cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.962
title: Data from: Nucleotide variation in the Egfr locus of Drosophila melanogaster

description: The Epidermal growth factor receptor is an essential gene with diverse
 pleiotropic roles in development throughout the animal kingdom. Analysis
 of sequence diversity in 10.9 kb covering the complete coding region and
 6.4 kb of potential regulatory regions in a sample of 250 alleles from
 three populations of Drosophila melanogaster suggests that the intensity
 of different population genetic forces varies along the locus. A total of
 238 independent common SNPs and 20 indel polymorphisms were detected, with
 just six common replacements affecting &gt;1475 amino acids, four of
 which are in the short alternate first exon. Sequence diversity is lowest
 in a 2-kb portion of intron 2, which is also highly conserved in
 comparison with D. simulans and D. pseudoobscura. Linkage disequilibrium
 decays to background levels within 500 bp of most sites, so haplotypes are
 generally restricted to up to 5 polymorphisms. The two North American
 samples from North Carolina and California have diverged in allele
 frequency at a handful of individual SNPs, but a Kenyan sample is both
 more divergent and more polymorphic. The effect of sample size on
 inference of the roles of population structure, uneven recombination, and
 weak selection in patterning nucleotide variation in the locus is
 discussed.
description: Supplementary GenBank
 FileGenBank File 17571116
 (Egfr Sequence)EGFRgenbank.docSupplementary Figure 1Fu and Li’s D* statistic across the EGFRPRBDG_SF1.pdfSupplementary Table 6Excel file with complete sequence of each of the allelesEGFRalleles.zipSupplementary Figure 3Conserved 30 bp sequence motif in D. melanogasterPRBDG_SF3.pdfSupplementary Figure 2Polymorphism and Divergence in the CN repeatPRBDG_SF2.pdfSupplementary Figure 4LD plot for all common polymorphismsPRBDG_SF4.pdfSupplementary Table 1List of Primers used in sequencingPRBDG_ST1.pdfSupplementary Table 2List of Amino Acid Replacement variants in DERPRBDG_ST2.pdfSupplementary Table 3Effect of sample size on estimation of nucleotide diversityPRBDG_ST3.pdfSupplementary Table 4Length distribution of microsatellite allelesPRBDG_ST4.pdfSupplementary Table 5Effect of sample size on estimation of Fst statisticsPRBDG_ST5.pdf
DOI: 10.5061/dryad.d5s92
title: Data from: Convergent evolution of vascular optimization in kelp (Laminariales)

description: Terrestrial plants and mammals, although separated by a great evolutionary
 distance, have each arrived at a highly conserved body plan in which
 universal allometric scaling relationships govern the anatomy of vascular
 networks and key functional metabolic traits. The universality of
 allometric scaling suggests that these phyla have each evolved an
 ‘optimal’ transport strategy that has been overwhelmingly adopted by
 extant species. To truly evaluate the dominance and universality of
 vascular optimization, however, it is critical to examine other,
 lesser-known, vascularized phyla. The brown algae (Phaeophyceae) are one
 such group—as distantly related to plants as mammals, they have
 convergently evolved a plant-like body plan and a specialized phloem-like
 transport network. To evaluate possible scaling and optimization in the
 kelp vascular system, we developed a model of optimized transport anatomy
 and tested it with measurements of the giant kelp, Macrocystis pyrifera,
 which is among the largest and most successful of macroalgae. We also
 evaluated three classical allometric relationships pertaining to plant
 vascular tissues with a diverse sampling of kelp species. Macrocystis
 pyrifera displays strong scaling relationships between all tested vascular
 parameters and agrees with our model; other species within the
 Laminariales display weak or inconsistent vascular allometries. The lack
 of universal scaling in the kelps and the presence of optimized transport
 anatomy in M. pyrifera raises important questions about the evolution of
 optimization and the possible competitive advantage conferred by optimized
 vascular systems to multicellular phyla.
description: Phloem Anatomy,
 LaminarialesThis file is a .csv
 database of individual measurements of sieve element diameter in six
 species of the Laminariales (Phaeophyceae, Ochrophyta).conduit_anatomy_table.csvPhloem Anatomy (Organismal Level)This .csv datafile contains averaged sieve element areas sampled at multiple intervals from multiple individuals from 6 species in the Laminariales, paired with other anatomical data and measures of error.data_for_model_load_unload2.csv
DOI: 10.5061/dryad.v0np1
title: Data from: A supermatrix phylogeny of corvoid passerine birds (Aves: Corvides)

description: The Corvides (previously referred to as the core Corvoidea) are a
 morphologically diverse clade of passerine birds comprising nearly 800
 species. The group originated some 30 million years ago in the
 proto-Papuan archipelago, to the north of Australia, from where lineages
 have dispersed and colonized all of the world’s major continental and
 insular landmasses (except Antarctica). During the last decade multiple
 species-level phylogenies have been generated for individual corvoid
 families and more recently the inter-familial relationships have been
 resolved, based on phylogenetic analyses using multiple nuclear loci. In
 the current study we analyse eight nuclear and four mitochondrial loci to
 generate a dated phylogeny for the majority of corvoid species. This
 phylogeny includes 667 out of 780 species (85.5%), 141 out of 143 genera
 (98.6%) and all 31 currently recognized families, thus providing a
 baseline for comprehensive macroecological, macroevolutionary and
 biogeographical analyses. Using this phylogeny we assess the temporal
 consistency of the current taxonomic classification of families and
 genera. By adopting an approach that enforces temporal consistency by
 causing the fewest possible taxonomic changes to currently recognized
 families and genera, we find the current familial classification to be
 largely temporally consistent, whereas that of genera is not.
description: Corvides
 alignmentCorvides alignment with
 partitionsCC_alignment.nexCorvides Maximum Clade Credibility (MCC) TreeCorvides Maximum Clade Credibility (MCC) TreeCC_MCC.treCorvides, 1000 trees from the posterior distributionCorvides, 1000 trees from the posterior distribution of the BEAST analysis (after having discarded the burn in).CC_1000Trees.nextemporal banding function R scriptThis function identifies where to cut the tree to cause least taxonomic disruption at a particular taxonomic rank.tempbanding_function_PW_210115.R
DOI: 10.5061/dryad.dq7qv
title: Data from: Stable eusociality via maternal manipulation when resistance is costless

description: In many eusocial species, queens use pheromones to influence offspring to
 express worker phenotypes. While evidence suggests that queen pheromones
 are honest signals of the queen's reproductive health, here I show
 that queen's honest signaling can result from ancestral maternal
 manipulation. I develop a mathematical model to study the coevolution of
 maternal manipulation, offspring resistance to manipulation, and maternal
 resource allocation. I assume that (1) maternal manipulation causes
 offspring to be workers against offspring's interests; (2) offspring
 can resist at no direct cost, as is thought to be the case with pheromonal
 manipulation; and (3) the mother chooses how much resource to allocate to
 fertility andmaternal care. In the coevolution of these traits, I find
 that maternal care decreases, thereby increasing the benefit that
 offspring obtain from help, which in the long run eliminates selection for
 resistance. Consequently, ancestral maternal manipulation yields stable
 eusociality despite costless resistance. Additionally, ancestral
 manipulation in the long run becomes honest signaling that induces
 offspring to help. These results indicate that both eusociality and its
 commonly associated queen honest signaling can be likely to originate from
 ancestral manipulation.
description: SupportingInformationS2A Mathematica notebook containing mathematical derivations and code to generate all the figures in the paper.SupportingInformationS3A zip file with MATLAB computer code to generate the numerical solutions of all the figures in the paper.
DOI: 10.5061/dryad.7f4v1
title: Data from: Dioecy does not consistently accelerate or slow lineage diversification across multiple genera of angiosperms

description: Dioecy, the sexual system in which male and female organs are found in
 separate individuals, allows greater specialization for sex-specific
 functions and can be advantageous under various ecological and
 environmental conditions. However, dioecy is rare among flowering plants.
 Previous studies identified contradictory trends regarding the relative
 diversification rates of dioecious lineages vs their nondioecious
 counterparts, depending on the methods and data used. We gathered detailed
 species-level data for dozens of genera that contain both dioecious and
 nondioecious species. We then applied a probabilistic approach that
 accounts for differential speciation, extinction, and transition rates
 between states to examine whether there is an association between dioecy
 and lineage diversification. We found a bimodal distribution, whereby
 dioecious lineages exhibited higher diversification in certain genera but
 lower diversification in others. Additional analyses did not uncover an
 ecological or life history trait that could explain a context-dependent
 effect of dioecy on diversification. Furthermore, in-depth simulations of
 neutral characters demonstrated that such bimodality is also found when
 simulating neutral characters across the observed trees. Our analyses
 suggest that – at least for these genera with the currently available data
 – dioecy neither consistently places a strong brake on diversification nor
 is a strong driver.
description: Phylogenetic trees and
 sexual system classificationsProvided are: (1) Trees
 - a directory with phylogenetic trees for all genera in the study. (2)
 Sexual_systems - a directory with sexual system assignments for all
 species. (3) sexual.system.classifications.csv - a file with the
 classifications of sexual system (per species) into "broad" and
 "strict" definitions.Data_from_Sabath_at_al_2015.zip
DOI: 10.5061/dryad.963
title: Data from: Association between nucleotide variation in Efgr and wing shape in Drosophila melanogaster

description: As part of an effort to dissect quantitative trait locus effects to the
 nucleotide level, association was assessed between 238 single-nucleotide
 and 20 indel polymorphisms spread over 11 kb of the Drosophila
 melanogaster Egfr locus and nine relative warp measures of wing shape. One
 SNP in a conserved potential regulatory site for a GAGA factor in the
 promoter of alternate first exon 2 approaches conservative experimentwise
 significance (P &lt; 0.00003) in the sample of 207 lines for
 association with the location of the crossveins in the central region of
 the wing. Several other sites indicate marginal association with one or
 more other aspects of shape. No strong effects of sex or population of
 origin were detected with measures of shape, but two different sites were
 strongly associated with overall wing size in interaction with these fixed
 factors. Whole-gene sequencing in very large samples, rather than
 selective genotyping, would appear to be the only strategy likely to be
 successful for detecting subtle associations in species with high
 polymorphism and little haplotype structure. However, these features
 severely limit the ability of linkage disequilibrium mapping in Drosophila
 to resolve quantitative effects to single nucleotides.
description: Supplementary Data
 1PG_SD1.zipSupplementary Data 2PG_ST2.xlsSupplementary Table 3PG_ST3.pdfSupplementary GenBank FileEGFRgenbank.doc
DOI: 10.5061/dryad.v8c4c
title: Data from: The functional significance of complex floral colour pattern in a food-deceptive orchid

description: Many non-rewarding orchid species mimic the signals of co-occurring food
 flowers and thereby attract food-seeking animal pollinators. These signals
 are often visually complex with a colour pattern that contrasts between
 outer and central parts. The significance of this colour complexity for
 the pollination success of flowers of deceptive orchids has scarcely been
 investigated. We tested the effects of the colour patterns of the
 food-deceptive orchid Paphiopedilum micranthum on bumblebee visitation
 choices and pollination success using behavioural experiments in a
 community context. Using comparative phylogenetic analysis and a bee
 vision model, we also compared the colour patterns of P. micranthum with
 those of its congeners and sympatric food flowers. The probability of both
 long-range approach and close-up choice by bumblebees to orchids was all
 enhanced in communities with food flowers similar in colour pattern to the
 orchid. Probability of long-range approach and close-up choice was
 negatively correlated with colour distance between orchid and food flowers
 in floral outer and centre, respectively. Flowers of P. micranthum that
 were manipulated to reduce visual complexity had reduced male and female
 pollination success. Phylogenetic analysis revealed that the outer floral
 colour of P. micranthum is apomorphic and thus likely represents an
 evolutionary innovation, whereas the central colour is plesiomorphic and
 thus likely to function in the bumblebee pollination system as an
 exaptation. The contrast between the inner and outer colours appears to
 exploit visual preferences of bumblebees acquired during foraging on local
 food plants with similar colour patterns. This study highlights the
 adaptive significance of colour patterns in successful food deception and
 the importance of complex signals in facilitating interspecific
 interactions.
description: Reflectance and colour
 lociReflectance and colour
 loci (bee vision) of flowers of each species and paper discs used in this
 studyVisitor
 assemblagesVisitor assemblages
 (number of visits) of Paphiopedilum micranthum and co-occurring species in
 2011Data of behaviour
 experimentsData of behaviour
 experiments (Bee-interview experiments; Orchid manipulation
 experiments)Abundance of
 co-occurring speciesData for calculating the
 Relative Abundance of co-occurring species in the habitat of Paphiopedilum
 micranthumFlower
 sizesFlower sizes (diameters,
 cm) of co-flowering species in the habitat of Paphiopedilum
 micranthum
DOI: 10.5061/dryad.25jp6
title: Data from: Behaviour-related scalar habitat use by Cape buffalo (Syncerus caffer caffer)

description: Studies of habitat use by animals must consider behavioural resource
 requirements at different scales, which could influence the functional
 value of different sites. Using Cape buffalo (Syncerus caffer caffer) in
 the Okavango Delta, Botswana, we tested the hypotheses that behaviour
 affected use between and within habitats, hereafter referred to as macro-
 and microhabitats, respectively. We fitted GPS-enabled collars to fifteen
 buffalo and used the distances and turning angles between consecutive
 fixes to cluster the resulting data into resting, grazing, walking and
 relocating behaviours. Distance to water and six vegetation characteristic
 variables were recorded in sites used for each behaviour, except for
 relocating, which occurred too infrequently. We used multilevel logistic
 regressions to identify variables that characterised macro- and
 microhabitats. Our results showed that macrohabitat use was linked to
 behaviour, although this was least apparent during the rainy season, when
 resources were most abundant. Behaviour-related microhabitat use was less
 significant, but variation in forage characteristics could predict
 behaviour within all macrohabitats. The variables predicting behaviour
 were not consistent, but resting and grazing sites were more readily
 identifiable than walking sites, highlighting the importance of resting,
 as well as foraging, site availability in buffalo spatial processes. Our
 results emphasise the importance of considering several behaviours and
 scales in studies of habitat use to understand the links between
 environmental resources and animal behavioural and spatial ecology.
description: Vegetation
 dataAll vegetation variables
 describing macro- and microhabitatsBehaviour
 dataProportional behaviour
 in macrohabitats and different seasons
DOI: 10.5061/dryad.964
title: Data from: Comparison of regional gene expression differences in the brains of the domestic dog and human

description: Comparison of the expression profiles of 2,721 genes in the cerebellum,
 cortex and pituitary gland of three American Staffordshire terriers, one
 beagle and one fox hound revealed regional expression differences in the
 brain but failed to reveal marked differences among breeds, or even
 individual dogs. Approximately 85 per cent (42 of 49 orthologue
 comparisons) of the regional differences in the dog are similar to those
 that differentiate the analogous human brain regions. A smaller percentage
 of human differences were replicated in the dog, particularly in the
 cortex, which may generally be evolving more rapidly than other brain
 regions in mammals. This study lays the foundation for detailed analysis
 of the population structure of transcriptional variation as it relates to
 cognitive and neurological phenotypes in the domestic dog.
description: Supplementary Table
 1KTOBG_Annotation.xlsSupplementary Table 2KTOBG_Results.xlsSupplementary Table 3BFSraw.xlsSupplementary File 4CanineMIAME.docSupplementary Table 5KTOBG_SupplTable5.xls
DOI: 10.5061/dryad.92137
title: Data from: Phylogeny and photosynthesis of the grass tribe Paniceae

description: PREMISE OF THE STUDY: The grass tribe Paniceae includes important food,
 forage, and bioenergy crops such as switchgrass, napiergrass, various
 millet species, and economically important weeds. Paniceae are also
 valuable for answering scientific and evolutionary questions about C4
 photosynthetic evolution, drought tolerance, and spikelet variation.
 However, the phylogeny of the tribe remains incompletely resolved.
 METHODS: Forty-five taxa were selected from across the tribe Paniceae and
 outgroups for genome survey sequencing (GSS). These data were used to
 build a phylogenetic tree of the Paniceae based on 102 markers (78
 chloroplast, 22 mitochondrial, 2 nrDNA). Ancestral state reconstruction
 analyses were also performed within the Paniceae using both the
 traditional and two subtype classification systems to test hypotheses of
 C4 subtype evolution. KEY RESULTS: The phylogenetic tree resolves many
 areas of the Paniceae with high support and provides insight into the
 origin and number of C4 evolution events within the tribe. The recovered
 phylogeny and ancestral state reconstructions support between four and
 seven independent origins of C4 photosynthesis within the tribe and
 indicate which species are potentially the closest C3 sister taxa of each
 of these events. CONCLUSIONS: Although the sequence of evolutionary events
 that produced multiple C4 subtypes within the Paniceae remains
 undetermined, the results presented here are consistent with only a subset
 of currently proposed models. The species used in this study constitute a
 panel of C3 and C4 grasses that are suitable for further studies on C4
 photosynthesis, bioenergy, food and forage crops, and various
 developmental features of the Paniceae.
description: fig1_for_dryadTree and alignment file for figure 1 of manuscriptGPWGII_and_Washburn_tree_matrixGrass phylogeny work group tree and alignment combined with tree and alignment from figure 1 of manuscript
DOI: 10.5061/dryad.rp77j
title: Data from: Strategies for a successful plant invasion: the reproduction of Phragmites australis in northeastern North America

description: 1. Knowing the relative contribution of vegetative propagation and sexual
 reproduction to the dispersal and establishment of exotic plants is
 crucial for devising efficient control strategies. This is particularly
 true for the common reed (Phragmites australis), one of the most invasive
 species in North America. 2. For the first time we combined in situ field
 observations and genetic evidence, based on two genotyping techniques,
 i.e., microsatellite markers (SSR) and genotyping-by-sequencing (GBS), to
 determine the propagation strategies of this invader at its northern
 distribution limit in North America, and especially in roadside ditches.
 3. Field observations revealed that, in a region where the common reed is
 already abundant, both seeds and plant fragments contributed to the
 establishment of new populations. Newly established individuals originated
 mostly (84%) from seeds rather than fragments, but a larger proportion of
 individuals originating from fragments survived the second year compared
 to seedlings. 4. High genetic diversity among marsh and roadside common
 reed stands indicated the prime role of sexual reproduction for dispersal.
 The vast majority of genotypes were found in only one stand; such high
 genetic variability can only be explained by sexual reproduction. Half the
 surveyed stands comprised a single clone, suggesting that local expansion
 mainly occurred vegetatively. As the small proportion of SSR genotypes
 initially thought to be common between distant stands proved to be
 distinct (as revealed by GBS data), it is likely that all the stands
 examined were initially founded by genetically distinct individuals. 5.
 Synthesis. Our study suggests that long-distance dispersal by seeds is
 important for the common reed, in marshes and roadsides, while both seeds
 and plant fragments contribute to short-distance dispersal along roads, at
 least in regions where the species is already abundant. The success of
 this invader in North America seems to be attributable to a reproduction
 strategy combining the advantages of sexuality with those of vegetative
 propagation. Moreover, this study shows that the GBS approach strongly
 reduces uncertainties associated with the use of a limited number of
 markers. This approach is especially valuable for ecologists dealing with
 an ever increasing number of invaders, of which few have identified
 microsatellite markers.
description: Albert_etal_JEcolGenetic data (SSR, SNP) from Phragmites australis populations sampled along highways and in marshes of southern Québec, Canada