cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.5tb2rbp0n
title: Microsatellite-based analysis of genetic structure and gene flow of Mythimna separata (Walker) (Lepidoptera: Noctuidae) in China

description: The oriental armyworm, Mythimna separata, is a serious
 agricultural pest in China. Seasonal and roundtrip migration has recently
 led to sudden, localized outbreaks and crop losses. To evaluate genetic
 differentiation between populations in eastern and western China and
 elucidate gene flow, the genetic structure of 20 natural populations from
 nine provinces was examined using seven microsatellite markers. The
 results indicated high genetic diversity. However, little to moderate
 (0 &lt; FST &lt; 0.15) genetic
 differentiation was detected, and there was no correlation between genetic
 distance and geographical distance. Bayesian clustering analysis
 identified three groups whereas discriminant analysis of principal
 components identified ten clusters that were considered as two clear‐cut
 clusters and one admixed group. Gene flow occurred frequently in most
 population pairs, and an asymmetrical migration rate was detected in
 several pairwise population comparisons. The bottleneck test showed that
 few populations had experienced recent bottlenecks. Correspondingly,
 large‐scale and long‐distance migration
 of M. separata has caused low genetic
 differentiation and frequent gene exchange. Our findings are important for
 studying genetic evolution and help to improve predictions
 of M. separata outbreaks in China.
description: The oriental armyworm larvae samples were collected from
 maize (<em>Z. mays</em>) fields from nine provinces at 20
 geographical sites in China. Seven  polymorphic microsatellite loci,
 A1–91, A3–81, JGTT29, MS1, MS2, MS3, and MS4, developed for <em>M.
 separata</em> were scored for genotyping. The PCR products of the
 target band were genotyped by capillary electrophoresis with two‐color
 fluorescent detection technique using an ABI3730XL  automatic
 sequencer. (Applied Biosystems). Microsatellite alleles for genotyping
 were estimated with GeneMarker 2.2 (SoftGenetics LLC) and were confirmed
 manually.
description: The microsatellite data file incorporates a total of 542
 individuals from 20 geographical populations of the oriental armyworm,
 <i>Mythimna separata</i> in China. Seven polymorphic
 microsatellite loci, including A3-91, A3-81, JGTT29, MS1, MS2, MS3, and
 MS4 are used to genotype. Twenty populations are HBB, HBC, HNH, HNL, HNX,
 JLC, JLS, LNF, NME, SDJ, SDW, SXB, SXF, SXH, SXL, SXM, SXW, SXX, SYC, and
 YNZ, respectively. This dataset are associated to the article
 “Microsatellite-based analysis of genetic structure and gene flow of
 <i>Mythimna separata</i> (Walker) (Lepidoptera: Noctuidae) in
 China (ECE-2019-03-00269.R2)”, which has been accepted by journal Ecology
 and Evolution. Seven polymorphic microsatellite loci,
 A1–91, A3–81, JGTT29, MS1, MS2, MS3, and MS4, developed for <em>M.
 separata </em>were scored for genotyping (Li et al., 2018; Zhang
 & Zhai, 2008). The missing values were denoted by 0.
DOI: 10.5061/dryad.qjq2bvqbv
title: Efficacy of treatments for polycystic ovarian syndrome management in adolescents: a systematic review and network meta-analysis

description: Limited evidence on treatment options for polycystic ovarian syndrome
 (PCOS) has led to considerable variation in healthcare
 practices. We aimed to compare the effects of metformin and/or
 oral contraceptive pills (OCPs) in combination with pioglitazone,
 spironolactone, flutamide, and lifestyle interventions among adolescents
 aged 11-19 years with PCOS. Literature searches were performed in Medline,
 Embase, and the Cochrane Central Register of Controlled Trials from
 database inception through December 2018, with no language restriction.
 Two reviewers screened titles and abstracts, assessed full text
 eligibility, and extracted information from eligible trials. Evidence was
 synthesized through network meta-analyses (NMA) using Bayesian
 random-effects approach. We identified 37 RCTs, in which 2400 patients
 were randomized. NMA showed no statistically important difference among
 all interventions to improve menstrual regulation, or body mass index.
 Moderate quality evidence showed hirsutism scores were reduced by multiple
 interventions that included single and combination medications namely;
 lifestyle intervention, metformin, OCP, spironolactone, pioglitazone,
 metformin-OCP, metformin-spironolactone, metformin-flutamide, against
 placebo. Moderate quality evidence showed OCP results in more dysglycaemia
 compared to metformin (odds ratio 2.98; 95%credible interval 1.02, 8.96),
 no intervention resulted in dysglycaemia reduction. In conclusion,
 metformin and OCP as monotherapy or in combination with other
 interventions compared to placebo can reduce hirsutism scores, but none of
 these medications lead to effective menstrual cycle regulation or weight
 reduction. However, the use of OCP leads to worse cardiometabolic risk
 factors. Further research into new treatment options is urgently needed.
description: PROSPERO registration number:
 CRD42015016148.
DOI: 10.5061/dryad.z34tmpg84
title: Maintaining genetic integrity with high promiscuity: Frequent hybridization with low introgression in multiple hybrid zones of Melocactus(Cactaceae)

description: Hybridization and introgression between species in contact/hybrid zones
 provide important insight into the genetic and ecological
 mechanisms of speciation. Cactaceae represents the most important
 radiation of true succulent angiosperms in the New World. This
 diversification continues to date, with species experiencing few
 intrinsic barriers to gene flow and the frequent occurrence of
 natural hybridization. Here, we used RAD-Seq single-nucleotide
 polymorphism (SNP) data to investigate  the
  genetic  architecture  of
  hybridization  in  four  hybrid
  zones  hosting  Melocactus concinnus
  and  four  congeneric  species
  (M.  ernestii,  M.  glaucescens,
  M.  paucispinus,  and M. zehntneri). Our
 results revealed that  M. concinnusis highly promiscuous in
 sympatric areas and hybridizes  with  various
  species  distributed  in  Morro
  do  Chapéu  (Diamantina  Plateau,
  Bahia), eastern Brazil. However, the contemporary
 genomic introgression among the investigated species is
  very  low  (c.  2–5%),
  confirming  that  even  in
  the  face  of  hybridization,
  Melocactus  species maintain  their
  genetic  integrity.  The  genomic
  cline  approach  showed  a
  large  fraction  of
  loci deviating from a model of neutral introgression,
 where most of the loci are consistent with selection favoring
  parental  genotypes.  Our  results
  suggest  the  occurrence  of
  weak  premating  but
  strong  postmating  reproductive
  isolation  in  the  analyzed
  cactus  species.  Furthermore,  as
  most  of  the Melocactus species
  are  restricted  in  distribution,
  hybridization  might  negatively
  affect  their integrity if hybrids replace the
 parental species.
DOI: 10.5061/dryad.547d7wm3x
title: Multilevel modeling of time-series cross-sectional data reveals the dynamic interaction between ecological threats and democratic development

description: What is the relationship between environment and democracy? The framework
 of cultural evolution suggests that societal development is an adaptation
 to ecological threats. Pertinent theories assume that democracy emerges as
 societies adapt to ecological factors such as higher economic wealth,
 lower pathogen threats, less demanding climates, and fewer natural
 disasters. However, previous research confused within-country processes
 with between-country processes and erroneously interpreted between-country
 findings as if they generalize to within-country mechanisms. In this
 article, we analyze a time-series cross-sectional dataset to study the
 dynamic relationship between environment and democracy (1949-2016),
 accounting for previous misconceptions in levels of analysis. By
 separating within-country processes from between-country processes, we
 find that the relationship between environment and democracy not only
 differs by countries but also depends on the level of analysis. Economic
 wealth predicts increasing levels of democracy in between-country
 comparisons, but within-country comparisons show that democracy declines
 as countries become wealthier over time. This relationship is only
 prevalent among historically wealthy countries but not among historically
 poor countries, whose wealth also increased over time. By contrast,
 pathogen prevalence predicts lower levels of democracy in both
 between-country and within-country comparisons. Our longitudinal analyses
 identifying temporal precedence reveal that not only reductions in
 pathogen prevalence drive future democracy, but also democracy reduces
 future pathogen prevalence and increases future wealth. These nuanced
 results contrast with previous analyses using narrow, cross-sectional
 data. As a whole, our findings illuminate the dynamic process by which
 environment and democracy shape each other.
description: Our Time-Series Cross-Sectional data combine various online
 databases. Country names were first identified and matched using R-package
 “countrycode” (Arel-Bundock, Enevoldsen, & Yetman, 2018) before
 all datasets were merged. Occasionally, we modified unidentified country
 names to be consistent across datasets. We then transformed “wide” data
 into “long” data and merged them using R’s Tidyverse framework (Wickham,
 2014). Our analysis begins with the year 1949, which was occasioned by the
 fact that one of the key time-variant level-1 variables, pathogen
 prevalence was only available from 1949 on. See our Supplemental Material
 for all data, Stata syntax, R-markdown for visualization, supplemental
 analyses and detailed results (available at https://osf.io/drt8j/).
DOI: 10.25338/b8h038
title: Multiple and extra-pair mating in a pair-living hermaphrodite, the intertidal limpet Siphonaria gigas

description: Pair-living is a common social system found across animal taxa, and the
 relationship between pair-living and reproduction varies greatly among
 species. Siphonaria gigas, hermaphroditic pulmonate gastropods, often live
 in pairs in the rocky intertidal zone of the tropical Eastern Pacific.
 Combining genetic parentage analysis using four polymorphic microsatellite
 loci with behavioral observations from a 10-week field study, we provide
 the first description of the mating system of a Siphonaria species
 incorporating genetic data. S. gigas mated both within-pair and extra-pair
 and three out of four paired S. gigas individuals produced egg masses with
 extra-pair paternity. Multiple paternity was detected, but at a relatively
 low frequency (19% of egg masses) compared to other marine gastropods.
 Behavioral data indicate one potential advantage of pair-living: paired S.
 gigas produced almost twice as many egg masses as their solitary
 counterparts over four reproductive cycles. These observations, together
 with constraints on the movement of S. gigas, suggest that pairing may
 ensure mate access and increase reproductive success.
description: This dataset includes genomic libraries for four
 <i>Siphonaria gigas</i> individuals. Foot tissue was collected
 from live adult <i>S. gigas</i> and stored in 99% ethanol. DNA
 was extracted from the tissue using the Qiagen DNeasy Blood and Tissue Kit
 with a modified elution step (see manuscript for details). Shotgun genomic
 libraries were prepared using a simplified restriction-associated
 digestion sequencing protocol (after Toonen et al. 2013), including
 digestion with DpnII. The digested DNA was purified and then prepared for
 sequencing using a KAPA Hyper Prep Kit (Kapa Biosystems Ltd.) and Illumina
 TruSeq adapters (Illumina Inc.). Libraries were sequenced on an Illumina
 MiSeq platform with V3 chemistry and 600 cycles to produce 300 bp
 paired-end reads. The raw sequence data from the four <i>S.
 gigas</i> are provided here; full methods are provided in the
 open-access publication. Further details of sequencing
 and processing included in manuscript.
DOI: 10.5061/dryad.t4b8gthxd
title: Microsatellite genotypes of Camellia oleifera for GenoDive analysis

description: Camellia oleifera, a hexaploid evergreen broadleaf shrub or small tree, is
 the dominant woody oilseed crop in China. Understanding the spatial
 pattern of genetic diversity in wild C. oleifera is essential for
 conservation and utilization of genetic resources. Six wild C. oleifera
 populations were sampled along a latitudinal gradient in subtropical
 evergreen broadleaf forests of Southern China. A new high-throughput
 sequencing-based microsatellite genotyping method was developed to resolve
 allele dosage uncertainty in hexaploid wild C. oleifera with 35
 microsatellite markers. Finally, the dataset of
 mcrosatellite genotypes was generated with corrected
 allele dosages. In addition, another dataset of
 microsatellite genotypes with uncorrected allele dosages (showing
 only different alleles) was generated, for mimicking the situation of
 current microsatellite genotyping methods.
DOI: 10.5061/dryad.mgqnk98vw
title: Data from: Larval development in the Pacific oyster and the impacts of ocean acidification: differential genetic effects in wild and domesticated stocks

description: The adaptive capacity of marine calcifiers to ocean acidification (OA) is
 a topic of great interest to evolutionary biologists and ecologists.
 Previous studies have provided evidence to suggest that larval resilience
 to high pCO­2 seawater for these species is a trait with a genetic basis
 and variability in natural populations. To date, however, it remains
 unclear how the selective effects of OA occur within the context of
 complex genetic interactions underpinning larval development in many of
 the most vulnerable taxa. Here we evaluated phenotypic and genetic changes
 during larval development of Pacific oysters (Crassostrea gigas) reared in
 ambient (~ 400 µatm) and high (~ 1600 µatm) pCO2 conditions, both in
 domesticated and naturalized ‘wild’ oysters from the Pacific Northwest,
 USA. Using pooled DNA samples, we determined changes in allele frequencies
 across larval development, from early “D-stage” larvae to metamorphosed
 juveniles (spat), in both groups and environments. Domesticated larvae had
 ~ 26% fewer loci with changing allele frequencies across developmental
 stages and &lt; 50% as many loci affected by acidified culture
 conditions, compared to larvae from wild brood stock. Functional
 enrichment analyses of genetic markers with significant changes in allele
 frequency revealed that the structure and function of cellular membranes
 were disproportionately affected by high pCO2 conditions in both groups.
 These results indicate the potential for a rapid adaptive response of
 oyster populations to OA conditions; however, underlying genetic changes
 associated with larval development differ between these wild and
 domesticated oyster stocks and influence their adaptive responses to OA
 conditions.
description: Pooled samples of oyster larvae  (n=200-3000) were collected at 2
 and 22 days post fertilization.  DNA was extracted in bulk, converted to
 2bRAD libraries (BCGI enzyme) and sequenced on an Illumina Hiseq (SE 50bp
 reads).   Samples represent two oyster populations (MBP or Wild) from the
 Pacific Northwest USA.  Larvae from each population was reared in ambient
 (~400 pCO2) and acidified (~1600 pCO2) conditions from fertilization to
 settlement (22 days post fertilization). 
description: FASTQ file labeling is as follows:  M= MBP, W=Wild, A= ambient
 pCO2, O= simulated OA (high pCO2), D2/22= days 2 or 22 post
 fertilization.  Numbers following group designation (e.g. 'MA')
 denote biological replicate (n=5 each group).  For example:
 'WA2_D22*.fastq' denotes 'Wild, Ambient, rep 2, Day
 22'.  Another example: 'MO3_D2*.fastq' refers to 'MBP
 larvae, in OA conditions, from day 2'. The CSV
 file contains all 1288 curated SNPs and read counts (A/B allele) for each
 replicate. Please see manuscript for experimental
 setup.
DOI: 10.5061/dryad.1vhhmgqp1
title: Data from: Attractive male sticklebacks carry more oxidative DNA damage in the soma and germline

description: Trade-offs between the expression of sexual signals and the maintenance of
 somatic and germline tissues are expected when these depend upon the same
 resources. Despite the importance of sperm DNA integrity, its trade-off
 with sexual signalling has rarely been explored. We experimentally tested
 the trade-off between carotenoid-based sexual colouration and oxidative
 DNA damage in skeletal muscle, testis and sperm by manipulating
 reproductive schedule (early vs. late onset of breeding) in male
 three-spined sticklebacks. Oxidative DNA damage was measured as the amount
 of 8-hydroxy-2-deoxy-Guanosine in genomic DNA. Irrespective of the
 experimentally manipulated reproductive schedule, individuals investing
 more in red colouration showed higher levels of oxidative DNA damage in
 muscle, testis and sperm during the peak breeding season. Our results show
 that the expression of red colouration traded off against the level of
 oxidative DNA damage possibly due to the competing functions of
 carotenoids as colorants and antioxidants. Thus, female sticklebacks may
 risk fertility and viability of offspring by choosing redder, more
 deteriorated partners with decreased sperm DNA integrity. The evolution of
 sexual signal may be constrained by oxidative DNA damage in the soma and
 germline.
DOI: 10.5061/dryad.41ns1rn9g
title: The spatial analysis of biological interactions: morphological variation responding to the co-occurrence of competitors and resources

description: By sharing geographic space, species are forced to interact with one
 another and the contribution of this process to evolutionary and
 ecological patterns of individual species is not fully understood. At the
 same time, species turnover makes that species composition varies from one
 area to another, so the analysis of biological interaction cannot be
 uncoupled from the spatial context. This is particularly important for
 clades that show high degree of specialization such as hummingbirds, where
 any variation in biotic pressures might lead to changes in morphology.
 Here, we describe the influence of biological interactions on the
 morphology of Hylocharis leucotis by simultaneously considering potential
 competition and diet resources. We characterized the extent of local
 potential competition and local available floral resources by correlating
 two measurements of hummingbird diversity, floral resources and the size
 of morphological space of H. leucotis along its geographic distribution.
 We found that H. leucotis shows an important morphological variability
 across its range and two groups can be recognized. Surprisingly,
 morphological variation is not always linked to local hummingbird richness
 or the phylogenetic similarity of. Only in the southern part of its
 distribution, H. leucotis is morphologically more variable in those
 communities where it coexist with closely related hummingbird species. We
 also found that morphological variation in H. leucotis is independent from
 the availability of floral resources. Our results suggest that abiotic
 factors might be responsible for morphological differences across
 populations in Hylocharis leucotis being biological interactions of minor
 importance.
DOI: 10.5061/dryad.crjdfn30r
title: The effects of management on vegetation trajectories during the early‐stage restoration of previously arable land after hay transfer

description: The restoration of floodplain grasslands has benefited from many studies
 of the underlying mechanisms. Among the operational tools that resulted,
 hay transfer is now used increasingly to alleviate the effects of limited
 seed dispersal and recruitment. To improve this method, we still need to
 understand how it can affect restoration trajectories, and particularly
 their direction and magnitude during the early stages of restoration.
 Based on concepts from the field of community ecology theory, we
 investigated the effects of early‐stage management through grazing or
 mowing on restoration trajectories after soil harrowing and hay transfer.
 We established a randomized block design experiment and quantified several
 community‐related metrics to formalize restoration trajectories for
 3 years after hay transfer on a previously arable alluvial island
 in southwestern France. Whatever the management treatment, the species
 richness and evenness were significantly higher in hay‐inoculated than in
 control plots. This effect was linked to the recruitment of species
 originating not only from the reference grassland through hay transfer,
 but also from the seed bank, a well‐known effect of soil harrowing.
 Although generally oriented toward the reference grassland, the origin,
 direction, and magnitude of the trajectory of hay‐inoculated plots all
 depended on the management applied. Sheep grazing applied at the same time
 as hay transfer enhanced the recruitment of reference species as from the
 first experimental year, because it controlled aboveground competition and
 maintained the window of opportunity open for a sufficiently longer period
 of time. Our findings show that the type of management applied
 simultaneously to hay transfer influences the origin of a grassland
 trajectory, while its direction and magnitude are dependent on the
 management applied in subsequent years. Grazing immediately after hay
 transfer may be appropriate to accelerate the recruitment of species from
 the reference grassland.