cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.c624907
title: Data from: The biggest losers: habitat isolation deconstructs complex food webs from top to bottom

description: Habitat fragmentation threatens global biodiversity. To date, there is
 only limited understanding of how the different aspects of habitat
 fragmentation (habitat loss, number of fragments and isolation) affect
 species diversity within complex ecological networks such as food webs.
 Here, we present a dynamic and spatially-explicit food web model which
 integrates complex food web dynamics at the local scale and
 species-specific dispersal dynamics at the landscape scale, allowing us to
 study the interplay of local and spatial processes in metacommunities. We
 here explore how the number of habitat patches, i.e. the number of
 fragments, and an increase of habitat isolation, affect the species
 diversity patterns of complex food webs (alpha-, beta-, gamma-diversity).
 We specifically test whether there is a trophic dependency in the effect
 of these two factors on species diversity. In our model, habitat isolation
 is the main driver causing species loss and diversity decline. Our results
 emphasise that large-bodied consumer species at high trophic positions go
 extinct faster than smaller species at lower trophic levels, despite being
 superior dispersers that connect fragmented landscapes better. We
 attribute the loss of top species to a combined effect of higher biomass
 loss during dispersal with increasing habitat isolation in general, and
 the associated energy limitation in highly fragmented landscapes,
 preventing higher trophic levels to persist. To maintain trophic-complex
 and species-rich communities calls for effective conservation planning
 which considers the interdependence of trophic and spatial dynamics as
 well as the spatial context of a landscape and its energy availability.
description: Ryser et al
 2019This data package
 includes the files needed to reproduce the data and analyses of the
 following paper: The biggest losers: habitat isolation deconstructs
 complex food webs from top to bottom, Ryser, Remo, Häussler, Johanna,
 Stark, Markus, Brose, Ulrich, Rall, Björn C., Guill,
 ChristianCode_S.zip
DOI: 10.5061/dryad.6dv4rj2
title: Data from: Host plant associations and geography interact to shape diversification in a specialist insect herbivore

description: Disentangling the processes underlying geographic and environmental
 patterns of biodiversity challenges biologists as such patterns emerge
 from eco-evolutionary processes confounded by spatial autocorrelation
 among sample units. The herbivorous insect, Belonocnema treatae
 (Hymenoptera: Cynipidae), exhibits regional specialization on three plant
 species whose geographic distributions range from sympatry through
 allopatry across the southern USA. Using range-wide sampling spanning the
 geographic ranges of the three host plants and genotyping-by-sequencing of
 1,217 individuals, we tested whether this insect herbivore exhibited
 host-plant-associated genomic differentiation while controlling for
 spatial autocorrelation among the 58 sample sites. Population genomic
 structure based on 40,699 SNPs was evaluated using the hierarchical
 Bayesian model ENTROPY to assign individuals to genetic clusters and
 estimate admixture proportions. To control for spatial autocorrelation,
 distance-based Moran’s eigenvector mapping was used to construct
 regression variables summarizing spatial structure inherent among sample
 sites. Distance based redundancy analysis (dbRDA) incorporating the
 spatial variables was then applied to partition host-plant-associated
 differentiation (HAD) from spatial autocorrelation. By combining ENTROPY
 and dbRDA to analyze SNP data we unveiled a complex mosaic of highly
 structured differentiation within and among gall former populations
 finding evidence that geography, HAD and spatial autocorrelation all play
 significant roles in explaining patterns of genomic differentiation in B.
 treatae. While dbRDA confirmed host association as a significant predictor
 of patterns of genomic variation, spatial autocorrelation among sites
 explained the largest proportion of variation. Our results demonstrate the
 value of combining dbRDA with hierarchical structural analyses to
 partition spatial/environmental patterns of genomic variation.
description: gprob_matrix_BtreataeThis file contains the genotypes at 40,699 SNPs for 1,217 Belonocnema treatae individuals.localityHostList_BtreataeList of sampled localities, coordinates and host association
DOI: 10.5061/dryad.p3123d8
title: Data from: Genome-wide association analyses reveal polygenic genomic architecture underlying divergent shell morphology in Spanish Littorina saxatilis ecotypes

description: Gene flow between diverging populations experiencing dissimilar ecological
 conditions can theoretically constrain adaptive evolution. To minimize the
 effect of gene flow, alleles underlying traits essential for local
 adaptation are predicted to be located in linked genome regions with
 reduced recombination. Local reduction in gene flow caused by selection on
 these alleles is expected to produce elevated divergence in these regions.
 The highly divergent crab-adapted and wave-adapted ecotypes of the marine
 snail Littorina saxatilis present a model system to test the predictions
 of this model. We used genome-wide association (GWA) analysis of geometric
 morphometric shell traits associated with microgeographic divergence
 between the two L. saxatilis ecotypes within three separate sampling
 sites. A total of 477 snails that had individual geometric morphometrics
 data and individual genotypes at 4066 single nucleotide polymorphisms
 (SNPs) were analyzed using GWA methods that corrected for population
 structure among the three sites. This allowed dissection of the genomic
 architecture of shell shape divergence between ecotypes across a wide
 geographic range, spanning two glacial lineages. GWA revealed 175
 quantitative trait loci (QTL) with shell size or shape differences between
 ecotypes, with most loci explaining a small proportion of phenotypic
 variation. We found that trait-associated loci were evenly distributed
 across 16 linkage groups, and exhibited elevated inter-chromosomal
 linkage, suggesting a genome-wide response to divergent selection on shell
 shape between the two ecotypes. Shell shape trait-associated loci showed
 partial overlap with previously identified outlier loci under divergent
 selection between the two ecotypes, supporting the hypothesis of
 diversifying selection on these genomic regions. These results suggest
 that genetic divergence in shell shape between the crab-adapted and
 wave-adapted ecotypes is produced predominantly by a polygenic genomic
 architecture with positive linkage disequilibrium among loci of small
 effect.
description: Phenotype and genotype
 data used in L. saxatilis GWAS4066 SNP loci from 477
 individuals identified using ddRAD, with minimum 70% genotyping rate, and
 no SNPs out of HWE. Phenotype file with aligned x and y coordinates,
 relative warps, partial warps, and centroid size.L Sax GWAS
 data.zip
DOI: 10.5061/dryad.30bf364
title: Data from: Hyperandrogenism and insulin resistance-induced fetal loss: evidence for placental mitochondrial abnormalities and elevated ROS production in pregnant rats that mimic the clinical features of PCOS

description: Women with polycystic ovary syndrome (PCOS) commonly suffer from
 miscarriage, but the underlying mechanism of PCOS‐induced fetal loss
 during pregnancy remains obscure and specific therapies are lacking. We
 used pregnant rats treated with 5α‐dihydrotestosterone (DHT) and insulin
 to investigate the impact of hyperandrogenism and insulin resistance on
 fetal survival and to determine the molecular link between PCOS conditions
 and placental dysfunction during pregnancy. Our study shows that pregnant
 rats chronically treated with a combination of DHT and insulin exhibited
 endocrine aberrations such as hyperandrogenism and insulin resistance that
 are strikingly similar to those in pregnant PCOS patients. Of
 pathophysiological significance, DHT+insulin‐treated pregnant rats had
 greater fetal loss and subsequently decreased litter sizes compared to
 normal pregnant rats. This negative effect was accompanied by impaired
 trophoblast differentiation, increased glycogen accumulation, and
 decreased angiogenesis in the placenta. Mechanistically, we report that
 over‐production of reactive oxygen species (ROS) in the placenta,
 mitochondrial dysfunction, and disturbed SOD1 and Keap1/Nrf2 antioxidant
 responses constitute important contributors to fetal loss in
 DHT+insulin‐treated pregnant rats. Many of the molecular pathways leading
 to placental abnormalities and fetal loss in DHT+insulin treatment were
 also seen in pregnant rats treated with DHT alone, whereas pregnant rats
 treated with insulin alone often exerted distinct effects on placental
 gene expression compared to insulin treatment in combination with DHT. We
 also found that treatment with the antioxidant N‐acetylcysteine (NAC)
 improved fetal survival in DHT+insulin‐treated pregnant rats, an effect
 related to changes in Keap1/Nrf2 and NFκB signaling. However, NAC
 administration resulted in fetal loss in normal pregnant rats, most likely
 due to PCOS‐like endocrine abnormality induced by the treatment. Our
 results suggest that the deleterious effects of hyperandrogenism and
 insulin resistance on fetal survival are related to a constellation of
 mitochondrial‐ROS‐SOD1/Nrf2 changes in the placenta. Our findings also
 suggest that physiological levels of ROS are required for normal placental
 formation and fetal survival during pregnancy.
description: Suppl Tables and
 FiguresSupplemental tables 1-3
 and supporting Figures 1 and 2 with legend.
DOI: 10.5061/dryad.87f53d7
title: Data from: Genotyping-by-sequencing reveals genomic homogeneity among overwintering Pacific Dunlin (Calidris alpina pacifica) aggregations along the Pacific coast of North America

description: Information on how migratory populations are genetically structured during
 the overwintering season of the annual cycle can improve our understanding
 of the strength of migratory connectivity and help identify populations as
 units for management. Here, we use a genotype-by-sequencing approach to
 investigate whether population genetic structure exists among
 overwintering aggregations of the Pacific Dunlin subspecies (Calidris
 alpina pacifica) sampled at two spatial scales (i.e. within and among
 overwintering sites) in the eastern Pacific Flyway. Genome-wide analyses
 of 874 single nucleotide polymorphisms across 80 sampled individuals
 revealed no evidence for genetic differentiation among aggregations
 overwintering at three locations within the Fraser River Estuary (FRE) of
 British Columbia. Similarly, comparisons of aggregations in the FRE and
 those overwintering in southern sites in California and Mexico indicated
 no genetic segregation between northern and southern overwintering areas.
 These results suggest that Pacific Dunlin residing within the FRE,
 Sacramento Valley (California) and Guerrero Negro (Mexico) are genetically
 homogeneous, with no evident genetic structure between sampled sites or
 regions across the overwintering range. Despite no evidence for
 differentiation among aggregations, we identified a significant effect of
 geographical distance between sites on the distribution of individual
 genotypes in a redundancy analysis; however, a small proportion of the
 total genotypic variance (R2 = 0.036, P = 0.011) was explained by the
 combined effect of latitude and longitude, suggesting weak genomic
 patterns of isolation-by-distance that are consistent with chain-like
 migratory connectivity between breeding and overwintering areas. Our study
 represents the first genome-scale investigation of population structure
 for a Dunlin subspecies and provides essential baseline estimates of
 genomic diversity and differentiation within the Pacific Dunlin.
description: Dunlin sample
 informationdryad_dunlin_sample_info.csvDunlin_HighSeq_2014_R1_001.fastqGenomic data from Illumina sequencing for DunlinToews_Dunlin_HighSeq_2014_R1.tarDunlin_HighSeq_2014_R2_001.fastqGenomic data from Illumina sequencing for DunlinToews_Dunlin_HighSeq_2014_R2.tar
DOI: 10.5061/dryad.96q5g80
title: Data from: Does past evolutionary history under different mating regimes influence the demographic dynamics of interspecific competition?

description: Interspecific interactions are contingent upon organism phenotypes, and
 thus phenotypic evolution can modify interspecific interactions and affect
 ecological dynamics. Recent studies have suggested that male-male
 competition within a species selects for capability to reproductively
 interfere with a closely related species. Here we examine the effect of
 past evolutionary history under different mating regimes on the
 demographic dynamics of interspecific competition in Callosobruchus seed
 beetles. We used previously established experimental evolution lines of C.
 chinensis that evolved under either forced lifelong monogamy or polygamy
 for 17 generations, and examined the demographic dynamics of competition
 between these C. chinensis lines and a congener, C. maculatus.
 Callosobruchus chinensis was competitively excluded by C. maculatus in all
 trials. Time series data analyses suggested that reproductive interference
 from C. chinensis was relatively more important in the trials involving
 polygamous C. chinensis than those involving monogamous C. chinensis, in
 accordance with the potentially higher reproductive interference
 capability of polygamous C. chinensis. However, the estimated signs and
 magnitudes of interspecific interactions were not fully consistent with
 this explanation, implying the evolution of not only reproductive
 interference but also other interaction mechanisms. Our study thus
 suggests multifaceted effects of sexually-selected traits on interspecific
 competitive dynamics.
description: Kyogoku.Kondoh.Sota.2019.Ecol.Evol.dataReplicated experimental evolution lines of Callosobruchus chinensis (beetle) first evolved under either polygamy or monogamy. These experimental evolution lines then competed with Callosobruchus maculatus. All trials resulted in the extinction of C. chinensis. The data file includes time until extinction, and demographyc dynamics of the competition for a subset of the replications.
DOI: 10.5061/dryad.4398b9f
title: Data from: De novo assembly of a chromosome-level reference genome of red spotted grouper (Epinephelus akaara) using nanopore sequencing and Hi-C

description: The red spotted grouper Epinephelus akaara (E. akaara) is one of the most
 economically important marine fish in China, Japan and Southeast Asia, and
 is a threatened species. The species is also considered a good model for
 studies of sex-inversion, development, genetic diversity and immunity.
 Despite its importance, molecular resources for E. akaara remain limited
 and no reference genome has been published to date. In this study, we
 constructed a chromosome-level reference genome of E. akaara by taking
 advantage of long-read single molecule sequencing and de novo assembly by
 Oxford Nanopore Technologies (ONT) and Hi-C. A red-spotted grouper genome
 of 1.135 Gb was assembled from a total of 106.29 Gb polished Nanopore
 sequence (GridION, ONT), equivalent to 96-fold genome coverage. The
 assembled genome represents 96.8% completeness (BUSCO) with a contig N50
 length of 5.25 Mb and a longest contig of 25.75 Mb. The contigs were
 clustered and ordered onto 24 pseudo-chromosomes covering approximately
 95.55% of the genome assembly with Hi-C data, with a scaffold N50 length
 of 46.03 Mb. The genome contained 43.02% repeat sequences and 5,480
 non-coding RNAs. Furthermore, after mining several RNA-seq datasets,
 23,809 (99.5%) genes were functionally annotated from a total of 23,924
 predicted protein-coding sequences. The high-quality chromosome-level
 reference genome of E. akaara was assembled for the first time and will be
 a valuable resource for molecular breeding and functional genomics studies
 of red-spotted grouper in the future.
description: Genome data of Red
 Spotted Grouper (Epinephelus akaara)1.
 rsg.genome.chr.fasta.gz The assembled genome sequences
 (Pseudo-chromosomes) with fasta format. 2. rsg.gene.gff.gz Gff files for
 gene models 3. rsg.gene.cds.fasta.gz Coding sequences for gene models 4.
 rsg.gene.protein.fasta.gz Protein sequences for gene
 models.Red
 Spotted Grouper genome data.zip
DOI: 10.5061/dryad.bg1kq06
title: Data from: Diet assessment of two land planarian species using high-throughput sequencing data

description: Geoplanidae (Platyhelminthes: Tricladida) feed on soil invertebrates.
 Observations of their predatory behavior in nature are scarce, and most of
 the information has been obtained from food preference experiments.
 Although these experiments are based on a wide variety of prey, this
 catalog is often far from being representative of the fauna present in the
 natural habitat of planarians. As some geoplanid species have recently
 become invasive, obtaining accurate knowledge about their feeding habits
 is crucial for the development of plans to control and prevent their
 expansion. Using high throughput sequencing data, we perform a metagenomic
 analysis to identify the in situ diet of two endemic and codistributed
 species of geoplanids from the Brazilian Atlantic Forest: Imbira marcusi
 and Cephaloflexa bergi. We have tested four different methods of taxonomic
 assignment and find that phylogenetic-based assignment methods outperform
 those based on similarity. The results show that the diet of I. marcusi is
 restricted to earthworms, whereas C. bergi preys on spiders, harvestmen,
 woodlice, grasshoppers, Hymenoptera, Lepidoptera and possibly other
 geoplanids. Furthermore, both species change their feeding habits among
 the different sample locations. In conclusion, the integration of
 metagenomics with phylogenetics should be considered when establishing
 studies on the feeding habits of invertebrates.
description: Sequences analysed in
 the publicationScaffolds obtained from
 Illumina pair-end reads and used as a query for the taxonomic assignment
 in the subject study.DATA_DRYAD.7z
DOI: 10.5061/dryad.6b9n240
title: Data from: Treatment of aquaculture effluent with Chlorella vulgaris and Tetradesmus obliquus: the effect of pretreatment on microalgae growth and nutrient removal efficiency

description: The ongoing and increasing worldwide demand for fish has caused a steady
 increase in aquaculture production during the last decades. This
 emphasizes the importance of farming systems with a low ecological
 footprint, like recirculating aquaculture systems (RAS), which are an
 alternative to traditional open systems. Furthermore, implementing
 microalgae treatments in RAS, sustainable water management and low
 discharge of concentrated wastewater could be achieved, allowing its reuse
 in the system. The influence of three factors on microalgae treatment
 efficiency in RAS water were studied: i) microalgae species (Chlorella
 vulgaris, Tetradesmus obliquus), ii) water pre-treatment (sterile
 filtration), and iii) sampling location within the RAS (e.g. from fish
 tank, after UV-disinfection, etc.). To this end, fully factorial,
 replicated cultivations were carried out in 100-ml flasks, and nutrient
 removal, microalgae growth, and density of bacteria and protozoa were
 measured for up to 18 days. Results show that both species are able to
 grow in RAS water and effectively remove nutrients in it, yet their
 performance depended greatly on water quality. In sterile RAS water,
 growth and nutrient removal efficiency of C. vulgaris surpassed that of T.
 obliquus. In non-sterile RAS water, the pattern reversed because of
 grazing proto- zoa. The location of sampling within the RAS had no
 discernible effect on microalgae growth or nutrient removal efficiency.
 The results confirm that a microalgae-based technology to treat and
 valorise RAS water is technically feasible, yet caution that inferences
 made can be reversed depending on the choice of the species and the pre-
 treatment of the RAS water prior to cultivation.
description: Data from cultivation
 experimentThis file contains all
 variables that were measured during the cultivation experiment. All
 figures were produced with these data. The file is in csv format. Note
 that the abbreviation for Chlorella is Cv and for Tetradesmus is Ao
 (Acutodesmus obliquus).Tejio_Nunez_2019_Ecol_Eng.csvR file to produce statistics and figuresThis file requires reads the data from Tejio_Nunez_2019_Ecol_Eng.csv and produces all figures (and more) and statistics that are used in the paper. Note that the file is best executed with source(). It then displays a primitive menu from which various figures or statistics can be selected to be produced. Apologies for a very basic R code!Tejio_Nunez_2019_Ecol_Eng.R
DOI: 10.5061/dryad.v34fd09
title: Data from: Large feet are beneficial for eiders Somateria mollissima

description: 1. Many waterbirds have fully (totipalmate) or partially webbed (palmate)
 feet that are used for locomotion in aquatic environments. 2. If webbed
 feet and wings both contribute to efficient diving, we predicted a
 positive association between the area of webbed feet and the size of the
 frontal locomotor apparatus (wing area, heart mass and breast muscle,
 after adjusting for any partial effects of body size). We predicted that
 individuals able to acquire more and better quality food due to larger
 webbed feet should have larger livers with higher concentrations of
 fat-soluble antioxidants such as vitamin E, and invest more in immune
 function as reflected by the relative size of the uropygial gland than
 individuals with small webbed feed. 3. Here we examine if the area of
 webbed feet is correlated with locomotion, diet and body condition in a
 sea-duck, the eider (Somateria mollissima). We analyzed an extensive data
 base of 233 eiders shot in Danish waters and at Åland, Finland during
 winter and early spring. 4. Eiders with larger webbed feet had a larger
 locomotor apparatus, but did not have larger body size, they had larger
 uropygial glands that waterproof the plumage, they had larger beak volume
 and larger gizzards, and they had higher body condition. 5. These findings
 imply that eiders with large webbed feet benefitted in terms of
 locomotion, feeding and reproduction.
description: Swimming-Feet-DataAll data