cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.kkwh70s3j
title: Comparative Phylogeography of Veronica spicata and V. longifolia (Plantaginaceae) Across Europe: Integrating Hybridization and Polyploidy in Phylogeography

description: Climatic fluctuations in the Pleistocene caused glacial
 expansion-contraction cycles in Eurasia and other parts of the world.
 Consequences of these cycles, such as population expansion and subsequent
 subdivision, have been studied in many taxa at intraspecific population
 level across much of the Northern Hemisphere. However, the consequences
 for the potential of hybridization and polyploidization are poorly
 understood. Here, we investigated the phylogeographic structure of two
 widespread, closely related species, Veronica
 spicata and Veronica longifolia, across their European
 distribution ranges. We assessed the extent and the geographic pattern of
 polyploidization in both species and hybridization between them. We used
 genome-scale SNP data to clarify phylogenetic relationships and detect
 possible hybridization/introgression events. In addition, crossing
 experiments were performed in different combination between V.
 spicata and V. longifolia individuals of two
 ploidy levels and of different geographic origins. Finally, we employed
 ecological niche modeling to infer macroclimatic differences between both
 species and both ploidy levels. We found a clear genetic structure
 reflecting the geographical distribution patterns in both species,
 with V. spicata showing higher genetic differentiation
 than V. longifolia. We retrieved significant signals of
 hybridization and introgression in natural populations from the genetic
 data and corroborated this with crossing experiments. However, there were
 no clear phylogeographic patterns and unequivocal macroclimatic niche
 differences between diploid and tetraploid lineages. This favors the
 hypothesis, that autopolyploidization has happened frequently and in
 different regions. The crossing experiments produced viable hybrids when
 the crosses were made between plants of the same ploidy levels but not in
 the interploidy crosses. The results suggest that hybridization occurs
 across the overlapping areas of natural distribution ranges of both
 species, with apparently directional introgression from V.
 spicata to V. longifolia. Nevertheless, the two species
 maintain their species-level separation due to their adaptation to
 different habitats and spatial isolation rather than reproductive
 isolation.
description: Through Next generation sequencing
DOI: 10.5061/dryad.c2fqz616m
title: Do avian species survive better on islands?

description: Island species are often predictably different from their mainland
 counterparts. Milder climates and reduced predation risk on islands have
 been involved to explain shifts in body size and a suite of life history
 traits such as clutch size and offspring growth rate. Despite the key role
 of adult survival on risk taking and reproduction, the prediction that
 living on islands increases adult survival has yet to be tested
 systematically. I gathered data on adult annual apparent survival from
 island and mainland year-round resident species of birds from around the
 world. With this large dataset (697 species), I found that species of
 birds living on islands showed higher apparent survival than their
 mainland counterparts in the two hemispheres and at all latitudes
 controlling for several known predictors of adult survival including body
 size, clutch size, and breeding system. These results shed light on the
 ecological factors that influence survival on islands and extend the life
 history island syndrome to adult survival.
description: I searched the literature for avian studies that reported
 survival rates. I focused on year-round resident species, as most island
 species are not migratory.
DOI: 10.5061/dryad.m905qfv05
title: Species delimitation and taxonomic revision of Oxyopes (Araneae: Oxyopidae) of Taiwan

description: This study revised the spider genus Oxyopes Latreille,
 1804 in Taiwan and delineated the species boundaries based on
 morphological and molecular characters. A total of
 seven Oxyopes spiders were recognized, including two
 newly described species, O. hasta sp.
 nov. and O. taiwanensis sp.
 nov. Oxyopes fujianicus Song & Zhu 1993
 from Yilan County, Nantou County, and Kaohsuing City, and O.
 striagatus Song 1999 from New Taipei City, Taichung City, Nantou
 County, and Kaohsiung City were recorded for the first time in Taiwan. An
 identification key and a distributional map of
 Taiwanese Oxyopes species were provided.
 Partial COI sequences were obtained for molecular
 phylogenetic and species delimitation analyses. Maximum likelihood and
 Bayesian phylogenies, and DNA barcoding gap analysis supported
 morphologically defined species. However, molecular species delimitation
 based on Automatic Barcode Gap Discovery(ABGD),
 PID (Liberal), and generalized mixed Yule
 coalescent (GMYC) were incongruent in species assignment. The
 results showed that the interspecific genetic divergence
 between O. sertatus and O.
 taiwanensis was relatively low (1.28 ± 0.43%), and the
 intraspecific genetic divergence of O. striagatus was
 relatively high (1.69 ± 0.35%). Ecological data, additional samples and
 genetic loci are required to further examine the level of reproductive
 isolation and patterns of population genetic structure in
 Taiwanese Oxyopes.
description: <strong>Supplementary Material</strong>
 Lo_etal_Zootaxa_SupplementaryMaterials.pdf
 <strong>mtDNA sequence for Oxyopes</strong>
 oxyopesCOIalign.fasta
DOI: 10.5061/dryad.n2z34tmvk
title: Field evidence for colour mimicry overshadowing morphological mimicry

description: 1. Imperfect mimicry may be maintained when the various components of an
 aposematic signal have different salience for predators. Experimental
 laboratory studies provide robust evidence for this phenomenon. Yet,
 evidence from natural settings remains scarce.  2. We studied how
 natural bird predators assess multiple features in a multicomponent
 aposematic signal in the Neotropical “clear wing complex” mimicry ring,
 dominated by glasswing butterflies.  3. We evaluated two
 components of the aposematic signal, wing colouration and wing morphology,
 in a predation experiment based on artificial replicas of glasswing
 butterflies (model) and Polythoridae damselflies (mimics) in their natural
 habitat. We also studied the extent of the colour aposematic signal in the
 local insect community. Finally, we inspected the nanostructures
 responsible for this convergent colour signal, expected to highly differ
 between these phylogenetically distinct species.  4. Our results
 provide direct evidence for a stronger salience of wing colouration than
 wing morphology, as well as stronger selection on imperfect than in
 perfect colour mimics. Additionally, investigations of how birds perceive
 wing colouration of the local insect community provides further evidence
 that a UV-reflective white colouration is being selected as the colour
 aposematic signal of the mimicry ring.  Using electron
 microscopy, we also suggest that damselflies have convergently evolved the
 warning colouration through a pre-adaptation.  5. These findings
 provide a solid complement to previous experimental evidence suggesting a
 key influence of the cognitive assessment of predators driving the
 evolution of aposematic signals and mimicry rings.
DOI: 10.15468/dl.cw5pzh
title: Occurrence Download

description: A dataset containing 124 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Copaifera religiosa",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 124 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002661-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.sqv9s4n2r
title: Plant-soil feedback and crop rotation

description: Plant-soil feedback (PSF) can be a major driver of plant performance in
 communities, and this concept can be used in selecting crop rotation
 sequences to maximize agricultural yields. Potential benefits of using PSF
 in this context include nutrient use optimization, pathogen reduction and
 enhancement of mutualisms between crops and microbes. Yet, the
 contributions of these combined mechanisms are poorly understood. Here we
 investigated the relative contributions of these mechanisms using five
 major crops commonly cultivated in rotation (alfalfa, canola, maize,
 soybean and wheat) under controlled conditions. We trained soil by growing
 each of the five crops in a ‘training phase’, and then reciprocally
 planted the five crops in the trained soils in a ‘feedback phase’. To
 tease out soil biota from nutrient effects, we established three
 treatments: ‘control’ (trained unsterilized soil used in the feedback
 phases), ‘biota’ (sterilized soil in the feedback phase inoculated with
 soil biota from the ‘control’ treatment after the training phase), and
 ‘nutrient’ (sterilized soils in both phases). Plant-soil feedback for each
 crop was calculated by comparing the total biomass of each crop grown in
 soils trained by each of the four other crops (i.e., in rotation) against
 total biomass in self-trained soil (i.e., monocropping). We found that PSF
 values varied among crop combinations in all the treatments, but such
 variation was the greatest in the ‘nutrient’ treatment. Overall, soil
 ‘biota’ feedback tended to be lower whereas ‘nutrient’ feedback tended to
 be greater compared to the unsterilized ‘control’ soil, suggesting that
 effects of antagonistic biota outweighed those of beneficial microbes in
 the ‘biota’ treatment, and that plants optimized nutrient uptake when the
 soil microbiome was absent in the ‘nutrient’ treatment. Furthermore, soils
 in the ‘nutrient’ treatment trained by the legume crops (alfalfa and
 soybean) tended to provide the greatest positive feedback, emphasizing the
 important legacy of N2-fixers in crop rotation. Taken together, our data
 demonstrate how nutrients and soil biota can be integral to PSFs among
 crops, and that assessing PSFs under controlled conditions can serve as a
 basis to determine the most productive crop rotation sequences prior to
 field testing.
description: The data set was collected during a greenhouse study at Ontario
 Forest Research Institute (OFRI) in Sault Ste. Marie, Ontario, Canada.
 Plant biomass data were used to calculate feedback values via
 bootstrapping. Fix-effect ANOVAs were used to test treatment effects. The
 data set resulted in a manuscript accepted in Ecological
 Applications
description: The README file contains an explanation of each of the variables
 in the dataset and its measurement units, n/a =  values not available.
 Information on how the measurements were done can be found in the
 associated manuscript referenced above.
DOI: 10.5061/dryad.gb5mkkwns
title: Environmental characteristics of the Mediterranean islands and the lizard assemblages

description: Aim: To identify and evaluate the environmental properties of the
 Mediterranean islands that make them a suitable habitat for their endemic
 lizards. This would represent an important improvement in our knowledge
 and would assist the conservation of these lizards, which are threatened
 by both the expansion of mainland species and the increasing intensity of
 human disturbance on these islands. Location: Mediterranean Basin.
 Methods: I assessed the environmental associations of 50 species
 of lizard (19 endemic) across 552 Mediterranean islands using outlying
 mean index analysis. The strength of the response of each species was
 assessed using binomial generalized linear models. Results: The presence
 of endemic species is positively correlated with the distance of the
 island from the mainland. Island connectivity is also positively
 correlated with an increased presence of endemic lizards, but not with an
 increased presence of mainland species (those with exclusive or mainly
 continental natural distribution). In addition, island size, temperature,
 and vegetation productivity are positively correlated with the presence of
 mainland species. Outlying mean index (OMI) analysis showed that the
 endemic species occupy niche positions that are similar to the average
 environmental conditions in the archipelago, but frequently without using
 the entire range of niches. The mainland species usually occur in more
 peripheral positions in the environmental space, except for some highly
 expansive species. Conclusions: Lizards that are endemic to the
 Mediterranean islands were found to be present on a large number of
 islands within an archipelago, but they quickly disappear as the
 conditions change, largely because of human activity. Large islands act as
 population reservoirs for mainland species, facilitating secondary
 colonization of peripheral islets.
DOI: 10.5061/dryad.hx3ffbgcq
title: Isoform specific activities of androgen receptor and its splice variants in prostate cancer cells

description: Androgen receptor (AR) signaling continues to drive castration resistant
 prostate cancer (CRPC) in spite of androgen deprivation therapy (ADT).
 Constitutively active shorter variants of AR, lacking the ligand binding
 domain, are frequently expressed in CRPC and have emerged as a potential
 mechanism for prostate cancer to escape ADT.  ARv7 and ARv567es
 are two of the most commonly detected variants of AR in clinical samples
 of advanced, metastatic prostate cancer. It is not clear if variants of AR
 merely act as weaker substitutes for AR or can mediate unique isoform
 specific activities different from AR. In this study, we employed LNCaP
 prostate cancer cell lines with inducible expression of ARv7 or ARv567es
 to delineate similarities and differences in transcriptomics, metabolomics
 and lipidomics resulting from the activation of AR, ARv7 or ARv567es.
 While the majority of target genes were similarly regulated by the action
 of all three isoforms, we found a clear difference in transcriptomic
 activities of AR versus the variants, and a few differences between ARv7
 and ARv567es. Some of the target gene regulation by AR isoforms was
 similar in the VCaP background as well. Differences in downstream
 activities of AR isoforms were also evident from comparison of the
 metabolome and lipidome in an LNCaP model. Overall our study implies that
 shorter variants of AR are capable of mediating unique downstream
 activities different from AR and some of these are isoform specific.
description: LNCaP cell lines with dox inducible expression of androgen
 receptor (AR) variants such as ARv7 and ARv567es were generated using
 lenti-virus. qPCR, metabolomic and lipidomic analysis were performed to
 compare activities of AR with ARv7 and ARv567es in LNCaP cells.
DOI: 10.5061/dryad.bk3j9kd9d
title: Data from: Effects of a major Amazonian river confluence on the distribution of floodplain forest avifauna

description: Aim: Although “river color” or water type is an important
 determinant of Amazonian floodplain biodiversity, the relevance of mixing
 distinct water types at river confluences to the distribution of
 terrestrial floodplain fauna has been largely overlooked. We investigated
 how the influx of a sediment-rich whitewater tributary affects the
 floodplain forest avifauna along the world’s largest blackwater river.
 Location: Northwestern Brazilian Amazon Taxon: Birds
 Methods: We sampled floodplain avifauna and retrieved estimates
 of sediment concentration in the water (the main parameter in river-water
 classification) at 52 sites, along the Negro (blackwater) and Branco
 (whitewater) rivers, above and below their confluence. We compared species
 richness and composition using analyses of variance, ordinations,
 generalized linear models and indicator species analyses.
 Results: Bird species composition on the lower Rio Negro (below
 the confluence) was distinct from both the upper Negro (above the
 confluence) and the Branco, and species richness on the Negro increased
 below the confluence. Typical whitewater bird species occurring on the
 Branco were found exclusively or predominantly along the left side of the
 lower Rio Negro, where the Branco’s muddy waters seem to be channeled.
 Overall avian compositional variation among sites was correlated
 with sediment concentration in the water, a determinant of floodplain
 forest structure. Main Conclusions: The influx of the muddy
 waters of the Rio Branco into the Rio Negro promotes the co-occurrence of
 bird species that upstream are segregated by river type, increasing
 species richness at the landscape scale. Rather than just representing a
 potential blackwater barrier between whitewater systems, the lower Rio
 Negro comprises a unique biogeographical transition zone, with a mixed
 avifauna occurring in a mosaic of varied floodplain forest types. Our
 results suggest that confluences of large rivers of distinct water types
 represent a significant factor determining species distributional
 boundaries and geographic patterns of Amazonian floodplain biodiversity.
DOI: 10.5061/dryad.dncjsxkxw
title: Sister-Species Diverge in Modality-Specific Courtship Signal Form and Function

description: Understanding the relative importance of different sources of selection
 (e.g. the environment, social/sexual selection) on the divergence or
 convergence of reproductive communication can shed light on the origin,
 maintenance, or even disappearance of species boundaries. Using a
 multi-step approach, we tested the hypothesis that two presumed
 sister-species of wolf spider with overlapping ranges and microhabitat
 use, yet differing degrees of sexual dimorphism, have diverged in their
 reliance on modality-specific courtship signaling. We predicted that male
 Schizocosa crassipalpata (no ornamentation) rely predominantly on
 diet-dependent vibratory signaling for mating success. In contrast, we
 predicted that male S. bilineata (black foreleg brushes) rely on
 diet-dependent visual signaling. We first tested and corroborated the
 sister-species relationship between S. crassipalpata and S. bilineata
 using phylogenomic scale data. Next, we tested for species-specific,
 diet-dependent vibratory and visual signaling by manipulating subadult
 diet and subsequently quantifying adult morphology and mature male
 courtship signals. As predicted, vibratory signal form was diet-dependent
 in S. crassipalpata while visual ornamentation (brush area) was
 diet-dependent in S. bilineata. We then compared the species-specific
 reliance on vibratory and visual signaling by recording mating across
 artificially manipulated signaling environments (presence/absence of each
 modality in a 2 x 2 full factorial design). In accordance with our diet
 dependence results for S. crassipalpata, the presence of vibratory
 signaling was important for mating success. In contrast, the light and
 vibratory environment interacted to influence mating success in S.
 bilineata, with vibratory signaling being important only in the absence of
 light. We found no differences in overall activity patterns. Given that
 these species overlap in much of their range and microhabitat use, we
 suggest that competition for signaling space may have led to the
 divergence and differential use of sensory modalities between these
 sister-species.
description: This excel file contains sheets with raw data for each species
 - <em>Schizocosa crassipalpata </em>and <em>S.
 bilineata</em> for Objectives II - IV. The data
 were not manipulated or processed in any way. Data were
 imported into JMP for analyses.
description: These excel files contain mostly raw values measured/quantified
 from specimen measurements or behavioral assays run in the laboratory.
 Details of data analysis can be found in the methods section of the
 manuscript, but these files were imported into JMP where statistical
 analyses were carried out. We don't believe that
 there is any additional knowledge required to use these
 datasets.
DOI: 10.5061/dryad.8kprr4xmd
title: Temporal variability is key to modelling the climatic niche

description: Aim: Niche-based species distribution models (SDMs) have become a
 ubiquitous tool in ecology and biogeography. These models relate species
 occurrences with the environmental conditions found at these sites.
 Climatic variables are the most commonly used environmental data, and are
 usually included in SDMs as averages of a reference period (30-50 years).
 In this study we analyze the impact of including inter-annual climatic
 variability on the estimation of species niches and predicted
 distributions when assessing plant demographic response to extreme
 climatic episodes. Location: Mediterranean basin, SE Iberian Peninsula.
 Methods: We first characterized species niches with inter-annual and
 average climate in the same environmental space. We then compare the
 respective capacities of climatic suitability obtained from averaged
 climate-based and from inter-annual variability-based niches to explain
 population demographic responses to extreme drought. Furthermore, we
 assessed the relative increase in niche size when including climatic
 variability for a set of Mediterranean species exhibiting a wide range of
 distribution areas. Results: We found that climatic suitability obtained
 from inter-annual variability-based niches showed higher explanatory
 capacity than average climate-based suitability, especially for
 populations living in climatically marginal conditions, although both
 niches quantifications significantly explained species demographic
 responses. In addition, species with restricted distribution ranges
 increased relatively more their niche space when considering climatic
 variability, probably because in widely distributed species spatial
 variability compensates for temporal variability. Main Conclusions: The
 common use of climatic averages when characterizing species niches could
 lead to underestimations of species distribution and misunderstanding of
 demographic behavior, with implications for conservation plans derived
 from SDMs, e.g. overestimations of species extinction risk under climate
 change, or underestimations of alien species invasion’ risk. We highlight
 that including climatic variability in niche modelling can be particularly
 important when dealing with species with restricted distribution and
 populations at the margin of their species niche.