cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8882
title: Data from: Testing the species–genetic diversity correlation in the Aegean archipelago: towards a haplotype-based macroecology?

description: A positive correlation between species and genetic diversity (SGDC) has
 been proposed, consistent with neutral predictions in macroecology. We
 assessed the SGDC in tenebrionid beetle communities of the Aegean
 archipelago on fifteen islands of different sizes, distances to mainland,
 and ages of isolation. Alpha- and beta-diversity of species and haplotypes
 were assessed using sequences of &gt;1000 individuals (mitochondrial
 Cytochrome Oxidase I and nuclear Muscular Protein 20) to test the SGDC. We
 show that: (i) there is a strong species-area and haplotype-area
 relationship; (ii) species richness in island communities is correlated
 with intraspecific genetic diversity in the constituent species except
 when island size or distance to mainland are factored out in partial
 correlations; (iii) community similarity declines exponentially at an
 increasing rate when calculated based on species, nuclear and mtDNA
 haplotypes; and (iv) distance decay of community similarity is slower in
 dispersive sand-dwelling lineages compared to less dispersive lineages
 that are not sand-obligate. Taken together, these correlated patterns at
 the species and haplotype level are consistent with individual-based
 stochastic dispersal proposed by neutral theories of biodiversity. The
 results also demonstrate the utility of haplotype data for exploring
 macroecological patterns in poorly known biota and predicting large-scale
 biodiversity patterns based on genetic inventories of local samples.
description: AmNat52448_FigureA2Newick.txtThis is the tree of Figure A2 (ML analysis including all Cox1 haplotypes) in newick format. See the corresponding pdf file (AmNat52448_FigureA2.pdf) for more information on taxon names and localities.AmNat52448_FigureA2.pdfMaximum likelihood cox1 tree including all sequenced individuals from 15 islands and two mainland regions and depicting the entities that were delimited by the GMYC model. The newick format is provided as a separate file ('AmNat52448_FigureA2Newick.tre').AmNat52448_TableA4.pdfList of the entities (clusters and singletons) delimited by the GMYC model for each genus, per island and mainland area. The GMYC clusters, with their corresponding capital letters, are also shown on the tree Figure A2 ('AmNat52448_FigureA2.pdf').AmNat52448_TableA3.pdfIncidence-based species richness estimators for the tenebrionid communities of 15 central Aegean islands.
DOI: 10.5061/dryad.qn82p
title: Data from: Racehorses are getting faster

description: Previous studies have concluded that thoroughbred racehorse speed is
 improving very slowly, if at all, despite heritable variation for
 performance and putatively intensive selective breeding. This has led to
 the suggestion that racehorses have reached a selection limit. However,
 previous studies have been limited, focusing only on the winning times of
 a few elite races run over middle and long distances, and failing to
 account for potentially confounding factors. Using a much larger dataset
 covering the full range of race distances and accounting for variation in
 factors such as ground softness, we show that improvement is, in fact,
 ongoing for the population as a whole, but driven largely by increasing
 speed in sprint races. In contrast, speed over middle and long distances,
 at least at the elite level, appears to be reaching an asymptote. Whether
 this reflects a selection limit to speed over middle and long distances or
 a shift in breeding practices to target sprint performances remains to be
 determined.
description: 1850_2012_elite_winnersSpeeds (yard/sec) of winners of elite thoroughbred horse races run in Great Britain on the turf (flat only) between 1850 and 2012. Data were sourced from Ruff’s Guide to the Turf (1850-1951 annual editions), the Raceform Flat Annual (1949-1994) and Raceform Interactive (1996-2012; www.raceform.co.uk).1997_2012Speed of horses in GB flat races run on the turf between 1997 and 20012. Data were sourced from Raceform Interactive ( www.raceform.co.uk).
DOI: 10.5281/zenodo.18391099
title: Ground truth: analysis of cereal species and definition of the agricultural knowledge  base
DOI: 10.5281/zenodo.18391100
title: Ground truth: analysis of cereal species and definition of the agricultural knowledge  base
DOI: 10.5878/002381
title: The Regional Skåne SOM Survey 2006
title: SOM-undersökningen i Skåne 2006
title: Syd-SOM 2006

description: This is the third SOM survey carried out in the Skåne region. Like Southern SOM 2004, the 2006 survey was carried out in the whole Skåne region. The questionnaire consists of nine coherent parts: news and daily papers; politics and society; society and service; media and society; holdings of technology and internet; traffic; activities and leisure habits; working life; and background.

Purpose:
Study attitudes and behaviour linked to local and regional issues.
description: Detta är den tredje SOM-undersökning som genomförts i Skåne. Liksom Syd-SOM 2004 har Syd-SOM 2006 genomförts i hela region Skåne. Frågeformuläret består av nio sammanhållna frågeområden: nyheter och dagstidningar; politik och samhälle; samhälle och service; medier och samhälle; teknikinnehav och Internet; trafik; aktiviter och fritidsvanor; arbetsliv; samt bakgrundsfrågor.

Syfte:
Studera attityder och beteenden som är knutna till lokala och regionala frågor och företeelser.
DOI: 10.5878/000452
title: The Regional Skåne SOM Survey 2006
title: SOM-undersökningen i Skåne 2006
title: Syd-SOM 2006

description: This is the third SOM survey carried out in the Skåne region. Like Southern SOM 2004, the 2006 survey was carried out in the whole Skåne region. The questionnaire consists of nine coherent parts: news and daily papers; politics and society; society and service; media and society; holdings of technology and internet; traffic; activities and leisure habits; working life; and background.

Purpose:
Study attitudes and behaviour linked to local and regional issues.
description: Detta är den tredje SOM-undersökning som genomförts i Skåne. Liksom Syd-SOM 2004 har Syd-SOM 2006 genomförts i hela region Skåne. Frågeformuläret består av nio sammanhållna frågeområden: nyheter och dagstidningar; politik och samhälle; samhälle och service; medier och samhälle; teknikinnehav och Internet; trafik; aktiviter och fritidsvanor; arbetsliv; samt bakgrundsfrågor.

Syfte:
Studera attityder och beteenden som är knutna till lokala och regionala frågor och företeelser.
DOI: 10.5061/dryad.kp93h
title: Data from: A robust semi-parametric test for detecting trait-dependent diversification

description: Rates of species diversification vary widely across the tree of life and
 there is considerable interest in identifying organismal traits that
 correlate with rates of speciation and extinction. However, it has been
 challenging to develop methodological frameworks for testing hypotheses
 about trait-dependent diversification that are robust to phylogenetic
 pseudoreplication and to directionally biased rates of character change.
 We describe a semi-parametric test for trait-dependent diversification
 that explicitly requires replicated associations between character states
 and diversification rates in order to detect effects. To use the method,
 diversification rates are reconstructed across a phylogenetic tree with no
 consideration of character states. A test statistic is then computed to
 measure the association between species-level traits and the corresponding
 diversification rate estimates at the tips of the tree. The empirical
 value of the test statistic is compared to a null distribution that is
 generated by structured permutations of evolutionary rates across the
 phylogeny. The test is applicable to binary discrete characters as well as
 continuous-valued traits and can accommodate extremely sparse sampling of
 character states at the tips of the tree. We apply the test to several
 empirical datasets and demonstrate that the method has acceptable Type I
 error rates.
description: PaperDatapackage
DOI: 10.5061/dryad.b6gj8
title: Data from: Resolving evolutionary relationships in closely related species with whole-genome sequencing data

description: Using genetic data to resolve the evolutionary relationships of species is
 of major interest in evolutionary and systematic biology. However,
 reconstructing the sequence of speciation events, the so-called species
 tree, in closely related and potentially hybridizing species is very
 challenging. Processes such as incomplete lineage sorting and
 interspecific gene flow result in local gene genealogies that differ in
 their topology from the species tree, and analyses of few loci with a
 single sequence per species are likely to produce conflicting or even
 misleading results. To study these phenomena on a full phylogenomic scale,
 we use whole-genome sequence data from 200 individuals of four
 black-and-white flycatcher species with so far unresolved phylogenetic
 relationships to infer gene tree topologies and visualize genome-wide
 patterns of gene tree incongruence. Using phylogenetic analysis in
 nonoverlapping 10-kb windows, we show that gene tree topologies are
 extremely diverse and change on a very small physical scale. Moreover, we
 find strong evidence for gene flow among flycatcher species, with distinct
 patterns of reduced introgression on the Z chromosome. To resolve species
 relationships on the background of widespread gene tree incongruence, we
 used four complementary coalescent-based methods for species tree
 reconstruction, including complex modeling approaches that incorporate
 post-divergence gene flow among species. This allowed us to infer the most
 likely species tree with high confidence. Based on this finding, we show
 that regions of reduced effective population size, which have been
 suggested as particularly useful for species tree inference, can produce
 positively misleading species tree topologies. Our findings disclose the
 pitfalls of using loci potentially under selection as phylogenetic markers
 and highlight the potential of modeling approaches to disentangle species
 relationships in systems with large effective population sizes and
 post-divergence gene flow.
description: Supporting
 Information_Tables S2-S4_Figures S1-S5Contains Supporting
 Tables S2-S4 and Supporting Figures S1-S5Supporting Table
 S1Supporting Table S1:
 List of all flycatcher samples used in the study.Supporting Figure
 S6Supporting Figure S6:
 Distribution of nucleotide diversity (π, panel A), genealogical sorting
 index (gsi, panel B), depth of the lowest common ancestor of all four
 flycatcher species relative to the root depth (panel C), frequencies of
 all 15 possible rooted tree topologies (panel D), and topology diversity
 index (tdi, panel E) for all chromosomes.Supporting Figure
 S7Supporting Figure S7:
 Frequencies of the three possible unrooted tree topologies (panel A) and
 the six possible internal species pairings (panel B) for all
 chromosomes.Data
 FilesContains input files for
 different species tree analyses and phylogenetic trees.data
 files.tar.gzScriptsContains all the scripts used for data analysis in the paper.scripts.tar.gz
DOI: 10.5061/dryad.mk3dc
title: Data from: Species-specific responses to island connectivity cycles: refined models for testing phylogeographic concordance across a Mediterranean Pleistocene Aggregate Island complex

description: The contribution of Pleistocene sea level changes to diversification
 patterns in archipelagos around the world, and specifically whether the
 repeated cycles of island connectivity and isolation acted as a ‘species
 pump’ is debated. The debate has been perpetuated in part because of the
 type of evidence used to evaluate the species-pump hypothesis.
 Specifically, existing tests of the ‘Pleistocene Aggregate Island Complex’
 (PAIC) model of diversification interpret the lack of concordant
 divergence times among multiple codistributed taxa as a rejection of the
 PAIC model. However, the null expectation of concordance disregards
 taxon-specific ecological traits and geographic characteristics that may
 affect population persistence and gene flow among islands. Here, we study
 the factors affecting population divergence in thirteen flightless
 darkling beetle species (Coleoptera: Tenebrionidae) across the PAIC system
 of the Cycladic plateau in the Aegean archipelago. Based on
 isolation-by-resistance analyses, hierarchical amova and the degree of
 genealogical sorting on individual islands, we identify a major effect of
 bathymetry and habitat stability on the levels of genetic divergence
 across the PAIC, with island size and body size playing a secondary role
 as well. We subsequently use bathymetric maps and habitat association to
 generate predictions about the set of islands and group of taxa expected
 to show phylogeographic concordance. We test these predictions using
 hierarchical approximate Bayesian computation and show how our
 interpretations regarding the role of PAICs as drivers of divergence
 change when relying on a null expectation of concordance compared to a
 refined model that takes geography and ecological traits into account.
description: Sequence Alignments
 (Cox1 & Mp20)Alignments of Cox1 and
 Mp20 sequences from 13 darkling beetle species distributed across the
 Cycladic plateauSequenceAlignments.zipTree files (calibrated Cox1 gene trees)These are calibrated Cox1 gene trees for 13 darkling beetle species distributed across the Cycladic plateauTreeFiles.zipInput files for hABC analyses in dpp-msbayesInput files for hABC analyses in dpp-msbayes that were used to test for simultaneous divergence between the Southern and Northern Cycladic plateau. There are two sets of input files: a) including all 13 taxa b) including only the 6 taxa associated with stable ("soil") habitatshABC_dppmsbayes_InputFiles.zipInput files for Mantel testsThis folder contains data files used to test for "isolation-by-distance" and "isolation-by-bathymetry" in 13 darkling beetle species distributed across the Cycladic plateauMantelTestInputFiles.zip
DOI: 10.5061/dryad.8908
title: Data from: Demersal fish diversity of the isolated Rockall plateau compared with the adjacent west coast shelf of Scotland.

description: This study compared the diversity of the demersal fish assemblage of an
 isolated shelf sea, the Rockall plateau, with that of the nearest adjacent
 continental shelf sea ecosystem, the west coast of Scotland. Bottom trawl
 surveys were carried out between 1986-2008 on the Rockall plateau and the
 adjacent shelf sea to the west of Scotland. All demersal fish were
 identified and counted. Analyses of species richness and abundance were
 undertaken. The fish assemblage of the Rockall plateau was less diverse
 and the proportional representation of species was markedly different. A
 number of species common at Rockall were rare on the west coast shelf and
 in general there were fewer common and temporally stable species and more
 rare and ephemeral species at Rockall. Some species absent from Rockall
 have life-history stages associated with inshore habitat. The Rockall
 plateau fish assemblage can be described as an impoverished subset of the
 NW European shelf sea fish assemblage. It is likely that there are
 constraints on diversity imposed by the relatively small area of the
 Rockall plateau and its degree of isolation by depth, distance and ocean
 currents
description: Trawl survey data
 Rockall Scotland 1986 2008Trawl survey data for
 Rockall plateau and west coast of scotland between depths of 90-250 m. See
 'read me' sheet in file for further details.
DOI: 10.7910/dvn/nhg62q
title: Replication Data for Political Preferences, Policy Loss and Shifting Support for European Integration

description: What explains the relationship between political preferences and support for European integration? Why did people on the Left oppose, and Right support, European integration in the 1980s, but this pattern reverse in the 2020s? We argue that citizens evaluate European integration in a transactional way in terms of their assessment of EU policy outputs. If the European Union offers citizens policies in line with their political preferences, they support it. If not, they oppose it. We find support for this argument using individual level public opinion data (n&gt;1,100,000) from all EU member states over almost 50 years (from the mid 1970s to the present) and novel approaches for measuring the left-right policy location of EU legislative outputs.
DOI: 10.15468/dl.rdyeg6
title: Occurrence Download

description: A dataset containing 102 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "GadmGid is CHL.12_1",
 "OccurrenceStatus is Present",
 "TaxonKey is Percilia gillissi",
 "Year 2000-2026"
 ]
}

 The dataset includes 102 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001640-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.5rs50
title: Data from: Phytochrome diversity in green plants and the origin of canonical plant phytochromes

description: Phytochromes are red/far-red photoreceptors that play essential roles in
 diverse plant morphogenetic and physiological responses to light. Despite
 their functional significance, phytochrome diversity and evolution across
 photosynthetic eukaryotes remain poorly understood. Using newly available
 transcriptomic and genomic data we show that canonical plant phytochromes
 originated in a common ancestor of streptophytes (charophyte algae and
 land plants). Phytochromes in charophyte algae are structurally diverse,
 including canonical and non-canonical forms, whereas in land plants,
 phytochrome structure is highly conserved. Liverworts, hornworts and
 Selaginella apparently possess a single phytochrome, whereas independent
 gene duplications occurred within mosses, lycopods, ferns and seed plants,
 leading to diverse phytochrome families in these clades. Surprisingly, the
 phytochrome portions of algal and land plant neochromes, a chimera of
 phytochrome and phototropin, appear to share a common origin. Our results
 reveal novel phytochrome clades and establish the basis for understanding
 phytochrome functional evolution in land plants and their algal relatives.
description: alignments_and_treesThis zip file contains the alignments and trees, as well as a ReadMe file.baits-120-60The probe sequences to target phytochrome, phototropin and neochrome genes, with a special focus on those of hornworts and ferns.
DOI: 10.5061/dryad.g31cv
title: Data from: Structure and extent of DNA methylation-based epigenetic variation in wild emmer wheat (T. turgidum ssp. dicoccoides) populations

description: Background: The genetic structure and differentiation of wild emmer wheat
 suggests that genetic diversity is eco-geographically structured. However,
 very little is known about the structure and extent of the heritable
 epigenetic variation and its influence on local adaptation in natural
 populations. Results: The structure and extent of the heritable
 methylation-based epigenetic variation were assessed within and among
 natural populations of Triticum turgidum ssp. dicoccoides. We used
 methylation sensitive amplified polymorphism (MSAP) and transposon
 methylation display (TMD) techniques, to assess the methylation status of
 random genomic CCGG sites and CCGG sites flanking transposable elements
 (TEs), respectively. Both techniques were applied to the DNA of 50 emmer
 accessions which were collected from five different geographically
 isolated regions. In order to ensure the assessment of heritable
 epigenetic variation, all accessions were grown under common garden
 conditions for two generations. In all accessions, the difference in
 methylation levels of CCGG sites, including CCGG sites that flanked TEs,
 were not statistically significant and relatively high, ranging between 46
 and 76 %. The pattern of methylation was significantly different among
 accessions, such that clear and statistically significant
 population-specific methylation patterns were observed. Conclusion: In
 this study, we have observed population-unique heritable methylation
 patterns in emmer wheat accessions originating from five geographically
 isolated regions. Our data indicate that methylation-based epigenetic
 diversity might be eco-geographically structured and might be partly
 determined by climatic and edaphic factors.
description: Primer6 workspace
 files
DOI: 10.5061/dryad.9rs25
title: Data from: Development of chloroplast genomic resources for Cynara

description: In this study, new chloroplast (cp) resources were developed for the genus
 Cynara, using whole cp genomes from 20 genotypes, by means of
 high-throughput sequencing technologies. Our target species included seven
 globe artichokes, two cultivated cardoons, eight wild artichokes, and
 three other wild Cynara species (C. baetica, C. cornigera, and C.
 syriaca). One complete cp genome was isolated using short reads from a
 whole genome sequencing project, while the others were obtained by means
 of long-range PCR, for which primer pairs are provided here. A de novo
 assembly strategy, combined with a reference based assembly allowed us to
 reconstruct each cp genome. Comparative analyses among the newly sequenced
 genotypes and two additional Cynara cp genomes (“Brindisino” artichoke and
 C. humilis) retrieved from public databases revealed 126 parsimony
 informative characters and 258 singletons in Cynara, for a total of 384
 variable characters. Thirty-nine SSR loci and 34 other INDEL events were
 detected. After data analysis, 37 primer pairs for SSR amplification were
 designed, and these molecular markers were subsequently validated in our
 Cynara genotypes. Phylogenetic analysis based on all cp variable
 characters provided the best resolution when compared to what was observed
 using only parsimony informative characters, or only short “variable” cp
 regions. The evaluation of the molecular resources obtained from this
 study led us to support the “super-barcode” theory and consider the total
 cp sequence of Cynara as a reliable and valuable molecular marker for
 exploring species diversity and examining variation below the species
 level.
description: Cynara
 MSACynara MSA for
 phylogenyCynara maximum parsimony
 treeCynara
 MP.nwkCynara neighbor joining
 treeCynara
 NJ.nwk