cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.g9s2k
title: Data from: Polyploidy and microsatellite variation in the relict tree Prunus lusitanica L.: how effective are refugia in preserving genotypic diversity of clonal taxa?

description: Refugia are expected to preserve genetic variation of relict taxa,
 especially in polyploids, because high gene dosages could prevent genetic
 erosion in small isolated populations. However, other attributes linked to
 polyploidy, such as asexual reproduction, may strongly limit the levels of
 genetic variability in relict populations. Here, ploidy levels and
 patterns of genetic variation at nuclear microsatellite loci were analysed
 in Prunus lusitanica, a polyploid species with clonal reproduction that is
 considered a paradigmatic example of a Tertiary relict. Sampling in this
 study considered a total of 20 populations of three subspecies: mainland
 lusitanica (Iberian Peninsula and Morocco), and island azorica (Azores)
 and hixa (Canary Islands and Madeira). Flow cytometry results supported an
 octoploid genome for lusitanica and hixa, whereas a 16-ploid level was
 inferred for azorica. Fixed heterozygosity of a few allele variants at
 most microsatellite loci resulted in levels of allelic diversity much
 lower than those expected for a high-order polyploid. Islands as a whole
 did not contain higher levels of genetic variation (allelic or genotypic)
 than mainland refuges, but island populations displayed more private
 alleles and higher genotypic diversity in old volcanic areas. Patterns of
 microsatellite variation were compatible with the occurrence of clonal
 individuals in all but two island populations, and the incidence of
 clonality within populations negatively correlated with the estimated
 timing of colonization. Our results also suggest that gene flow has been
 very rare among populations, and thus population growth following founder
 events was apparently mediated by clonality rather than seed recruitment,
 especially in mainland areas. This study extends to clonal taxa the idea
 of oceanic islands as important refugia for biodiversity, since the
 conditions for generation and maintenance of clonal diversity (i.e.
 occasional events of sexual reproduction, mutation and/or seed
 immigration) appear to have been more frequent in these enclaves than in
 mainland areas.
description: Prunus_lusitanica_Table
 S4Sampled individuals,
 populations and vouchersPrunus_lusitanica_nSSRMicrosatellite data for P. lusitanica individuals. Data follows FDASH software format. Columns are separated by TABs. Alleles are separated by "," whereas "?" indicates missing data. Due to the polyploid constitution of these taxa, multiple alleles per individual and locus were scored, but fixed heterozygosity of a few allele variants can be observed at several loci.Prunus_lusitanica-flow cytometry2C values obtained through FCM for a subset of individuals representing P. lusitanica subspecies
DOI: 10.15468/dl.x9a5cz
title: Occurrence Download

description: A dataset containing 11 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is The InBIO Barcoding Initiative Database: A taxonomic revision of the Western Palaearctic genus Cacochroa Heinemann, 1870 (Lepidoptera, Depressariidae)"
 ]
}

 The dataset includes 11 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000611-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.03kb7
title: Data from: When are adaptive radiations replicated in areas? Ecological opportunity and unexceptional diversification in West Indian dipsadine snakes (Colubridae: Alsophiini)

description: AIM: We examine diversification in Caribbean alsophiine snakes and
 hypothesize that, given ecological opportunity presented by colonizing the
 West Indies, alsophiines should show the signature of an early burst of
 diversification and associated low-within clade ecological and
 morphological disparification. We also test if changes in morphology or
 ecology are associated with changes in diversification rate, as
 trait-dependent diversification is hypothesized to affect historical
 inferences of diversification and disparification. Finally, as replicated
 radiations are found across the West Indies in the anoles, we test for
 significant differences in ecological and morphological assemblages and
 rates among the major island groups. LOCATION: The West Indies. METHODS: A
 time-calibrated phylogeny produced from six genes using relaxed clock
 methods in BEAST was constructed to examine ancestral area using LAGRANGE.
 Maximum body size and ecological niche were scored for all species in the
 phylogeny, and comparative phylogenetic methods in R using GEIGER, LASER,
 APE and our own code were used to examine diversification through time,
 disparification and trait-dependent diversification from this dated
 phylogeny. RESULTS: The pattern of species diversification did not differ
 significantly from the Yule model of diversification. Morphology and
 ecology fit a Brownian and white noise model of diversification,
 respectively. Although not significantly different, morphological
 disparification was lower than the Brownian null model, whereas ecological
 disparification was significantly greater than the null. Trait-dependent
 diversification analyses suggested that the constant null models provided
 the best fit to these data. There was no significant signal of rate
 variation among the major island groups for size, but moderate evidence
 for niche. MAIN CONCLUSIONS: Although ecological opportunity was similarly
 present for alsophiines as it was for anoles, the snakes fail to show an
 early burst of speciation. Potential reasons for this include the young
 age of the group, and staggered diversification due to waiting times
 between island colonization. In turn, ecological and morphological
 disparity do not necessarily follow predictable patterns related to
 species diversification. Thus, the presence of ecological opportunity
 alone is not necessarily sufficient to trigger replicated adaptive
 radiations in areas.
description: Alsophiini_DNA_1Alsophiini_DNA_2
DOI: 10.5061/dryad.3v0n3
title: Data from: An experimental test of whether cheating is context dependent

description: Microbial cells rely on cooperative behaviours that can breakdown as a
 result of exploitation by cheats. Recent work on cheating in microbes,
 however, has produced examples of populations benefiting from the presence
 of cheats and/or cooperative behaviours being maintained despite the
 presence of cheats. These observations have been presented as evidence for
 selection favouring cheating at the population level. This apparent
 contradiction arises when cheating is defined simply by the reduced
 expression of a cooperative trait and not in terms of the social costs and
 benefits of the trait under investigation. Here, we use two social traits,
 quorum sensing and iron-scavenging siderophore production in Pseudomonas
 aeruginosa, to illustrate the importance of defining cheating by the
 social costs and benefits. We show that whether a strain is a cheat
 depends on the costs and benefits associated with the social and abiotic
 environment and not the absolute expression of a cooperative trait.
description: Comp assays, lasR,
 PAO1OD600 monocultures
 strain A,B,COD600, RFU, strains
 A,B,CW values of strains
 A,B,CSupp data-PAO1-LasI,
 lasB OD600, RLU-gene expressions
DOI: 10.5061/dryad.4890t057
title: Data from: Rapid evolution of sex frequency and dormancy as hydroperiod adaptations

description: Dormancy can serve as an adaptation to persist in variable habitats, and
 often is coupled with sex. In cyclically parthenogenetic rotifers an
 asexual phase enables rapid population growth, whereas sex results in
 diapausing embryos capable of tolerating desiccation. Few studies have
 experimentally tested whether sex-dormancy associations in temporary
 waters reflect evolution in response to the short hydroperiod selecting
 for diapause ability. Here we demonstrate evolution of higher propensity
 for sex and dormancy in ephemeral rotifer cultures mimicking temporary
 ponds, and lower propensity in permanent cultures. Results are consistent
 with rapid evolution, with evolutionary changes occurring in a short
 timeframe (385 d, ≤84 generations). We also provide insight into
 mechanisms for rapid evolution in basal metazoans, discussing potential
 roles of new mutations, recombination, and clonal selection.
description: ReadMe1_Sex_Induction_Density2_Sex_Frequency3_Diapausing_Embryo_Production4_Diapausing_Embryo_Hatching5_DensityCounts6_Fecundity7_Lifespan
DOI: 10.5061/dryad.t9584
title: Data from: Insights into the origin and distribution of biodiversity in the Brazilian Atlantic forest hotspot: a statistical phylogeographic study using a low-dispersal organism

description: The relative importance of the processes that generate and maintain
 biodiversity is a major and controversial topic in evolutionary biology
 with large implications for conservation management. The Atlantic Forest
 of Brazil, one of the world's richest biodiversity hotspots, is
 severely damaged by human activities. To carry out an efficient
 conservation policy, a good understanding of spatial and temporal
 biodiversity patterns and their underlying evolutionary mechanisms is
 required. With this aim, we performed a comprehensive phylogeographic
 study using a low-dispersal organism, the land planarian species
 Cephaloflexa bergi (Platyhelminthes, Tricladida). Applying a multi-locus
 DNA sequence variation approach under the ABC framework we evaluated two
 scenarios proposed to explain the diversity of SAF region. We found that
 most sampled localities harbour high levels of genetic diversity, with
 lineages sharing old common ancestors that predate the Pleistocene.
 Remarkably, we detected the molecular hallmark of the
 isolation-by-distance effect and little evidence of a recent colonization
 of SAF localities; some populations nevertheless might result from very
 recent secondary contacts. We conclude that extant SAF biodiversity
 originated and has been shaped by complex interactions between ancient
 geological events and more recent evolutionary processes, while
 Pleistocene climate changes would have a minor influence in generating
 present day diversity. We also demonstrate that land planarians are an
 advantageous biological model for making phylogeographic and,
 particularly, fine-scale evolutionary inferences, and propose appropiate
 conservation policies.
description: COI
 alignmentAlignment of cytochrome
 oxidase I sequences resulted in an 822 bp matrix with no gaps used for
 phylogenetic analyses.COIalignmentDryad.phyITS-1 alignmentAlignment of 133 internal transcribed spacer 1 sequences (130 of Cephaloflexa bergi species and 3 of Cephaloflexa sp. as outgroup) used for the phylogenetic analyses.ITSalignmentDryad.phy
DOI: 10.5061/dryad.7530v
title: Data from: Infrageneric revision of the fern genus Deparia (Athyriaceae, Aspleniineae, Polypodiales)

description: Current molecular phylogenetic analyses support the monophyly and
 circumscription of the athyrioid fern genus Deparia (Athyriaceae), which
 includes previously recognized genera including Athyriopsis, ×Depazium,
 Dictyodroma, Dryoathyrium (= Parathyrium), Lunathyrium, and Triblemma.
 This broad generic concept has been adopted in several recent taxonomic
 treatments, including the Pteridophyte Phylogeny Group I. However, the
 infrageneric taxonomy of Deparia still needs further revision. In this
 study, we provide a new infrageneric classification with five sections and
 three subsections based on the phylogenetic evidence. We recognize two new
 sections, sect. Dictyodroma and sect. Erectus, and two new subsections,
 sect. Deparia subsect. Caespites and subsect. Athyriopsis. In addition, we
 provide a key to the sections and subsections, a table of diagnostic
 characters, new combinations for three Deparia and one Diplazium species,
 and a list of species assigned to the sections/subsections. Hybrids
 derived from crosses between the sections and subsections are also noted.
description: Deparia
 4_cpDNA_region_alignmenttrnL-L-F + rps16-matK
 IGS + matK + rbcL alignment in nexus with partition and model for Mr.
 Bayes and Garli.Deparia
 4_cpDNA_region_ML_bestreetrnL-L-F + rps16-matK
 IGS + matK + rbcL ML most likely phylogeny inferred by
 Garli
DOI: 10.5061/dryad.fm7b5
title: Data from: Late spring nitrate distributions beneath the ice-covered northeastern Chukchi Shelf

description: Measurements of late springtime nutrient concentrations in Arctic waters
 are relatively rare due to the extensive sea ice cover that makes sampling
 difficult. During the SUBICE cruise in May-June 2014, an extensive survey
 of hydrography and pre-bloom concentrations of inorganic macronutrients,
 oxygen, particulate organic carbon and nitrogen, and chlorophyll a was
 conducted in the northeastern Chukchi Sea. Cold (&lt; -1.5°C) winter
 water was prevalent throughout the study area, and the water column was
 weakly stratified. Nitrate (NO3-) concentration averaged 12.6±1.92 μM in
 surface waters and 14.0±1.91 μM near the bottom and was significantly
 correlated with salinity. The highest NO3- concentrations were associated
 with winter water within the Central Channel flow path. NO3-
 concentrations were much reduced near the northern shelfbreak within the
 upper halocline waters of the Canada Basin and along the eastern side of
 the shelf near the Alaskan coast. Net community production (NCP),
 estimated as the difference in depth-integrated NO3- content between
 spring (this study) and summer (historical), varied from 28-38 g C m-2
 a-1. This is much lower than previous NCP estimates that used NO3-
 concentrations from the southeastern Bering Sea as a baseline. These
 results demonstrate the importance of using profiles of NO3- measured as
 close to the beginning of the spring bloom as possible when estimating
 local NCP. They also show that once the snow melts in spring, increased
 light transmission through the sea ice to the waters below the ice could
 fuel large phytoplankton blooms over a much wider area than previously
 known.
description: WOCE WHP Bottle Exchange
 FileBottle file containing
 CTD sensor data as well as bottle measurements like nutrients and Chl
 a.SUBICE_high_NO3_hy1.csv
DOI: 10.5061/dryad.nm5ns
title: Data from: Effects of ambient noise on detectability and localization of avian songs and tones by observers in grasslands

description: Probability of detection and accuracy of distance estimates in aural avian
 surveys may be affected by the presence of anthropogenic noise, and this
 may lead to inaccurate evaluations of the effects of noisy infrastructure
 on wildlife. We used arrays of speakers broadcasting recordings of
 grassland bird songs and pure tones to assess the probability of
 detection, and localization accuracy, by observers at sites with and
 without noisy oil and gas infrastructure in south-central Alberta from
 2012 to 2014. Probability of detection varied with species and with
 speaker distance from transect line, but there were few effects of noisy
 infrastructure. Accuracy of distance estimates for songs and tones
 decreased as distance to observer increased, and distance estimation error
 was higher for tones at sites with infrastructure noise. Our results
 suggest that quiet to moderately loud anthropogenic noise may not mask
 detection of bird songs; however, errors in distance estimates during
 aural surveys may lead to inaccurate estimates of avian densities
 calculated using distance sampling. We recommend caution when applying
 distance sampling if most birds are unseen, and where ambient noise varies
 among treatments.
description: playbacktransects20132014 for DryadData on detectability of bird song recordings in grasslands, in the presence and absence of noise
DOI: 10.5061/dryad.n9j60
title: Data from: Chronic protein restriction in mice impacts placental function and maternal body weight before fetal growth

description: Mechanisms of resource allocation are essential for maternal and fetal
 survival, particularly when the availability of nutrients is limited. We
 investigated the responses of feto-placental development to maternal
 chronic protein malnutrition to test the hypothesis that maternal low
 protein diet produces differential growth restriction of placental and
 fetal tissues, and adaptive changes in the placenta that may mitigate
 impacts on fetal growth. C57BL/6J female mice were fed either a
 low-protein diet (6% protein) or control isocaloric diet (20% protein). On
 embryonic days E10.5, 17.5 and 18.5 tissue samples were prepared for
 morphometric, histological and quantitative RT-PCR analyses, which
 included markers of trophoblast cell subtypes. Potential endocrine
 adaptations were assessed by the expression of Prolactin-related hormone
 genes. In the low protein group, placenta weight was significantly lower
 at E10.5, followed by reduction of maternal weight at E17.5, while the
 fetuses became significantly lighter no earlier than at E18.5. Fetal head
 at E18.5 in the low protein group, though smaller than controls, was
 larger than expected for body size. The relative size and shape of the
 cranial vault and the flexion of the cranial base was affected by E17.5
 and more severely by E18.5. The junctional zone, a placenta layer rich in
 endocrine and energy storing glycogen cells, was smaller in low protein
 placentas as well as the expression of Pcdh12, a marker of glycogen
 trophoblast cells. Placental hormone gene Prl3a1 was altered in response
 to low protein diet: expression was elevated at E17.5 when fetuses were
 still growing normally, but dropped sharply by E18.5 in parallel with the
 slowing of fetal growth. This model suggests that nutrients are
 preferentially allocated to sustain fetal and brain growth and suggests
 the placenta as a nutrient sensor in early gestation with a role in
 mitigating impacts of poor maternal nutrition on fetal growth.
description: Gonzalez_et_al_Brain_SizeThis file lists the centroid size of the brain for specimens at 18.5DPCGonzalez_et_al_DamThis file contains the weight of the dams at each DPC before and after dissection.Gonzalez_et_al_Embryo_PlacentaThis file contains the weight of embryos and placentas at the three DPC sampledGonzalez_et_al_genesThis file contains the gene expression in the placentas of the low protein groups in relation to control placentas. Data are expresses as fold changes.Gonzalez_et_al_Morphometric_skullThis file conains the raw coordinates of landmarks of the skull and the centroid size for specimens at 17.5 and 18.5DPCPcdh12 area E10 E17 E18 dataThis file contains the area of Pchd12 expression at the three age stages analyzed.Placenta layers areas E10 E17 E18 dataThis file contains the area of the three layers of the placenta at the three age stages analyzed.
DOI: 10.5061/dryad.270h8
title: Data from: Men’s preferences for women’s body odours are not associated with HLA

description: Body odours reportedly portray information about an individual's
 genotype at the major histocompatibility complex (MHC, called human
 leucocyte antigen, HLA, in humans). While there is strong experimental
 support for MHC-associated mating behaviour in animals, the situation in
 humans is more complex. A lot of effort has been spent on testing
 HLA-associated odour preferences of women. To date, only very few studies
 have looked at HLA-linked olfactory preferences in men and these studies
 have revealed inconsistent results. Here, we investigate men's
 HLA-associated preferences for women's body odours. Importantly, and
 in contrast to previous studies, these odours were gathered at peak
 fertility (i.e. just before ovulation) when any HLA-associated odour
 preferences should be strongest. We scrutinized whether men's
 preference for women's body odours is influenced by (i) the number of
 shared HLA alleles between men and women, (ii) HLA heterozygosity, and
 (iii) the frequency of rare HLA alleles. We found that men could readily
 differentiate between odours they found attractive and odours they found
 less attractive, but that these preferences were not associated with HLA.
 Specifically, men did not prefer odours from women who are HLA dissimilar,
 HLA heterozygous, or who have rare HLA alleles. Together, these findings
 suggest that HLA has no effect on men's odour preferences.
description: supporting
 data
DOI: 10.5061/dryad.11p01
title: Data from: Using a comprehensive DNA barcode library to detect novel egg and larval host plant associations in a Cephaloleia Rolled-leaf Beetle (Coleoptera: Chrysomelidae)

description: To fully understand the ecology and evolution of plant-herbivore
 interactions, information regarding the life history of both immature and
 adult insect stages is essential. However, most knowledge of
 plant-herbivore associations is derived from observations of adults. One
 reason for this bias is that species identification of immature stages is
 usually challenging. DNA barcodes can be used to identify immature stages
 to the species-level. This technique compares short sequences of the
 appropriate DNA barcode loci (e.g., mitochondrial COI gene for insects) of
 an unidentified specimen to a known DNA barcode library. The accuracy of
 DNA-based identifications depends on the comprehensiveness of the DNA
 barcode library. We generated a comprehensive DNA barcode library for a
 community of Rolled-leaf Beetles (Coleoptera: Chrysomelidae) in a
 premontane tropical forest in Costa Rica. The DNA barcode COI accurately
 identified all beetle species included in this study. Using this DNA
 barcode library, we identified eggs and larvae of Cephaloleia histrionica
 Baly with 100% confidence. This new record of C. histrionica is unique in
 that this species completes its life cycle on a bromeliad, whereas most
 Cephaloleia species are associated with plants from the order
 Zingiberales. The life cycle, diet breadth, immature stages, and sexual
 dimorphism are described for C. histrionica.
description: Samples included in DNA
 barcode analysesSupplement S1. Samples
 included in DNA barcode analyses. Tables summarize collection information,
 the life stage of each sample (egg, larva or adult), host plant family /
 species and sequence quality (percentage of untrimmed bases of
 high-quality, HQ%). DNA amplifications were performed with the Folmer
 primers: GGTCAACAAATCATAAAGATATTGG (F) and TAAACTTCAGGGTGACCAAAAAATCA
 (R).SuppInfo.docDNA sequences (COI) of limited quality and not deposited in GenBank (FASTA format).Supplement S2. DNA sequences (COI) of limited quality and not deposited in GenBank (FASTA format). Sequences in this supplement were included in the analyses as they successfully identified individuals to the species level with 100% confidence. Numbers at the beginning of each sequence represent collection numbers. Information for each collection was included in Supplement S1.SuppInfo2.doc