cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1b15j
title: Data from: Sexual conflict and correlated evolution between male persistence and female resistance traits in the seed beetle Callosobruchus maculatus

description: Traumatic mating (or copulatory wounding) is an extreme form of sexual
 conflict whereby male genitalia physically harm females during mating. In
 such species females are expected to evolve counter-adaptations to reduce
 male-induced harm. Importantly, female counter-adaptations may include
 both genital and non-genital traits. In this study, we examine
 evolutionary associations between harmful male genital morphology and
 female reproductive tract morphology and immune function across 13
 populations of the seed beetle Callosobruchus maculatus. We detected
 positive correlated evolution between the injuriousness of male genitalia
 and putative female resistance adaptations across populations. Moreover,
 we found evidence for a negative relationship between female immunity and
 population productivity, which suggests that investment in female
 resistance may be costly due to the resource trade-offs that are predicted
 between immunity and reproduction. Finally, the degree of female tract
 scarring (harm to females) was greater in those populations with both
 longer aedeagal spines and a thinner female tract lining. Our results are
 thus consistent with a sexual arms race, which is only apparent when both
 male and female traits are taken into account. Importantly, our study
 provides rare evidence for sexually antagonistic coevolution of male and
 female traits at the within-species level.
description: Female trait
 dataImmunity, tract volume
 and tract scarring data for all femalesfemale_traits.xlsxpopulation_means_finalPopulation mean values for all male and female traits used in the analysis. Male data and standard female scarring data taken with permission from Hotzy & Arnqvist (2009), and population fitness data taken with permission from Rankin & Arnqvist (2008). See main text for details.
DOI: 10.5061/dryad.mg040
title: Data from: New approaches for unravelling reassortment pathways

description: BACKGROUND: Every year the human population encounters epidemic outbreaks
 of influenza, and history reveals recurring pandemics that have had
 devastating consequences. The current work focuses on the development of a
 robust algorithm for detecting influenza strains that have a composite
 genomic architecture. These influenza subtypes can be generated through a
 reassortment process, whereby a virus can inherit gene segments from two
 different types of influenza particles during replication. Reassortant
 strains are often not immediately recognised by the adaptive immune system
 of the hosts and hence may be the source of pandemic outbreaks. Owing to
 their importance in public health and their infectious ability, it is
 essential to identify reassortant influenza strains in order to understand
 the evolution of this virus and describe reassortment pathways that may be
 biased towards particular viral segments. Phylogenetic methods have been
 used traditionally to identify reassortant viruses. In many studies up to
 now, the assumption has been that if two phylogenetic trees differ, it is
 because reassortment has caused them to be different. While phylogenetic
 incongruence may be caused by real differences in evolutionary history, it
 can also be the result of phylogenetic error. Therefore, we wish to
 develop a method for distinguishing between topological inconsistency that
 is due to confounding effects and topological inconsistency that is due to
 reassortment. RESULTS: The current work describes the implementation of
 two approaches for robustly identifying reassortment events. The
 algorithms rest on the idea of significance of difference between
 phylogenetic trees or phylogenetic tree sets, and subtree pruning and
 regrafting operations, which mimic the effect of reassortment on tree
 topologies. The first method is based on a maximum likelihood (ML)
 framework (MLreassort) and the second implements a Bayesian approach
 (Breassort) for reassortment detection. We focus on reassortment events
 that are found by both methods. We test both methods on a simulated
 dataset and on a small collection of real viral data isolated in Hong Kong
 in 1999. CONCLUSIONS: The nature of segmented viral genomes present many
 challenges with respect to disease. The algorithms developed here can
 effectively identify reassortment events in small viral datasets and can
 be applied not only to influenza but also to other segmented viruses.
 Owing to computational demands of comparing tree topologies, further
 development in this area is necessary to allow their application to larger
 datasets.
description: Alignments for each gene
 segmentalignments.zipScripts for MLreassort and MBreassortscripts_reassort.zip
DOI: 10.5061/dryad.ss08k
title: Data from: Patriline differences reveal genetic influence on forewing size and shape in a yellowjacket wasp (Hymenoptera: Vespidae: Vespula flavopilosa Jacobson, 1978)

description: The wing venation is frequently used as a morphological marker to
 distinguish biological groups among insects. With geometric morphometrics,
 minute shape differences can be detected between closely related species
 or populations, making this technique useful for taxonomy. However, the
 direct influence of genetic differences on wing morphology has not been
 explored within colonies of social insects. Here, we show that the
 father’s genotype has a direct effect on wing morphology in colonies of
 social wasps. Using geometric morphometrics on the venation pattern, we
 found significant differences in wing size and shape between patrilines of
 yellowjackets, taking allometry and measurement error into account. The
 genetic influence on wing size accounted for a small part of the overall
 size variation, but venation shape was highly structured by the
 differences between patrilines. Overall, our results showed a strong
 genetic influence on wing morphology likely acting at multiple levels of
 venation pattern development. This confirmed the pertinence of this marker
 for taxonomic purposes and suggests this phenotype as a potentially useful
 marker for phylogenies. This also raises doubts about the strength of
 selective pressures on this phenotype, which highlights the need to
 understand better the role of wing venation shape in insect flight.
description: Landmark-Data-Perrard-Loope-2015Specimen information (colony, patriline) and landmark data of the wing shape of workers of Vespula flavopilosa studied in Perrard & Loope, 2015.Script R from Perrard & Loope, 2015Script R used for the analyses of Perrard & Loope, 2015. This file contains both the script and the function "regallom" to compute multigroup allometry and allometric residuals using the multivariate regression approach.ScriptR-Perrard-Loope-2015.R
DOI: 10.5061/dryad.cg10d
title: Data from: Human-facilitated metapopulation dynamics in an emerging pest species, Cimex lectularius

description: The number and demographic history of colonists can have dramatic
 consequences for the way in which genetic diversity is distributed and
 maintained in a metapopulation. The bed bug (Cimex lectularius) is a
 re-emerging pest species whose close association with humans has led to
 frequent local extinction and colonisation, i.e. to metapopulation
 dynamics. Pest control limits the lifespan of sub-populations, causing
 frequent local extinctions, and human-facilitated dispersal allows the
 colonisation of empty patches. Founder events often result in drastic
 reductions in diversity and an increased influence of genetic drift.
 Coupled with restricted migration this can lead to rapid population
 differentiation. We therefore predicted strong population structuring.
 Here, using 21 newly characterised microsatellite markers and Approximate
 Bayesian Computation (ABC), we investigate simplified versions of two
 classical models of metapopulation dynamics, in a coalescent framework, in
 order to estimate the number and genetic composition of founders in the
 common bed bug. We found very limited diversity within infestations but
 high degrees of structuring across the city of London, with extreme levels
 of genetic differentiation between infestations (FST = 0.59). ABC results
 suggest a common origin of all founders of a given sub-population and that
 the numbers of colonists were low; implying that even a single mated
 female is enough to found a new infestation successfully. These patterns
 of colonisation are close to the predictions of the propagule pool model,
 where all founders originate from the same parental infestation. These
 results show that aspects of metapopulation dynamics can be captured in
 simple models and provide insights that are valuable for the future
 targeted control of bed bug infestations.
description: Fountain et al. 2014
 genotypesMicrosatellite genotypes
 presented in Cervus input format for markers used in study. Divided into
 within infestation genotypes and within city genotypes as referred to in
 text. Populations correspond to those within
 manuscript.
DOI: 10.5061/dryad.302jc
title: Data from: Post-copulatory opportunities for sperm competition and cryptic female choice provide no offspring fitness benefits in externally fertilizing salmon

description: There is increasing evidence that females can somehow improve their
 offspring fitness by mating with multiple males, but we understand little
 about the exact stage(s) at which such benefits are gained. Here, we
 measure whether offspring fitness is influenced by mechanisms operating
 solely between sperm and egg. Using externally fertilizing and polyandrous
 Atlantic salmon (Salmo salar), we employed split-clutch and
 split-ejaculate in vitro fertilization experiments to generate offspring
 using designs that either denied or applied opportunities for sperm
 competition and cryptic female choice. Following fertilizations, we
 measured 140 days of offspring fitness after hatch, through growth and
 survival in hatchery and near-natural conditions. Despite an average
 composite mortality of 61%, offspring fitness at every life stage was
 near-identical between groups fertilized under the absence versus presence
 of opportunities for sperm competition and cryptic female choice. Of the
 21 551 and 21 771 eggs from 24 females fertilized under monandrous versus
 polyandrous conditions, 68% versus 67.8% survived to the 100-day juvenile
 stage; sub-samples showed similar hatching success (73.1% versus 74.3%),
 had similar survival over 40 days in near-natural streams (57.3% versus
 56.2%) and grew at similar rates throughout. We therefore found no
 evidence that gamete-specific interactions allow offspring fitness
 benefits when polyandrous fertilization conditions provide opportunities
 for sperm competition and cryptic female choice.
description: GAGE ET AL OPEN SCIENCE
 POLYANDRY BENEFITS IN SALMON RAW DATARaw study data in
 excel
DOI: 10.5061/dryad.k7v4811k
title: Data from: Effects of the landscape on boreal toad gene flow: does the pattern-process relationship hold true across distinct landscapes at the northern range margin?

description: Understanding the impact of natural and anthropogenic landscape features
 on population connectivity is a major goal in evolutionary ecology and
 conservation. Discovery of dispersal barriers is important for predicting
 population responses to landscape and environmental changes, particularly
 for populations at geographic range margins. We used a landscape genetics
 approach to quantify the effects of landscape features on gene flow and
 connectivity of boreal toad (Bufo boreas) populations from two distinct
 landscapes in Southeast Alaska (Admiralty Island, ANM, and the Chilkat
 River Valley, CRV). We used two common methodologies for calculating
 resistance distances in landscape genetics studies (resistance based on
 least-cost paths and circuit theory). We found a strong effect of
 saltwater on genetic distance of CRV populations, but no landscape effects
 were found for the ANM populations. Our discordant results show the
 importance of examining multiple landscapes that differ in the variability
 of their features, in order to maximize detectability of underlying
 processes and allow results to be broadly applicable across regions.
 Saltwater serves as a physiological barrier to boreal toad gene flow and
 affects populations on a small geographic scale, yet there appear to be
 few other barriers to toad dispersal in this intact northern region.
description: Boreal toad
 microsatellite genotypesToad_genotypes.xlsx
DOI: 10.5061/dryad.0735s
title: Data from: Self-fertilization and the role of males in populations of tadpole shrimp (Branchiopoda: Notostraca: Triops)

description: Self-fertilization has both negative and positive fitness effects on
 species evolution. Selfing can increase inbreeding depression, thereby
 decreasing genetic diversity. In contrast, self-fertilization can preserve
 beneficial gene combinations and facilitate colonization success. Within
 the class of crustaceans Branchiopoda, selfing is a primary reproductive
 mode. Some species of Triops, in the family Notostraca, are a few of the
 animal species thought to have a mixed mating system between
 hermaphrodites and males termed androdioecy. The objective of this study
 is to validate the reproductive mode utilized by Triops newberryi in
 southern New Mexico by the use of progeny arrays and population
 simulations. Individuals were reared in the lab from dried soil collected
 from temporary ponds inhabited by T. newberryi. The adults reared and the
 encysted embryos contained within their brood pouches were genotyped using
 seven T. newberryi specific microsatellite markers to determine the
 relatedness between parent and offspring. Overall microsatellite diversity
 was low with few heterozygous individuals and limited polymorphisms.
 Simulated populations and allele segregation analysis suggest
 hermaphroditism is the primary reproductive mode for T. newberryi. In
 addition, based on the offspring’s alleles, there was no direct evidence
 that a male (ovisacless) T. newberryi outcrossed with a female. Population
 simulations further suggest that the rate of successful outcrossing events
 must be low and could explain why outcrossing was not observed in the
 laboratory rearing trials.
description: Horn&Cowley_Tnewberryi GenotypesThe microsatellite genotypes for the adult and offspring samples from the Horn and Cowley manuscript.Horn&Cowley_Easypop_RunWindowsA text file containing the input parameters for the program EASYPOP used to generate the simulated datasets.Horn&Cowley_GeneticStatistics_SimulationsA file containing the genetic statistics (FIS, number of alleles, levels of heterozygosity, etc.) generated from the simulated datasets. This data was used to build figure 1 in the manuscript associated with this entry, i.e. Horn and Cowley(2016).
DOI: 10.5061/dryad.8r6m4
title: Data from: Extrapolating multi-decadal plant community changes based on medium-term experiments can be risky: evidence from high-latitude tundra

description: For most experimental studies the short-term responses to manipulation
 often differ from the long-term changes in the community composition,
 dynamics or functioning. Such discrepancy limits the translation of
 experimental results into key ecological topics such as global
 environmental change. Here we analyzed plant community dynamics from a
 23-year transplant experiment in the Fennoscandian mountain tundra and
 explored how well the pattern of responses over the first 12 years of the
 experiment can predict longer-term changes. Sod-blocks of tundra heath
 vegetation were transplanted to a snowbed 150 m higher in elevation from
 their origin, where, with contrasting levels of soil wetness, half of the
 transplants were protected from mammalian herbivores. Throughout the
 experiment, community changes strongly depended on both plant functional
 types and experimental treatments. The first 12 years were characterized
 by a response to transplantation to the snowbed showing a strong increase
 of graminoid and a decrease of shrub abundances in the transplants. In the
 longer term, the community divergence increased in particular in response
 to grazing and soil wetness within the snowbed, while graminoid dominance
 disappeared. Markov chain models captured the main trends during the first
 12 years but they failed to predict their relative abundance after 23
 years. In particular, the late dominance of bryophytes in the wet snowbed,
 the recovery of shrubs in the dry exclosures, and the subordinate status
 of graminoids deviated from the extrapolation based on the medium-term
 trends. Despite clear community dynamical trajectories detected in the
 first decade, the differences in the temporal scale of both treatment
 effects and plant functional type responses limited their ability to
 extrapolate longer-term trajectories. We find that increasing focus on
 long-term experiments is a crucial step to understanding the processes
 involved in the response of plant communities to global environmental
 change.
description: SacconeVirtanen-Oikos-02399-Plant-CompositionTable of 300 observations and 109 variables. Variables (columns) 1 to 4 = Year, treatment, replicate number, soil moisture. variables 5 to 104 = species abundances. variables 105 to 109 = accumulated plant functional type abundancesSacconeVirtanen-oik-02399.txt
DOI: 10.5061/dryad.qc57j
title: Data from: Long-term benefit of hepatitis C therapy in a safety net hospital system: a cross-sectional study with median 5-year follow-up

description: Objectives: To demonstrate the effectiveness of hepatitis C virus (HCV)
 therapy and survival benefit from sustained virologic remission (SVR) in a
 safety net hospital population with limited resources. Design and setting:
 We conducted a retrospective cross-sectional study at an urban safety-net
 hospital in the U.S. Participants and intervention: 242 patients receiving
 standard HCV therapy between 2001 and 2006. Primary and secondary outcome
 measures: Response rates, including sustained virologic response (SVR),
 were recorded for each patient. Univariate and multivariate analyses were
 performed to identify predictors of SVR and 5 year survival. Results: A
 total of 242 eligible patients were treated. Treatment was completed in
 197 (81%) patients, with 43 patients discontinuing therapy early – 32 due
 to adverse events and 11 due to non-compliance. Complications on treatment
 were frequent, including 3 deaths. SVR was achieved in 83 patients (34%).
 On multivariate analysis, independent predictors of a decreased likelihood
 of achieving SVR included African American race (OR 0.20, 95% CI 0.07 –
 0.54), genotype 1 HCV infection (OR 0.25, 95% CI 0.13 – 0.50) and the
 presence of cirrhosis (OR 0.26, 95% CI 0.12 – 0.58). Survival was 98% in
 those achieving SVR (median follow-up 72 months) and 71% in non-responders
 and those discontinuing therapy (n = 91, median known follow-up 65 and 36
 months respectively). On multivariate analysis, the only independent
 predictor of improved survival was SVR (HR 0.12, 95% CI 0.03 – 0.52). Both
 cirrhosis and hypoalbuminemia were independent predictors of increased
 mortality. Conclusions: HCV therapy can be effective despite limited
 resources. Survival is improved in those achieving SVR. Treatment before
 histologic cirrhosis develops, in combination with careful selection, may
 improve long-term outcomes without compromising other health care
 endeavors in safety net hospitals and areas with financial limitations.
description: Demographics,
 laboratory, imaging and treatment characteristicsAnonymized medical
 record data from individual subjectsHCVRxDryad.v3.xlsx
DOI: 10.5061/dryad.m2h55
title: Data from: Meiotic drive changes sperm precedence patterns in house mice: potential for male alternative mating tactics

description: Background - With female multiple mating (polyandry), male-male
 competition extends to after copulation (sperm competition). Males respond
 to this selective pressure through physiological, morphological and
 behavioural adaptations. Sperm competitiveness is commonly decreased in
 heterozygote carriers of male meiotic drivers, selfish genetic elements
 that manipulate the production of gametes in males. This might give
 carriers an evolutionary incentive to reduce the risk of sperm
 competition. Here, we explore this possibility in house mice. Natural
 populations frequently harbour a well-characterised male driver (t
 haplotype), which is transmitted to 90% of heterozygous (+/t) males'
 offspring. Previous research demonstrated strong detrimental effects on
 sperm competitiveness, and suggested that +/t males are particularly
 disadvantaged against wild type males when first-to-mate. Low paternity
 success in the first-to-mate role is expected to favour male adaptations
 that decrease the risk of sperm competition by preventing female remating.
 Genotype-specific paternity patterns (sperm precedence) could lead to
 genetically determined alternative reproductive tactics that can spread
 through gene level selection. Here, we seek confirmation that +/t males
 are generally disadvantaged when first-to-mate and address whether males
 of different genotypes differ in reproductive tactics (copulatory and
 morphological) to maximise individual or driver fitness. Finally, we
 attempt to explain the mechanistic basis for alternative sperm precedence
 patterns in this species. Results - We confirmed that +/t males are weak
 sperm competitors when first to mate. When two +/t males competed, the
 second-to-mate was more successful, which contrasts with first male sperm
 precedence when wild type males competed. However, we found no differences
 between male genotypes in reproductive behaviour or morphology that were
 consistent with alternative reproductive tactics. Sperm of +/+ and +/t
 males differed with respect to in vitro sperm features. Premature
 hypermotility in +/t males' sperm can potentially explain why +/t
 males are very weak sperm competitors when first-to-mate. Conclusions -
 Our results demonstrate that meiotic drivers can have strong effects on
 sperm precedence patterns, and may provide a heritable basis for
 alternative reproductive tactics motivated by reduced sperm
 competitiveness. We discuss how experimental and evolutionary constraints
 may help explain why male genotypes did not show the predicted
 differences.
description: Data from Sperm
 competition trials, male reproductive organs and sperm
 measurementsSheet1 contains
 behavioural data and paternity outcome from sperm competition trials;
 Sheet2 contains data from computer assisted sperm analysis; Sheet3
 contains data on male reproductive organ weights; Sheet4 contains variable
 descriptions20160601_forDryad.xlsx