cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.t0910
title: Data from: Decoupled diversification dynamics of feeding morphology following a major functional innovation in marine butterflyfishes

description: The diversity of fishes on coral reefs is influenced by the evolution of
 feeding innovations. For instance, the evolution of an intramandibular jaw
 joint has aided shifts to corallivory in Chaetodon butterflyfishes
 following their Miocene colonization of coral reefs. Today, over half of
 all Chaetodon species consume coral, easily the largest concentration of
 corallivores in any reef fish family. In contrast with Chaetodon, other
 chaetodontids, including the long-jawed bannerfishes, remain less
 intimately associated with coral and mainly consume other invertebrate
 prey. Here, we test (i) if intramandibular joint (IMJ) evolution in
 Chaetodon has accelerated feeding morphological diversification, and (ii)
 if cranial and post-cranial traits were affected similarly. We measured 19
 cranial functional morphological traits, gut length and body elongation
 for 33 Indo-Pacific species. Comparisons of Brownian motion rate
 parameters revealed that cranial diversification was about four times
 slower in Chaetodon butterflyfishes with the IMJ than in other
 chaetodontids. However, the rate of gut length evolution was significantly
 faster in Chaetodon, with no group-differences for body elongation. The
 contrasting patterns of cranial and post-cranial morphological evolution
 stress the importance of comprehensive datasets in ecomorphology. The IMJ
 appears to enhance coral feeding ability in Chaetodon and represents a
 design breakthrough that facilitates this trophic strategy. Meanwhile,
 variation in gut anatomy probably reflects diversity in how coral tissues
 are procured and assimilated. Bannerfishes, by contrast, retain a
 relatively unspecialized gut for processing invertebrate prey, but have
 evolved some of the most extreme cranial mechanical innovations among bony
 fishes for procuring elusive prey.
description: RSPB-2017-0906_Data4DryadThe R script is an example and not the entire analysis as it was batch processed (the simulation for the bootstrapping takes a lot of time and was sped up by running each trait on a separate CPU). All data files needed to run the R script are provided. Sequence alignments are also provided and refer to Bellwood et al. 2010. Evolutionary history of the butterflyfishes (f: Chaetodontidae) and the rise of coral feeding fishes. J. Evol. Biol. 23:335-349
DOI: 10.5061/dryad.mr401g7
title: Data from: Biotic and abiotic factors shape the microbiota of wild-caught populations of the arbovirus vector Culicoides imicola

description: Biting midges of the genus Culicoides are known vectors of arboviruses
 affecting human and animal health. However, little is known about
 Culicoides imicola microbiota and its influence on this insect’s biology.
 In this study, the impact of biotic and abiotic factors on C. imicola
 microbiota was characterized using shotgun-metagenomic sequencing of whole
 body DNA samples. Wild-caught C. imicola adult nulliparous females were
 sampled in two locations from Sicily, Italy. The climatic variables of
 temperature and soil moisture from both localities were recorded together
 with potential host blood meal sources. Shared core microbiome among C.
 imicola populations included Pseudomonas, Escherichia, Halomonas,
 Candidatus Zinderia, Propionibacterium, and Schizosaccharomyces. Specific
 and unique taxa were also found in C. imicola from each location,
 highlighting similarities and differences in microbiome composition
 between both populations. DNA and protein identification showed
 differences in host preferences between both populations with Homo sapiens
 and Canis lupus familiaris L. being the preferred blood meal source in
 both locations. A principal component analysis showed that the combined
 effect of host preferences (H. sapiens) and local soil moisture factors
 shape the microbiome composition of wild-caught populations of C. imicola.
 These results contribute to characterizing the role of the microbiome in
 insect adaptation and its utility in predicting geographic expansion of
 Culicoides species with potential implications for the control of
 vector-borne diseases.
description: Culicoides_all_fasta_samplesThis file contain all the fasta files from the Culicoides imicola samples from Collesano and TrapaniCulicoides_all_samples.zipmass_espectrometry_profile_all_samples
DOI: 10.5061/dryad.j2641
title: Data from: Modeling angle-resolved photoemission of graphene and black phosphorus nano structures

description: Angle-resolved photoemission spectroscopy (ARPES) data on electronic
 structure are difficult to interpret, because various factors such as
 atomic structure and experimental setup influence the quantum mechanical
 effects during the measurement. Therefore, we simulated ARPES of
 nano-sized molecules to corroborate the interpretation of experimental
 results. Applying the independent atomic-center approximation, we used
 density functional theory calculations and custom-made simulation code to
 compute photoelectron intensity in given experimental setups for every
 atomic orbital in poly-aromatic hydrocarbons of various size, and in a
 molecule of black phosphorus. The simulation results were validated by
 comparing them to experimental ARPES for highly-oriented pyrolytic
 graphite. This database provides the calculation method and every file
 used during the work flow.
description: Dataset of ARPES
 simulation for graphene and black phosphorusThe dataset of ARPES
 simulation consist of DFT calculation results using Gaussian 09 and
 photoelectron intensity calculations using home-made
 code.Dataset.zipPES_programThis is stand alone version of photoelectron intensity calculation program. This code can calculate photoelectron intensity for a atomic orbital with independent atomic center approximation.experimental ARPES dataThis file contains experimental ARPES data of HOPG. The emission angles of HOPG were measured with respect to the normal and tilted direction (2, 4, and 6 degree) using 100 eV photon. Also, photon energies varied from 100 eV to 400 eV for the case of the normal direction.
DOI: 10.5061/dryad.v2g01
title: Data from: Comparative genomics of color morphs In the coral Montastraea cavernosa

description: Montastraea cavernosa is a common coral in the Caribbean basin found in
 several color morphs. To investigate the causes for brown and orange
 morphs we undertook a genomics approach on corals collected at the same
 time and depth in the Bahamas. The coral holobiont includes the host,
 symbiotic dinoflagellates (Symbiodinium spp.), and a diverse microbiome.
 While the coral host showed significant genetic differentiation between
 color morphs both the composition of the Symbiodinium spp. communities and
 the prokaryotic communities did not. Both targeted and global gene
 expression differences in the transcriptome of the host show no difference
 in fluorescent proteins while the metatranscriptome of the microbiome
 shows that pigments such as phycoerythrin and orange carotenoid protein of
 cyanobacterial origin are significantly greater in orange morphs, which is
 also consistent with the significantly greater number of cyanobacteria
 quantified by 16S rRNA reads and flow cytometry. The microbiome of orange
 color morphs expressed significantly more nitrogenase (nifH) transcripts
 consistent with their known ability to fix nitrogen. Both coral and
 Symbiodinium spp. transcriptomes from orange morphs had significantly
 increased expression of genes related to immune response and apoptosis,
 which may potentially be involved in maintaining and regulating the unique
 symbiont population in orange morphs.
description: Mcav microbiome 16S
 assemblyAssembled reads for 16S
 pyrosequencing following quality filtering, chimera removal, and
 clustering at 97% similarity.LSI.Mc.seqs_cleaned.fnaSymbiodinium ITS2 Sanger readsSanger sequencing reads for 107 clones recovered from PCR amplification of ITS2 amplicons from Montastrea cavernosa samples.Mcav ITS2 Sanger.fastaMetatranscriptome assembly filtered annotatedTranscripts from Montastrea cavernosa metatranscriptome following assembly with Trinity/BinPacker/Tranfuse, BLAST-filtering, and annotation with Dammit.metatranscriptome.fasta.dammit.fastaSymbiodinium transcriptome filtered annotatedTranscripts classified as Symbiodinium following holobiont transcriptome assembly with Trinity/BinPacker/Tranfuse, BLAST-filtering, and annotation with Dammit.Symb_v1.0.0.fasta.dammit.fastaMcav transcriptome assembly filtered annotatedTranscripts classified as Montastrea cavernosa following holobiont transcriptome assembly with Trinity/BinPacker/Tranfuse, BLAST-filtering, and annotation with Dammit.Montastrea_v1.0.2.fasta.dammit.fastaSymbiodinium transcript annotations GFF3Annotation results for Symbiodinium transcripts output by DammitSymb_v1.0.0.fasta.dammit.gff3Microbial transcript annotation GFF3Annotation results for microbial transcripts output by Dammitmetatranscriptome.fasta.dammit.gff3Montastrea cavernosa transcript annotations GFF3Annotation results for coral transcripts output by DammitMontastrea_v1.0.2.fasta.dammit.gff3.txt
DOI: 10.5061/dryad.c50hm00
title: Data from: Step-wise evolution of complex chemical defenses in millipedes: a phylogenomic approach

description: With fossil representatives from the Silurian capable of respiring
 atmospheric oxygen, millipedes are among the oldest terrestrial animals,
 and likely the first to acquire diverse and complex chemical defenses
 against predators. Exploring the origin of complex adaptive traits is
 critical for understanding the evolution of Earth’s biological complexity,
 and chemical defense evolution serves as an ideal study system. The
 classic explanation for the evolution of complexity is by gradual increase
 from simple to complex, passing through intermediate “stepping stone”
 states. Here we present the first phylogenetic-based study of the
 evolution of complex chemical defenses in millipedes by generating the
 largest genomic-based phylogenetic dataset ever assembled for the group.
 Our phylogenomic results demonstrate that chemical complexity shows a
 clear pattern of escalation through time. New pathways are added in a
 stepwise pattern, leading to greater chemical complexity, independently in
 a number of derived lineages. This complexity gradually increased through
 time, leading to the advent of three distantly related chemically complex
 evolutionary lineages, each uniquely characteristic of each of the
 respective millipede groups.
description: Transcriptome
 assembliesAssemblies for
 transcriptomes generated by this study and sra files downloaded from
 NCBIfastas.zip
DOI: 10.5061/dryad.527pn
title: Data from: Strategies for sustainable management of renewable resources during environmental change

description: As a consequence of global environmental change, management strategies
 that can deal with unexpected change in resource dynamics are becoming
 increasingly important. In this paper we undertake a novel approach to
 studying resource growth problems using a computational form of adaptive
 management to find optimal strategies for prevalent natural resource
 management dilemmas. We scrutinize adaptive management, or
 learning-by-doing, to better understand how to simultaneously manage and
 learn about a system when its dynamics are unknown. We study important
 trade-offs in decision-making with respect to choosing optimal actions
 (harvest efforts) for sustainable management during change. This is
 operationalized through an artificially intelligent model where we analyze
 how different trends and fluctuations in growth rates of a renewable
 resource affect the performance of different management strategies. Our
 results show that the optimal strategy for managing resources with
 declining growth is capable of managing resources with fluctuating or
 increasing growth at a negligible cost, creating in a management strategy
 that is both efficient and robust towards future unknown changes. To
 obtain this strategy, adaptive management should strive for: high learning
 rates to new knowledge, high valuation of future outcomes and modest
 exploration around what is perceived as the optimal action.
description: Source code
 filesSource code of the
 Agent, Files for running the agent simulations, and analyzing the
 data.SourceCode_LindkvistEtAl.zipSimulation data filesThe simulated data used in the paperSimulationData_LindkvistEtAl.zip
DOI: 10.5061/dryad.7368cc2
title: Data from: QuLinePlus: extending plant breeding strategy and genetic model simulation to cross-pollinated populations – case studies in forage breeding

description: Plant breeders are supported by a range of tools that assist them to make
 decisions about the conduct or design of plant breeding programs.
 Simulations are a strategic tool that enable the breeder to integrate the
 multiple components of a breeding program into a number of proposed
 scenarios that are compared by a range of statistics measuring the
 efficiency of the proposed systems. A simulation study for the trait
 growth score compared two major strategies for breeding forage species,
 among half-sib family selection and among and within half-sib family
 selection. These scenarios highlighted new features of the QuLine program,
 now called QuLinePlus, incorporated to enable the software platform to be
 used to simulate breeding programs for cross pollinated species. Each
 strategy was compared across three levels of HS family mean heritability
 (0.1, 0.5 and 0.9), across three sizes of the initial parental population
 (10, 50, and 100), and across three genetic effects models (fully additive
 model, a mixture of additive, partial and over dominance model, and a
 mixture of partial dominance and over dominance model). Among and within
 half-sib selection performed better than among half-sib selection for all
 scenarios. The new tools introduced into QuLinePlus should serve to
 accurately compare among methods and provide direction on how to achieve
 specific goals in the improvement of plant breeding programs for cross
 breeding species.
description: HDY-18-A0216RRSimulation results files and data input files to replicate simulation experiments in QuLinePlus.
DOI: 10.5061/dryad.2p1t8
title: Data from: 18S rRNA V9 metabarcoding for diet characterization: a critical evaluation with two sympatric zooplanktivorous fish species

description: The potential of the 18S rRNA V9 metabarcoding approach for diet
 assessment was explored using MiSeq paired-end (PE; 2 × 150 bp)
 technology. To critically evaluate the method′s performance with
 degraded/digested DNA, the diets of two zooplanktivorous fish species from
 the Bay of Biscay, European sardine (Sardina pilchardus) and European
 sprat (Sprattus sprattus), were analysed. The taxonomic resolution and
 quantitative potential of the 18S V9 metabarcoding was first assessed both
 in silico and with mock and field plankton samples. Our method was capable
 of discriminating species within the reference database in a reliable way
 providing there was at least one variable position in the 18S V9 region.
 Furthermore, it successfully discriminated diet between both fish species,
 including habitat and diel differences among sardines, overcoming some of
 the limitations of traditional visual-based diet analysis methods. The
 high sensitivity and semi-quantitative nature of the 18S V9 metabarcoding
 approach was supported by both visual microscopy and qPCR-based results.
 This molecular approach provides an alternative cost and time effective
 tool for food-web analysis.
description: Metabarcoding samples
 details (mapping file)Metabarcoding samples´
 details including library tags and sample
 correspondence.MAPPING_FILE_ALBAINAETAL2016.xlsxFASTA file (metabarcoding data; zipped)Metabarcoding data (quality filtered chimera-free merged reads) from the two MiSeq runs needed to generate the paper dataset.ALL_filtered_seqs.zip
DOI: 10.5061/dryad.2qd07
title: Data from: New findings in a 400 million-year-old Devonian placoderm shed light on jaw structure and function in basal gnathostomes

description: Arthodire placoderms have been proposed as the sister group of Chinese
 ‘maxillate’ placoderms plus all the more crownward gnathostomes. These
 basal groups provide key information for understanding the early evolution
 of jaws. Here, we test previous assumptions about placoderm jaw structure
 and function by using high-resolution computed tomography, digital
 dissection, and enlarged 3D printouts on a unique articulated 400
 million-year-old buchanosteid arthrodire. The upper jaw has a double
 ethmoid and a palatobasal connection, but no otic connection; the dermal
 bone attachment for the quadrate is different to other placoderms. A
 separately ossified cartilage behind the mandibular joint is comparable to
 the interhyal of osteichthyans. Two articular facets on the braincase
 associated with the hyomandibular nerve foramen supported a possible
 epihyal element and a separate opercular cartilage. Reassembling and
 manipulating 3D printouts demonstrates the limits of jaw kenetics. The new
 evidence indicates unrecognized similarities in jaw structure between
 arthrodires and osteichthyans, and will help to clarify the sequence of
 character acquisition in the evolution of basal gnathostome groups. New
 details on the hyoid arch will help to reformulate characters that are key
 in the heated debate of placoderm monophyly or paraphyly.
description: 3D model of anterior
 supragnathalASG.ply3D model of infragnathalIG.ply3D model of Meckel's cartilageMk.ply3D model of suborbital plateSO.plyPSG_LG movieMovie, ANU 244, rotation of the in situ posterior supragnathal and infragnathal
DOI: 10.5061/dryad.00731
title: Data from: Membrane proteins are dramatically less conserved than water-soluble proteins across the tree of life

description: Membrane proteins are crucial in transport, signaling, bioenergetics,
 catalysis, and as drug targets. Here we show that membrane proteins have
 dramatically fewer detectable orthologs than water-soluble proteins, less
 than half in most species analyzed. This sparse distribution could reflect
 rapid divergence or gene loss. We find that both mechanisms operate.
 First, membrane proteins evolve faster than water-soluble proteins,
 particularly in their exteriorfacing portions. Second, we demonstrate that
 predicted ancestral membrane proteins are preferentially lost compared
 with water-soluble proteins in closely related species of archaea and
 bacteria. These patterns are consistent across the whole tree of life, and
 in each of the three domains of archaea, bacteria, and eukaryotes. Our
 findings point to a fundamental evolutionary principle: membrane proteins
 evolve faster due to stronger adaptive selection in changing environments,
 while cytosolic proteins are under more stringent purifying selection in
 the homeostatic interior of the cell. This effect should be strongest in
 prokaryotes, weaker in unicellular eukaryotes (with intracellular
 membranes), and weakest in multicellular eukaryotes (with extracellular
 homeostasis). We demonstrate that this is indeed the case. Similarly, we
 show that extracellular water-soluble proteins exhibit an even stronger
 pattern of low homology than membrane proteins. These striking differences
 in conservation of membrane proteins versus water-soluble proteins have
 important implications for evolution and medicine.
description: Main results file with
 countsThe file contains counts
 of species of each domain that compose the OG, the membrane-protein and
 signal-peptide classifications, plus evolutionary rates. The first row
 gives a brief description of the values in each column.OG_DomainCounts_MP_SP_dNdS_NeisPis_analysis.csvProtein sequences for the selected orthologs in OMAFor each ortholog group (OG) in OMA, we selected only one ortholog per species. For example, there are dozens of E. coli strains in OMA, so if an OG had multiple E. coli orthologs, we picked only one of these and ignored the others. We did this to avoid oversampling and guarantee a wider phylogenetic distribution. We only kept OGs with orthologs from 3 or more separate clades. That is, if an OG was composed of, say, orthologs from 4 different E. coli strains and 2 from B. subtilis strains, we ignored it, since there were only 2 strains represented in total.oma_OGs_protein_sequences.tar.gz
DOI: 10.5061/dryad.d62p2
title: Data from: Evolution of thorax architecture in ant castes highlights trade-off between flight and ground behaviors

description: The concerted evolution of morphological and behavioral specializations
 has compelling examples in ant castes. Unique to ants is a marked
 divergence between winged queens and wingless workers, but morphological
 specializations for behaviors on the ground have been overlooked. We
 analyzed thorax morphology of queens and workers in species from 21 of the
 25 ant subfamilies. We uncovered unique skeletomuscular modifications in
 workers that presumably increase power and flexibility of head–thorax
 articulation, emphasizing that workers are not simply wingless versions of
 queens. We also identified two distinct types of queens and showed
 repeated evolutionary associations with strategies of colony foundation.
 Solitary founding queens that hunt have a more worker-like thorax. Our
 results reveal that ants invest in the relative size of thorax segments
 according to their tasks. Versatility of head movements allows for better
 manipulation of food and objects, which arguably contributed to the ants’
 ecological and evolutionary success.
description: RAKeller-Figure1_source_data_finalMeasurements of length of the first, second and third thoracic segments, as well as total thoracic lengths, for representative queens and workers of different ant species. Different ratios between body parts are included. Measurements were taken from microscope images.RAKeller-Figure1_source_images-finalSource images of queens and workers from different representative ant species. Each individual is represented by a dorsal view and a profile view.
DOI: 10.5061/dryad.pg0hd0c
title: Data from: WRF 1960-2014 winter season simulations of particulate matter in the Sahel: implications for air quality and respiratory health

description: We use the Weather Research and Forecast model using the GOCART dust
 module (WRF-CHEM) to simulate the particulate matter variations in the
 Sahel during the winter seasons (January-March) of 1960-2014. Two
 simulations are undertaken where the direct aerosol feedback is turned
 off, and only transport is considered and where the direct aerosol
 feedback is turned on. We find that simulated Sahelian PM10 and PM2.5
 concentrations were lower in the 1960s and after 2003, and higher during
 the period between 1988 and 2002. Higher Sahelian PM10 concentrations are
 due to stronger winds between the surface and 925 hPa over the Sahara,
 which transport dust into the Sahel. Negative PM10 concentration anomalies
 are found over the Bodele Depression and associated with weaker 925 wind
 anomalies after 1997 through 2014. Further west, positive PM10
 concentration anomalies are found across the Adrar Plateau in the Sahara
 and responsible for dust transport to the Western Sahel. The North
 Atlantic Oscillation (NAO) is positively correlated to Sahelian dust
 concentrations especially during the periods of 1960-1970 and 1988-2002.
 The temporal/spatial patterns of PM10 concentrations have significant
 respiratory health implications for inhabitants of the Sahel.
description: jfm6014nofeedTime averaged January-february-march monthly 1960-2014 WRF-CHEM data files.janmar6014feedmTime-averaged January-March netcdf file with variables from WRF-CHEM model. Aerosol direct radiation feedback included.sahara_pm10_naoPM10 anomalies for the Sahara and sub-regions around Bodele and Adrar mountains and the NAO index for 1960-2014 JFM.sahel_pm10_naoPM10 anomalies for the Sahel, West, Central and Eastern Sahel regions.