cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8931zcrnp
title: Species complex diversification by host plant use in an herbivorous insect: The source of Puerto Rican cactus mealybug pest and implications for biological control

description: Cryptic taxa have often been observed in the form of host‐associated
 species that diverged as the result of adaptation to alternate host
 plants. Untangling cryptic diversity in species complexes that encompass
 invasive species is a mandatory task for pest management. Moreover,
 investigating the evolutionary history of a species complex may help to
 understand the drivers of their diversification. The mealybug
 Hypogeococcus pungens was believed to be a polyphagous species from South
 America and has been reported as a pest devastating native cacti in Puerto
 Rico, also threatening cactus diversity in the Caribbean and North
 America. There is neither certainty about the identity of the pest, nor
 the source population from South America. Recent studies pointed to
 substantial genetic differentiation among local populations, suggesting
 that H. pungens is a species complex. In this study, we used a combination
 of genome-wide SNPs and mtDNA variation to investigate species diversity
 within H. pungens sensu lato to establish host plant ranges of each one of
 the putative members of the complex, to evaluate whether the pattern of
 host plant association drove diversification in the species complex, and
 to determine the source population of the Puerto Rican cactus pest. Our
 results suggested that H. pungens comprises at least five different
 species, each one strongly associated with specific host plants. We also
 established that the Puerto Rican cactus pest derives from southeastern
 Brazilian mealybugs. This is an important achievement because it will help
 to design reliable strategies for biological control using natural enemies
 of the pest from its native range.
description: The Variant Calling File (VCF) was filtered to remove individuals
 with more than 10% missing data, sites with more than 20% missing
 genotypes and loci with minor allele frequency (MAF) lower than 0.01 using
 VCFtools v1.15 (Danecek et al., 2011). We randomly selected one SNP per
 contig to minimize linkage disequilibrium (LD) and to ensure the
 independence of the SNPs.
DOI: 10.5061/dryad.tb2rbnzz1
title: Genotyping by sequencing data of five legume tree species widespread in the rainforests of West and Central Africa

description: Although today the forest cover is continuous in Central Africa this may
 have not always been the case, as the scarce fossil record in this region
 suggests that arid conditions might have significantly reduced tree
 density during the Ice Ages. Our aim was to investigate whether the dry
 ice-age periods left a genetic signature on tree species that can be used
 to infer the date of the past fragmentation of the rainforest. We
 sequenced reduced representation libraries of 182 samples representing
 five widespread Legume trees and seven outgroups. Phylogenetic analyses
 identified an early divergent lineage for all species in West Africa
 (Upper Guinea), and two clades in Central Africa: Lower Guinea-North and
 Lower Guinea-South. As the structure separating the Northern and Southern
 clades -congruent across species- cannot be explained by geographic
 barriers, we tested other hypotheses with demographic model testing using
 ∂a∂I. The best estimates indicate that the two clades split between the
 Upper Pliocene and the Pleistocene, a date compatible with forest
 fragmentation driven by ice-age climatic oscillations. Furthermore, we
 found remarkably older split dates for the shade-tolerant tree species
 with non-assisted seed dispersal than for light-demanding species with
 long-distance wind dispersal. Different recolonisation abilities after
 recurrent cycles of forest fragmentation seem to explain why species with
 long-distance dispersal show more recent genetic admixture between the two
 clades than species with limited seed dispersal. Despite their old
 history, our results depict the African rainforests as a dynamic biome
 where tree species have expanded relatively recently after the last
 glaciation.
description: vcf and fasta files of Genotyping By Sequencing data of five
 Legume tree species widespread in the rainforests of West and Central
 Africa <i>Pericopsis elata</i> (Harms) Meeuwen,<i>
 Distemonanthus benthamianus</i> Baill., <i>Erythrophleum
 ivorense</i> A. Chev., <i>Erythrophleum suaveolens
 </i>(Guill. & Perr.) Brenan,and <i>Scorodophloeus
 zenkeri</i> Harms. Seven outgroup species (OUT) were also sequenced:
 <i>Pericopsis laxiflora</i> (Benth. Ex Baker) Meewen,<i>
 Dicorynia guianensis</i> Amshoff, <i>Dialium
 guianense</i> (Aubl.) Sandwith, <i>Erythrophleum
 africanum</i> (Welw. Ex Benth.) Harms, <i>Erythrophleum
 chlorostachys</i> Baill., <i>Calpocalyx
 brevibracteatus</i> Harms, and <i>Hymenostegia
 afzelii</i> (Oliv.) Harms. The genetic clusters were Upper Guinea
 (UG), Dahomey Gap, (DG), Lower Guinea North (LG-North), Lower Guinea South
 (LG-South), Lower Guinea East (LG-East), and Congo.
DOI: 10.5061/dryad.dbrv15dzg
title: Movement rules determine nomadic species’ responses to resource supplementation and degradation

description: 1. In environments that vary unpredictably, many animals are nomadic,
 moving in an irregular pattern that differs from year to year. Exploring
 the mechanisms of nomadic movement is needed to understand how animals
 survive in highly variable environments, and to predict behavioral and
 population responses to environmental change. 2. We developed a network
 model to identify plausible mechanisms of nomadic animal movement by
 comparing the performance of multiple movement rules along a continuum
 from nomadism to residency. Using simulations and analytical results, we
 explored how different types of habitat modifications (that augment or
 decrease resource availability) might affect the abundance and movement
 rates of animals following each of these rules. 3. Movement rules for
 which departure from patches depended on either resource availability or
 competition performed almost equally well and better than residency or
 uninformed movement under most conditions, even though animals using each
 rule moved at substantially different rates. Habitat modifications that
 stabilized resources, either by resource supplementation or degradation,
 eroded the benefits of informed nomadic movements, particularly for
 movements based on resource availability alone. 4. These results suggest
 that simple movement rules can explain nomadic animal movements and
 determine species’ responses to environmental change. In particular,
 landscape stabilization and supplementation might be useful strategies for
 promoting populations of resident animals, but would be less beneficial
 for managing highly mobile species, many of which are threatened by
 habitat disruption and changes in climate.
DOI: 10.5061/dryad.nk98sf7rb
title: Intersexual differences in density-dependent dispersal and their evolutionary drivers

description: Dispersal is well recognised as a major driver of evolutionary processes
 in local populations. Nevertheless, dispersal abilities should also be
 perceived as a life history trait, being subject to evolutionary changes
 in response to various drivers. Empirical studies investigating these
 drivers rarely consider that they may influence male and female dispersal
 differently. The purpose of our study was to document intersexual
 differences in density-dependent emigration from local habitat patches. As
 a model system we used a metapopulation of Maculinea (Phengaris) teleius
 butterfly, in which densities of both sexes vary greatly throughout the
 flying season. Following intensive mark-release-recapture surveys, the
 parameters and predictors of dispersal were analysed with the Virtual
 Migration model and the multi-state recapture model. The emigration rate
 in males was substantially higher in the early season, especially at
 smaller habitat patches. With the proportion of females increasing with
 the season progression, males became reluctant to emigrate from their
 natal patches. In turn, higher female emigration in the later part of the
 season was most strongly associated with female tendency to reduce
 intraspecific competition experienced by their offspring. Our findings
 provide evidence for the impact of reproductive strategies on dispersal in
 both sexes. The difference in reproductive strategies of males and females
 explain sex-biased dispersal in different parts of the season, which
 carries important implications for metapopulation functioning.
description: Following intensive mark-release-recapture surveys,
 the parameters and predictors of dispersal were analysed with the Virtual
 Migration model and the Brownie's multi-state recapture
 model.
DOI: 10.5061/dryad.95x69p8hd
title: Effect of wind farms on wintering ducks at an important wintering ground in China along the East Asian-Australasian Flyway

description: Wind farms offer a cleaner alternative to fossil fuels and can mitigate
 their negative effects on climate change. However, wind farms may have
 negative impacts on birds. The East China Coast forms a key part
 of the East Asian-Australasian Flyway and it is a crucial region for wind
 energy development in China. However, despite ducks being the
 dominant animal taxon along the East China Coast in winter and considered
 as particularly vulnerable to the effects of wind farms, the potential
 negative impacts of wind farms on duck populations remain unclear. We
 therefore assessed the effects of wind farms on duck abundance,
 distribution, and habitat use at Chongming Dongtan, which is a major
 wintering site for ducks along the East Asian-Australasian Flyway, using
 field surveys and satellite tracking. We conducted seven paired field
 surveys of ducks inside (IWF) and outside wind farm (OWF) sites in
 artificial brackish marsh, paddy fields, and aquaculture ponds. Duck
 abundance was significantly higher in OWF compared with IWF sites, and
 significantly higher in artificial brackish marsh than in aquaculture
 ponds and paddy fields. Based on 1,918 high-resolution satellite tracking
 records, the main habitat types of ducks during the day and at night were
 artificial brackish marsh and paddy fields, respectively. Furthermore,
 grid-based analysis showed overlaps between ducks and wind farms, with
 greater overlap at night than during the day. According to resource
 selection functions, habitat use by wintering ducks was impacted by
 distance to water, land cover, human activity, and wind-farm effects, and
 the variables predicted to have significant impacts on duck habitat use
 differed between day and night. Our study suggests that wintering ducks
 tend to avoid wind turbines at Chongming Dongtan, and landscape of paddy
 fields and artificial wetlands adjoining natural wetlands is crucial for
 wintering ducks
DOI: 10.5061/dryad.612jm641m
title: Environmental determinants of leaf-litter ant community composition along an elevational gradient

description: Ant communities are extremely diverse and provide a wide variety of
 ecological functions in tropical forests. Here we investigated the abiotic
 factors driving ant composition turnover across an elevational gradient at
 Mont Itoupé, French Guiana. Mont Itoupé is an isolated mountain whose top
 is covered by cloud forests, a biogeographical rarity that is likely to be
 threatened according to climate change scenarios in the region. We
 examined the influence of six soil, climatic and LiDAR-derived vegetation
 structure variables on leaf-litter ant assembly (267 species) across nine
 0.12-ha plots disposed at three elevations (ca. 400, 600 and 800m asl). We
 tested (a) whether species co-occurring within a same plot or a same
 elevation were more similar in terms of taxonomic, functional and
 phylogenetic composition, than species from different plots/elevations,
 and (b) which environmental variables significantly explained
 compositional turnover among plots. We found that the distribution of
 species and traits of ant communities along the elevational gradient was
 significantly explained by a turnover of environmental conditions,
 particularly in soil phosphorus and sand content, canopy height and mean
 annual relative humidity of soil. Our results shed light on the role
 exerted by environmental filtering in shaping ant community assembly in
 tropical forests. Identifying the environmental determinants of ant
 species distribution along tropical elevational gradients could help
 predicting the future impacts of global warming on biodiversity
 organization in vulnerable environments such as cloud forests.
DOI: 10.15468/dl.zwfa38
title: Occurrence Download

description: A dataset containing 643 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cajanus acutifolius",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 643 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002491-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6078/d10t3p
title: Plumage patterns: ecological functions, evolutionary origins, and advances in quantification

description: Birds exhibit remarkable variation in plumage patterns, both within
 individual feathers and among plumage patches. Differences in the size,
 shape, and location of pigments and structural colors comprise important
 visual signals involved in mate choice, social signaling, camouflage, and
 many other functions. While ornithologists have studied plumage patterns
 for centuries, recent technological advances in digital image acquisition
 and processing have transformed pattern quantification methods,
 enabling  comprehensive, detailed data sets of pattern phenotypes
 that were heretofore inaccessible. In this review, we synthesize recent
 and classic studies of plumage patterns at different evolutionary and
 organismal scales and discuss the various roles that plumage patterns play
 in avian biology. We dissect the role of plumage patches as signals within
 and among species. We also consider the evolutionary history of plumage
 patterns, including phylogenetic comparative studies and evolutionary
 developmental research of the genetic architecture underlying plumage
 patterns. We also survey an expanding toolbox of new methods that
 characterize and quantify the size, shape, and distribution of plumage
 patches. Finally, we provide a worked exampled to illustrate a potential
 workflow with dorsal plumage patterns among subspecies of the Horned Lark
 (Eremophila alpestris) in western North America. Studies of plumage
 patterning and coloration have played a prominent role in ornithology thus
 far, and recent methodlogical and conceptual advances have opened new
 avenues of research on the ecology and evolutionary origins of plumage
 patterning in birds.
description: These data were collected through digital photography. We
 processed RAW photographs using the image calibration and analysis
 toolkit, which is a plugin for ImageJ. We subsequently used R to perform a
 suite of downstream statistical analyses (PCA, boxplots) to characterize
 'pluamge pattern space' in Horned Larks (<i>Eremophila
 alpestris</i>), as a worked exampleof how one can use new pattern
 analysis methods in ornithology.
description: These data include a data frame of plumage pattern characters
 following data processing with ImageJ and the Image Calibration Analysis
 toolkit. We've also included RAW format photos and the regions of
 interest that we generated using ImageJ.
DOI: 10.25338/b82d07
title: Transportation Network Company (TNC) taxes/fees by state/city in the United States

description: Cities and states across the U.S. are assessing fees or taxes on
 transportation network company (TNC) platforms, such as Uber and Lyft. The
 goals of these policies include traffic and emissions mitigation, as well
 as revenue generation, among other objectives. Our research aims to assess
 the goals and effectiveness of these fees in achieving some of these
 policy objectives, primarily congestion and emissions mitigation. The
 analysis addresses a core difficulty in comparing TNC fees—some fees are
 assessed per mile and others per trip. We compare 21 fees implemented by
 state and local governments across the United States and apply a
 methodology to compare these diverse fees and taxes based on a
 hypothetical ride informed by Uber’s fare calculator, as well as other
 sources. Our findings show that when adjusted for comparison, the highest
 fees, by a wide margin, are assessed in downtown New York City and Chicago
 (during peak hours). A key policy implication of this research is that
 most fees or taxes are not large enough to affect enough travelers'
 choices to hail a TNC, and most do not differentiate between solo and
 pooled/shared rides. Only San Francisco, Chicago, New York City, and New
 Jersey differentiate between solo and shared rides, which is likely to
 influence travelers in choosing to share a ride. This is problematic given
 that increasing passengers per vehicle mile traveled is an essential
 strategy in managing congestion and reducing emissions associated with all
 vehicle travel, including TNCs.
description: This data was collected online using government websites and
 archives. It has been processed.
description: No additional information is needed for re-using this data.
DOI: 10.5061/dryad.3tx95x6d7
title: GPR120 in control of pancreatic polypeptide secretion from male mouse islets via phospholipase C-mediated calcium mobilization

description: GPR120-IRES-EGFP mice were generated on C57BL/6J background. The sequence
 of IRES-EGFP was inserted into the genome behind the gene termination
 codon TAA of GPR120 gene by targeted integration with CRISPR/Cas9
 technology to generate the knockin (KI) mice that express EGFP under the
 control of GPR120 expression. In brief, the recombinant donor vector
 containing IRES-EGFP element was constructed and identified by double
 enzyme digestion. The Cas9 mRNA, guide RNA and the donor vector were
 transferred into the fertilized eggs of C57BL/6J mice by microinjection
 and the founder mice were generated. The positive founder mice with right
 homologous recombination were mated with wild C57BL/6J mice to obtain F1
 generation. The F1 mice were back-crossed with wild type C57BL/6J mice for
 6 generations and then the homologous KI mice were mass-produced for
 experiments. The GPR120 expression in mouse islets was knockdown by GPR120
 siRNA transfection, and the reduction of GPR120 expression was observed by
 western blot after 3 days culture. The specificity of PP ELISA kits was
 measured by pre-absorption with PP antibodies. Samples with PP antibody
 pre-absorption had undetectable PP levels while the samples without
 antibody treatment were measured positively for PP levels.
description: The attached file includes: The
 data for generation of GPR120-IRES-EGFP knockin mouse
 The knockdown of GPR120 expression in mouse islets
 The specificity testing of mouse PP ELISA kit
DOI: 10.5061/dryad.cz8w9gj1m
title: Life history genomic regions explain differences in Atlantic salmon marine diet specialization

description: Abstract 1. Animals employ various foraging strategies along their
 ontogeny to acquire energy, and with varying degree of efficiencies, to
 support growth, maturation and subsequent reproduction events. Individuals
 that can efficiently acquire energy early are more likely to mature at an
 earlier age, as a result of faster energy gain which can fuel maturation
 and reproduction. 2. We aimed to test the hypothesis that heritable
 resource acquisition variation that co-varies with efficiency along the
 ontogeny would influence maturation timing of individuals. 3. To test this
 hypothesis, we utilized Atlantic salmon as a model which exhibit a simple,
 hence trackable, genetic control of maturation age. We then monitored the
 variation in diet acquisition (quantified as stomach fullness and
 composition) of individuals with different ages, and linked it with
 genomic regions (haploblocks) that were previously identified to be
 associated with age-at-maturity. 4. Consistent with the hypothesis, we
 demonstrated that one of the life history genomic regions tested six(6)
 was indeed associated with age-dependent differences in stomach fullness.
 Prey composition was marginally linked to six(6), and suggestively (but
 non-significantly) to vgll3 genomic regions. We further showed Atlantic
 salmon switched to the so-called “feast and famine” strategy along the
 ontogeny, where older age groups exhibited heavier stomach content, but
 that came at the expense of running on empty more often. 5. These results
 suggest genetic variation underlying resource utilization may explain the
 genetic basis of age structure in Atlantic salmon. Given that ontogenetic
 diet has a genetic component and the strong spatial diversity associated
 with these genomic regions, we predict populations with diverse maturation
 age will have diverse evolutionary responses to future changes in marine
 food-web structures. 28-Jul-2020
description: ## code and files to replicate main results presented in Aykanat
 et al (2020) Life history genomic regions explain differences in Atlantic
 salmon marine diet specialization, Journal fo Animal Ecology.<br> ##
 "code_Aykanat_etal_JAE_2020": code to replicate main
 results<br> ## phenotype_Aykanat_etal_JAE_2020.xlsx": Input
 phenotype file. The worksheet "SC.PHEN3" refer to
 "SC.PHEN3.txt" in the R code.<br> ##
 "genotype_Aykanat_etal_JAE_2020": Input genotype file as an R
 object. The object name is "SC.genoNUM2", same as in the R code.
  <br>
DOI: 10.7291/d1z08b
title: Data From: Ecosystem size shapes antipredator trait evolution in estuarine threespine stickleback

description: Ecosystem size is known to influence both community structure and
 ecosystem processes. Less is known about the evolutionary consequences of
 ecosystem size. A few studies have shown that ecosystem size shapes the
 evolution of trophic diversity by shaping habitat heterogeneity, but the
 effects of ecosystem size on antipredator trait evolution have not been
 explored. Ecosystem size may impact antipredator trait evolution by
 shaping predator presence (larger ecosystems have longer food chains) and
 habitat complexity (larger ecosystems may have more diverse habitat
 structure). We tested these effects using threespine stickleback from
 bar-built estuaries along the Central Coast of California. These
 stickleback populations are polymorphic for Ectodysplasin-A (Eda), a gene
 that controls bony lateral plates used as antipredator defense. We
 inferred Eda genotypes from lateral plate phenotypes and show that the
 frequency of the complete (C) allele, which is associated with greater
 number of lateral plates, increases as a function of ecosystem size.
 Predator presence and habitat complexity are both correlated to ecosystem
 size. The strongest proximate predictor of Eda allele frequencies was the
 presence of predatory fishes (steelhead trout and sculpin). Counter to
 expectations, habitat complexity did not have a strong modifying effect on
 Eda allele frequencies. Our results point to the importance of ecosystem
 size for determining predator presence as being the primary pathway to
 evolutionary effects.  Ecosystem size has received much attention
 in ecology. Our work shows that it may be an important determinant of
 adaptive evolution in wild populations.