
 pronounced loss of phylogenetic diversity. Furthermore, the standard
 effect size of mean pairwise distance indicated a gradual change from
 clustered to overdispersed phylogenetic community structure with
 increasing land use intensity from forest over jungle rubber to the
 monoculture plantations. In most land use systems, the presence or absence
 of alien plant species did not affect phylogenetic structure. Only in oil
 palm plantations, removing alien species from the data led to a more
 overdispersed structure. In conclusion, conserving the phylogenetic
 diversity and structure requires efficient protection of the last
 remaining rainforests. 5. Synthesis and applications. Forest conversion
 into agricultural areas negatively affects phylogenetic understorey plant
 diversity and leads to a shift from clustered to overdispersed
 phylogenetic community structure. These trends are partly driven by alien
 species particularly in oil palm plantations. Protecting the remaining
 rainforests, and considering multi-species agroforestry systems in favour
 of intensive monoculture plantations are thus imperative to conserve
 phylogenetic plant diversity and community structure.
description: phylo_sumatraThe phylogeny used in the paper in newick format.metrics_sumatraThe community data used in the paper in csv format.
DOI: 10.5061/dryad.7h7tk
title: Data from: Reciprocal behavioral plasticity and behavioral types during predator-prey interactions

description: How predators and prey interact has important consequences for population
 dynamics and community stability. Here we explored how predator-prey
 interactions are simultaneously affected by reciprocal behavioral
 plasticity (i.e., plasticity in prey defenses countered by plasticity in
 predator offenses and vice versa) and consistent individual behavioral
 variation (i.e., behavioral types) within both predator and prey
 populations. We assessed the behavior of a predator species (northern
 pike) and a prey species (three-spined stickleback) during one-on-one
 encounters. We also measured additional behavioral and morphological
 traits in each species. Using structural equation modeling, we found that
 reciprocal behavioral plasticity as well as predator and prey behavioral
 types influenced how individuals behaved during an interaction. Thus, the
 progression and ultimate outcome of predator-prey interactions depend on
 both the dynamic behavioral feedback occurring during the encounter and
 the underlying behavioral type of each participant. We also examined
 whether predator behavioral type is underlain by differences in metabolism
 and organ size. We provide some of the first evidence that behavioral type
 is related to resting metabolic rate and size of a sensory organ (the
 eyes). Understanding the extent to which reciprocal behavioral plasticity
 and intraspecific behavioral variation influence the outcome of species
 interactions could provide insight into the maintenance of behavioral
 variation as well as community dynamics.
description: Individual Northern pike
 traits - behavior, metabolism & organ massesMcGhee_etal_pike_traits.xlsStickleback-alone behavior & stickleback-pike behavior during interactionsMcGhee_etal_stickle-pike.xls
DOI: 10.5061/dryad.565r1
title: Data from: The distribution of mutational fitness effects of phage ϕX174 on different hosts

description: Adaptation depends greatly on the distribution of mutation fitness effects
 (DMFE), but the phenotypic expression of mutations is often
 environment-dependent. The environments of multi-host pathogens are mostly
 governed by their hosts and therefore measuring the DMFE on multiple hosts
 can inform on the likelihood of short-term establishment and longer-term
 adaptation of emerging pathogens. We explored this by measuring the growth
 rate of 36 mutants of the lytic bacteriophage ϕX174 on two host
 backgrounds, Escherichia coli (EcC) and Salmonella typhimurium (StGal).
 The DMFE showed higher mean and variance on EcC than on StGal. Most
 mutations were either deleterious or neutral on both hosts, but a greater
 proportion of mutations were deleterious on StGal. We identified two
 mutations with beneficial fitness effects on EcC that were neutral on
 StGal. Host-specific differences in fitness were associated with
 particular functional classes of genes involved in the initial stages of
 infection in accordance with previous studies of host specificity.
 Overall, there was a positive correlation between the effects of mutations
 on each host, suggesting that most new mutations will have general, rather
 than host-specific fitness effects. We consider these results in light of
 simple fitness landscape models of adaptation and discuss the relevance of
 context-dependent DMFE for multi-host pathogens.
description: analysesR codes and data files.
DOI: 10.5061/dryad.1436s
title: Data from: Breaking out of the comfort zone: El Niño-Southern Oscillation as a driver of trophic flows in a benthic consumer of the Humboldt Current ecosystem

description: The trophic flow of a species is considered a characteristic trait
 reflecting its trophic position and function in the ecosystem and its
 interaction with the environment. However, climate patterns are changing
 and we ignore how patterns of trophic flow are being affected. In the
 Humboldt Current ecosystem, arguably one of the most productive marine
 systems, El Niño-Southern Oscillation is the main source of interannual
 and longer-term variability. To assess the effect of this variability on
 trophic flow we built a 16-year series of mass-specific somatic production
 rate (P/B) of the Peruvian scallop (Argopecten purpuratus), a species
 belonging to a former tropical fauna that thrived in this cold ecosystem.
 A strong increase of the P/B ratio of this species was observed during
 nutrient-poor, warmer water conditions typical of El Niño, owing to the
 massive recruitment of fast-growing juvenile scallops. Trophic ecology
 theory predicts that when primary production is nutrient limited, the
 trophic flow of organisms occupying low trophic levels should be
 constrained (bottom-up control). For former tropical fauna thriving in
 cold, productive upwelling coastal zones, a short time of low food
 conditions but warm waters during El Niño could be sufficient to waken
 their ancestral biological features and display massive proliferations.
description: Growth parameters of
 Argopecten purpuratus and associated statisticsEstimation of growth
 parameters of Argopecten purpuratus using the ELEFAN_SA optimization
 procedure implemented in TropFishR. Ncohort: is the number of yearly
 repeating cohorts; Agemax: maximum age of the population; L∞ L asymptotic
 total length; K: von Bertalanffy growth constant; t_anchor: is the
 fraction of the year (ranging between 0 and 1) where yearly repeating
 growth curves cross length equal to zero; C: is a constant indicating the
 amplitude of the growth oscillation; ts is the fraction of a year where
 the sine wave oscillation begins; Φ´: growth performance index (see eq.
 3); Rn_max: maximum possible score obtained during the fitness
 maximization process; ASP: available sum of peaks (for details see
 Mildenberger et al. 2017 [30]). CI: confidence intervals for growth
 parameters calculated with the jack knife technique
 [30]Dataset
 1.xlsxP/B ratio of Argopecten
 purpuratus and environmental factorsAnnual changes in the
 production to biomass ratio of Argopecten purpuratus and environmental
 factors potentially affecting themDataset
 2.xlsxPopulation parameters of
 Argopecten purpuratusMonthly estimation of
 population parameters of Argopecten purpuratus in Bahia independencia:
 Mean abundance (number of individuals per square meter); Individual mass
 (g ash-free dry mass estimated for a standard individual of 65 mm in shell
 length); body size (mm, mean, minimum, Q1 percentil, Q2 percentil and
 maximum)Dataset
 3.xlsx