cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.298b1
title: Data from: pavo: an R package for the analysis, visualization and organization of spectral data

description: 1. Recent technical and methodological advances have led to a dramatic
 increase in the use of spectrometry to quantify reflectance properties of
 biological materials, as well as models to determine how these colours are
 perceived by animals, providing important insights into ecological and
 evolutionary aspects of animal visual communication. 2. Despite this
 growing interest, a unified cross-platform framework for analyzing and
 visualizing spectral data has not been available. We introduce pavo, an R
 package that facilitates the organization, visualization, and analysis of
 spectral data in a cohesive framework. pavo is highly flexible, allowing
 users to (a) organize and manipulate data from a variety of sources, (b)
 visualize data using R's state-of-the-art graphics capabilities, and
 (c) analyze data using spectral curve shape properties and visual system
 modeling for a broad range of taxa. 3. In this paper, we present a summary
 of the functions implemented in pavo and how they integrate in a workflow
 to explore and analyze spectral data. We also present an exact solution
 for the calculation of colour volume overlap in colourspace, thus
 expanding previously published methodologies. 4. As an example of
 pavo's capabilities, we compare the colour patterns of three African
 Glossy Starling species, two of which have diverged very recently. We
 demonstrate how both colour vision models and direct spectral measurement
 analysis can be used to describe colour attributes and differences between
 these species. Different approaches to visual models and several plotting
 capabilities exemplify the package's versatility and streamlined
 workflow. 5. pavo provides a cohesive environment for handling spectral
 data and addressing complex sensory ecology questions, while integrating
 with R's modular core for a broader and comprehensive analytical
 framework, automated management of spectral data, and reproducible
 workflows for colour analysis.
description: Reflectance spectra from
 Glossy StarlingsA compressed file
 including raw spectral files (Avantes .ttt files) of reflectance
 measurements from three species of African Glossy Starlings (Lamprotornis
 acuticaudus, L. chloropterus and L. elisabeth). Three replicate
 measurements from 11 plumage patches were taken from four museum specimens
 from each species.starlingspectra.zip
DOI: 10.5061/dryad.28n35
title: Data from: Genome-wide association study identifies vitamin B5 biosynthesis as a host specificity factor in Campylobacter

description: Genome-wide association studies have the potential to identify causal
 genetic factors underlying important phenotypes but have rarely been
 performed in bacteria. We present an association mapping method that takes
 into account the clonal population structure of bacteria and is applicable
 to both core and accessory genome variation. Campylobacter is a common
 cause of human gastroenteritis as a consequence of its proliferation in
 multiple farm animal species and its transmission via contaminated meat
 and poultry. We applied our association mapping method to identify the
 factors responsible for adaptation to cattle and chickens among 192
 Campylobacter isolates from these and other host sources. Phylogenetic
 analysis implied frequent host switching but also showed that some
 lineages were strongly associated with particular hosts. A seven-gene
 region with a host association signal was found. Genes in this region were
 almost universally present in cattle but were frequently absent in
 isolates from chickens and wild birds. Three of the seven genes encoded
 vitamin B5 biosynthesis. We found that isolates from cattle were better
 able to grow in vitamin B5-depleted media and propose that this difference
 may be an adaptation to host diet.
description: DryadWhole genome sequencing
 reads for the 80 BIGSdb Campylobacter isolates referred to in the
 associated publication.
DOI: 10.5061/dryad.31072
title: Data from: The developmental plasticity and functional significance of an additional sperm storage compartment in female yellow dung flies

description: 1. The mechanistic basis for, and adaptive significance of variation in
 female sperm storage organs is important for a range of questions
 concerning sexual selection and speciation, as such variation influences
 the evolutionary trajectories of male fertilization related traits and may
 facilitate speciation through its effects on gamete recognition. 2. Female
 yellow dung flies (Scathophaga stercoraria) usually develop three sperm
 storage compartments, and this subdivision may be an adaptation for
 sorting sperm during post-copulatory choice. 3. Using lines artificially
 selected to express four spermathecae (4s), we explored the fitness
 consequences of the novel phenotype relative to the naturally prevalent
 three-spermatheca (3s) phenotype by manipulating the opportunity for
 post-copulatory sexual selection (females mated either with three or only
 one male prior to oviposition). In addition, we examined the developmental
 plasticity of spermathecal number in response to different larval food
 environments and estimated its genetic correlation with growth rate. 4.
 Mating treatments with and without the opportunity for post-copulatory
 sexual selection revealed no significant fitness differences between
 alternative spermathecal phenotypes within selection lines despite overall
 benefits associated with multiple mating, and moderate egg-to-adult
 survival costs in response to artificial selection for 4s. Manipulations
 of the larval food environment revealed that the expression of 4s is
 highly plastic and tightly linked to environmental conditions promoting
 fast somatic growth and development. Likewise, siblings with fast
 intrinsic (genetic) growth were more likely to express 4s within and
 across food environments. 5. The present results highlight a great
 potential for rapid evolutionary change in female sperm storage morphology
 through indirect selection on life-history traits, and further suggest
 genetic assimilation as a potential mechanism facilitating phylogenetic
 transitions in spermatheca number as frequently observed within the
 Dipterans.
description: The developmental
 plasticity and functional significance of an additional sperm storage
 compartment in female yellow dung fliesThe data files contain
 information on maternal and offspring spermatheca phenotype, offspring
 development time, body size, growth rate and survival from five artificial
 selection lines of Scathophaga stercoraria. The data are provided based on
 family means and individual female offspring.FE-2013-00198R1.xls
DOI: 10.5061/dryad.n5h13
title: Data from: Increased accuracy of species lists developed for alpine lakes using morphology and cytochrome oxidase I for identification of specimens

description: The first step in many community ecology studies is to produce a species
 list from a sample of individuals. Community ecologists now have two
 viable ways of producing a species list: morphological and barcode
 identification. In this study, we compared the taxonomic resolution gained
 by a combined use of both methods and tested whether a change in taxonomic
 resolution significantly impacted richness estimates for benthic
 macroinvertebrates sampled from ten lakes in Sequoia National Park, USA.
 Across all lakes, 77 unique taxa were identified and 42% (32) were
 reliably identified to species using both barcode and morphological
 identification. Of the 32 identified to species, 63% (20) were identified
 solely by comparing the barcode sequence from cytochrome oxidase I to the
 Barcode of Life reference library. The increased resolution using a
 combined identification approach compared to identifications based solely
 on morphology resulted in a significant increase in estimated richness
 within a lake at the order, family, genus and species levels of taxonomy
 (P &lt; 0.05). Additionally, young or damaged individuals that could
 not be identified using morphology were identified using their COI
 sequences to the genus or species level on average 75% of the time. Our
 results demonstrate that a combined identification approach improves
 accuracy of benthic macroinvertebrate species lists in alpine lakes and
 subsequent estimates of richness. We encourage the use of barcodes for
 identification purposes and specifically when morphology is insufficient,
 as in the case of damaged and early life stage specimens of benthic
 macroinvertebrates.
description: COI alignment used to
 generate barcode treeSequence alignment of
 COI sequences used for identification. This alignment was used to generate
 the neighbor joining tree for figure 2 of manuscript.COI_MER
 alignment.fastaCOI tree
 fileTree file used to build
 tree in Figure 2.COI_MER alignment tree
 2.nexSource modifyer
 listFile sent along with
 Genbank submission identifying each isolate from which the sequence was
 generated. Extractions are archived at the Genomic Variation Laboratory at
 UC Davis.Analysis
 filesEach tab contains file
 used to execute statistical test performed in JMP.COI Sequencer
 fileSequences used for
 identification. Raw .ab1 files edited and aligned using Sequencher
 software.Biodiversity Barcoding SNL
 ALL.SPF
DOI: 10.5061/dryad.8t6c0
title: Data from: Mechanisms of macroevolution: polyphagous plasticity in butterfly larvae revealed by RNA-Seq

description: Transcriptome studies of insect herbivory are still rare, yet studies in
 model systems have uncovered patterns of transcript regulation that appear
 to provide insights into how insect herbivores attain polyphagy, such as a
 general increase in expression breadth and regulation of ribosomal,
 digestion- and detoxification-related genes. We investigated the potential
 generality of these emerging patterns, in the Swedish comma, Polygonia
 c-album, which is a polyphagous, widely-distributed butterfly. Urtica
 dioica and Ribes uva-crispa are hosts of P. c-album, but Ribes represents
 a recent evolutionary shift onto a very divergent host. Utilizing the
 assembled transcriptome for read mapping, we assessed gene expression
 finding that caterpillar life-history (i.e. 2nd vs. 4th-instar regulation)
 had a limited influence on gene expression plasticity. In contrast,
 differential expression in response to host-plant identified genes
 encoding serine-type endopeptidases, membrane-associated proteins and
 transporters. Differential regulation of genes involved in nucleic acid
 binding was also observed suggesting that polyphagy involves large scale
 transcriptional changes. Additionally, transcripts coding for structural
 constituents of the cuticle were differentially expressed in caterpillars
 in response to their diet indicating that the insect cuticle may be a
 target for plant defence. Our results state that emerging patterns of
 transcript regulation from model species appear relevant in species when
 placed in an evolutionary context.
description: P. c-album de novo
 trancriptome assembly (TA)P. c-album de novo
 TA.fastaP. c-album TA-contig
 expressionUnique number of reads
 per P. c-album TA-contig in each treatment. Treatment is denoted as AX-Y,
 where A is the host, U. dioica or R. uva-crispa; X is the biological
 replicate number and Y indicates the developmental stage of the
 caterpillars composing the sample (2nd or 4th instar). Additionally, the
 best hit homolog to each TA-contig obtained from the NCBI database using
 BLAST is provided (description and accession number). Each TA-contig was
 assigned to a database of predicted proteins from D. plexippus using
 BLASTx. The identification number obtained from the UniProt database and
 the corresponding gene ontology (GO) classification is provided for each
 D. plexippus predicted protein.P. c-album whole gene
 expressionPolygonia c-album total
 number of raw reads and RPKM values per corresponding Danaus plexippus
 transcript for each treatment. Each D. plexippus transcript (Feature ID)
 identifies the nucleotide sequence of the corresponding D. plexippus
 protein ortholog obtained for each P. c-album TA-contig using BLASTx.
 Treatment is denoted as AX-Y, where A is the host, U. dioica or R.
 uva-crispa; X is the biological replicate number and Y indicates the
 developmental stage of the caterpillars composing the sample (2nd or 4th
 instar).
DOI: 10.5061/dryad.4d236
title: Data from: Size variation, growth strategies and the evolution of modularity in the mammalian skull

description: Allometry is a major determinant of within-population patterns of
 association among traits and, therefore, a major component of
 morphological integration studies. Even so, the influence of size
 variation over evolutionary change has been largely unappreciated. Here,
 we explore the interplay between allometric size variation, modularity,
 and life history strategies in the skull from representatives of 35
 mammalian families. We start by removing size variation from
 within-species data and analyzing its influence on integration magnitudes,
 modularity patterns and responses to selection. We also carry out a
 simulation in which we artificially alter the influence of size variation
 in within-taxa matrices. Finally, we establish the relationship between
 size variation and different growth strategies. We demonstrate that a
 large portion of the evolution of modularity in the mammalian skull is
 associated to the evolution of growth strategies. Lineages with highly
 altricial neonates have adult variation patterns dominated by size
 variation, leading to high correlations among traits regardless of any
 underlying modular process and impacting directly their potential to
 respond to selection. Greater influence of size variation is associated to
 larger inter-module correlations, less individualized modules, and less
 flexible responses to natural selection.
description: Growth
 dataProportion of the total
 metabolic power devoted to growth (Eg) and the overall integration
 magnitude (ICV) calculated for each mammal family, as well as the original
 neonate and adult body mass measurements used in the calculation of Eg.
 Sources for the body mass data can be obtained from the text of the
 manuscript.Growth
 strategiesdata.xlsxDatabase of skull
 measurementsEach text file contains
 the residuals from the MANOVA carried out in each of the mammal families
 ,as described in the original manuscript. All results published in the
 manuscript can be obtained from these residuals. Rows represent each
 specimen measured. And columns represent each of the 35 skull
 measurements, in the same order as they appear in the manuscript. All
 measurements were obtained from museum specimens using a 3D digitizer.
 Please contact the main author if you have any
 questions.database of skull
 measurements.zip
DOI: 10.5061/dryad.51np1
title: Data from: Phylogeography of poorly dispersing net-winged beetles: a role of drifting India in the origin of Afrotropical and Oriental fauna

description: Ancient dispersal history may be obscured by subsequent dispersal events.
 Therefore, we intend to investigate the biogeography of metriorrhynchine
 net-winged beetles, a group characterized by limited dispersal propensity.
 We used DNA data to construct phylogenies and the BayesTraits and RASP
 programs to identify putative ancestral areas. Further, we inferred
 ultrametric trees to estimate the ages of selected nodes. The time frame
 is inferred from tectonic calibrations and the general mutation rate of
 the mitochondrial genes. Metriorrhynchini consists of two lineages with
 Afro/Oriental and Australian distributions. The basal lineages originated
 in Eastern Gondwana after the split of Australia, India and Madagascar;
 the Afrotropical and Madagascar Metriorrhynchini separated from the
 Oriental clades 65 and 62 mya. Several already diversified lineages
 colonized continental Asia 55–35 mya. A few genera of the Australian clade
 dispersed to the Oriental region 5–15 mya and reached Eastern India and
 Southern China. Only Xylobanus crossed the Makassar Strait to Sulawesi and
 does not occur further to the east. The current distribution of
 Metriorrhynchini is a result of drifting on continental fragments and
 over-sea dispersal events limited to a few hundreds of kilometers. We
 conclude that: (1) Afrotropical and Madagascar lineages originated
 independently from dispersal events during India's drift to the north
 and the Mozambique Channel completely isolates the respective faunas since
 then; (2) Oriental fauna is a recently established mixture of the Indian
 and Australian lineages, with predominance of the older Indian clades; (3)
 The fauna of islands located north of Australia colonized Sulawesi after
 collision with the Sundaland margin and the species rich Australian
 lineages did not reach Western Wallacea or the Philippines. Our results
 suggest an impact of subtle differences in biological characteristics on
 biogeographic history of individual lineages, when mostly lowland and
 flower-visiting lineages were able to disperse across sea channels.
description: alignment_blastdata set of 249 analysed sequences - alignment from BlastAlign 1.2 (under default parameters)curr_sup_blast249.dat.fastaalignment_muscledata set of 249 analysed sequences - alignment from Muscle 3.6 (under the gap opening parameter -600 and gap extension parameter -40)curr_sup_muscle249.dat.fasta
DOI: 10.5061/dryad.3nc54
title: Data from: Targeted sequence capture and resequencing implies a predominant role of regulatory regions in the divergence of a sympatric lake whitefish species pair (Coregonus clupeaformis)

description: Latest technological developments in evolutionary biology bring new
 challenges in documenting the intricate genetic architecture of species in
 the process of divergence. Sympatric populations of lake whitefish
 represent one of the key systems to investigate this issue. Despite the
 value of random genotype-by-sequencing methods and decreasing cost of
 sequencing technologies, it remains challenging to investigate variation
 in coding regions, especially in the case of recently duplicated genomes
 as in salmonids, as this greatly complicates whole genome resequencing. We
 thus designed a sequence capture array targeting 2773 annotated genes to
 document the nature and the extent of genomic divergence between sympatric
 dwarf and normal whitefish. Among the 2728 genes successfully captured, a
 total of 2182 coding and 10 415 noncoding putative single-nucleotide
 polymorphisms (SNPs) were identified after applying a first set of basic
 filters. A genome scan with a quality-refined selection of 2203 SNPs
 identified 267 outlier SNPs in 210 candidate genes located in genomic
 regions potentially involved in whitefish divergence and reproductive
 isolation. We found highly heterogeneous FST estimates among SNP loci.
 There was an overall low level of coding polymorphism, with a predominance
 of noncoding mutations among outliers. The heterogeneous patterns of
 divergence among loci confirm the porous nature of genomes during
 speciation with gene flow. Considering that few protein-coding mutations
 were identified as highly divergent, our results, along with previous
 transcriptomic studies, imply that changes in regulatory regions most
 likely had a greater role in the process of whitefish population
 divergence than protein-coding mutations. This study is the first to
 demonstrate the efficiency of large-scale targeted resequencing for a
 nonmodel species with such a large and unsequenced genome.
description: Python scripts - File
 formatting - Sequence CaptureAll relevant scripts
 used to format files, analyse data and obtain results from sequence
 capture experiment on two sympatric populations of whitefish ecotypes in
 the process of speciation.MEC-13-0265_seq-capt.tar.gzWhitefish sequence capture assemblyFasta file containing 2,228 genes de novo assembled after conducting a targeted enrichment and re-sequencing experiment on two sympatric populations of whitefish (Coregonus clupeaformis) currently in the process of speciation.assembled_genes.fasta
DOI: 10.5061/dryad.bg006
title: Data from: A revised taxonomy of crested newts in the Triturus karelinii group (Amphibia: Caudata: Salamandridae), with the description of a new species

description: We present a taxonomic revision of the crested newt Triturus karelinii
 sensu lato. Based on the presence of discrete nuclear DNA gene pools, deep
 genetic divergence of mitochondrial and nuclear DNA, and no indication of
 gene flow, we interpret this taxon as comprising two species: one covering
 the southern Caspian Sea shore, the Caucasus and the Crimea, i.e. the
 eastern part of the total range and another covering northern Asiatic
 Turkey and western Asiatic Turkey plus the south-eastern Balkan Peninsula,
 i.e. the central and western part of the total range. We acknowledge that
 the central/western species should likely be further subdivided into a
 central and a western taxon, but we prefer to await a more detailed
 genetic analysis of the putative contact zone, positioned in northwestern
 Asiatic Turkey. The name T. karelinii (Strauch, 1870) applies to the
 eastern species as the type locality is positioned along the coast of the
 Gulf of Gorgan, Iran. The name T. arntzeni has been applied to the
 central/western species with Vrtovać, Serbia as the type locality. We show
 that not T. karelinii sensu lato but T. macedonicus occurs at Vrtovać.
 Hence, the name T. arntzeni Litvinchuk, Borkin, Džukić and Kalezić, 1999
 (in Litvinchuk et al., 1999) is a junior synonym of T. macedonicus
 (Karaman, 1922) and should not be used for the central/western species. We
 propose the name T. ivanbureschi sp. nov. for the central/western species
 and provide a formal species description.
description: Wielstra_Triturus_taxonomy_Online_appendix1Wielstra_Triturus_taxonomy_Online_appendix2Online Appendix 2 – Number of rib-bearing vertebrae (NRBV) for newts from Vrtovać, Serbia.Wielstra_Triturus_taxonomy_Online_appendix3Online Appendix 3 – Genome size data from Litvinchuk et al. (1999) for individual newts.Wielstra_Triturus_taxonomy_Online_appendix4Online Appendix 4 – Allozyme data from Litvinchuk et al. (1999) for individual newts and the BAPS group they were assigned to.Wielstra_Triturus_taxonomy_Online_appendix5Online Appendix 5 – Pictures of the ventral side of the holotype and paratypes of Triturus ivanbureschi sp. nov.Wielstra_Triturus_taxonomy_Online_appendix6Online Appendix 6 – X-ray photographs of the holotype and paratypes of Triturus ivanbureschi sp. nov.