cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.n8s6t
title: Data from: Antennal lobe organization and pheromone usage in bombycid moths

description: We investigated the neuroanatomy of the macroglomerular complex, which is
 dedicated for sex pheromone processing, in five species belonging to the
 subfamily Bombycinae, Ernolatia moorei, Trilocha varians, Rondotia
 menciana, Bombyx mandarina, and Bombyx mori. The glomerulus located at the
 dorsal-most part of the olfactory center shows the largest volume in most
 of the moth species studied thus far. Such normal glomerular organization
 has been observed in E. moorei and T. varians, which use a two-component
 mixture, including the compound bombykal as a mating signal. On the other
 hand, the other three species, which use another component as a single
 attractant, exhibit a modified arrangement of the macroglomerular complex.
 This correlation between pheromone usage and neural organization might be
 helpful for understanding speciation.
description: Bombyx_mandarinaConfocal microscopic image of the antennal lobe in the brain of male Bombyx mandarinaBombyx_moriConfocal microscopic image of the antennal lobe in the brain of male Bombyx moriErnolatia_mooreiConfocal microscopic image of the antennal lobe in the brain of male Ernolatia mooreiRondotia_mencianaConfocal microscopic image of the antennal lobe in the brain of male Rondotia mencianaTrilocha_variansConfocal microscopic image of the antennal lobe in the brain of male Trilocha varians
DOI: 10.5061/dryad.804j3
title: Data from: A reduced-dimensionality approach to uncovering dyadic modes of body motion in conversations

description: Face-to-face conversations are central to human communication and a
 fascinating example of joint action. Beyond verbal content, one of the
 primary ways in which information is conveyed in conversations is body
 language. Body motion in natural conversations has been difficult to study
 precisely due to the large number of coordinates at play. There is need
 for fresh approaches to analyze and understand the data, in order to ask
 whether dyads show basic building blocks of coupled motion. Here we
 present a method for analyzing body motion during joint action using
 depth-sensing cameras, and use it to analyze a sample of scientific
 conversations. Our method consists of three steps: defining modes of body
 motion of individual participants, defining dyadic modes made of
 combinations of these individual modes, and lastly defining motion motifs
 as dyadic modes that occur significantly more often than expected given
 the single-person motion statistics. As a proof-of-concept, we analyze the
 motion of 12 dyads of scientists measured using two Microsoft Kinect
 cameras. In our sample, we find that out of many possible modes, only two
 were motion motifs: synchronized parallel torso motion in which the
 participants swayed from side to side in sync, and still segments where
 neither person moved. We find evidence of dyad individuality in the use of
 motion modes. For a randomly selected subset of 5 dyads, this
 individuality was maintained for at least 6 months. The present approach
 to simplify complex motion data and to define motion motifs may be used to
 understand other joint tasks and interactions. The analysis tools
 developed here and the motion dataset are publicly available.
description: Timeseries of joints
 positions of participantsTracked positions of 25
 skeletal joints of 12 dyads (24 participants) who were recorded during
 scientific conversations. All participants had at least three consecutive
 rounds of conversation on their primary session. Five dyads participated
 in an additional round conducted six months after the primary session.
 Rounds ranged up to 15min each. Data in each file corresponds to a
 specific dyad, round, and participant. The data is synchronized both in
 time and space. Namely, data points of a specific dyad are synchronized in
 their timestamps (between participants, but also across rounds 1-3) and
 share a global spatial coordinate system.body_movement_rawdata_0.01.rar
DOI: 10.5061/dryad.4f99c46
title: Data from: Bats enhance their call identities to solve the cocktail party problem

description: Echolocating bats need to solve the problem of signal jamming by
 conspecifics when they are in a group. However, while several mechanisms
 have been suggested, it remains unclear how bats avoid confusion between
 their own echoes and interfering sounds in a complex acoustic environment.
 Here, we fixed on-board microphones onto individual frequency-modulating
 bats flying in groups. We found that group members broaden the
 inter-individual differences in the terminal frequencies of pulses,
 thereby decreasing the similarity of pulses among individuals. To
 understand what features most affect similarity between pulses, we
 calculated the similarity of signals mimicking pulses. We found that the
 similarity between those artificial signals was decreased most by
 manipulation of terminal frequency. These results demonstrate that the
 signal jamming problem is solved by this simple strategy, which may be
 universally used by animals that use active sensing, such as echolocating
 bats and electric fish, thereby transcending species and sensory
 modalities.
description: SoundFileSound files (number of channels = 1; data length = 10 seconds) of echolocation pulses recorded with microphones mounted directly on bats flying alone or in groups of four individuals. The data were digitized using a high-speed data-acquisition card (National Instruments, Model NI PXI-6358, Tokyo, Japan, 16 bit, fs = 500 kHz). File names are as below. "batID"_"flight condition".bin
DOI: 10.5061/dryad.9pg8d
title: Data from: Replicated divergence in cichlid radiations mirrors a major vertebrate innovation

description: Decoupling of the upper jaw bones—jaw kinesis—is a distinctive feature of
 the ray-finned fishes, but it is not clear how the innovation is related
 to the extraordinary diversity of feeding behaviours and feeding ecology
 in this group. We address this issue in a lineage of ray-finned fishes
 that is well known for its ecological and functional diversity—African
 rift lake cichlids. We sequenced ultraconserved elements to generate a
 phylogenomic tree of the Lake Tanganyika and Lake Malawi cichlid
 radiations. We filmed a diverse array of over 50 cichlid species capturing
 live prey and quantified the extent of jaw kinesis in the premaxillary and
 maxillary bones. Our combination of phylogenomic and kinematic data
 reveals a strong association between biting modes of feeding and reduced
 jaw kinesis, suggesting that the contrasting demands of biting and suction
 feeding have strongly influenced cranial evolution in both cichlid
 radiations.
description: SRA-files.xlsxAccession numbers for raw-reads in NCBI SRA.trinity-assemblies-for-dryad.tar.gzDe novo Trinity (trinityrnaseq_r2013-02-25) assemblies of raw-reads for all individuals included in study.outgroup-data.tar.gzOutgroup data included in analysis from genome-enabled cichlids.11-20-2014-malfaro-cichlids-taxa.confConfiguration file used with PHYLUCE for taxon-set extraction.skull-mobility-contig-and-alignment-data.tar.gzUCE contigs, alignments, trimmed alignments, coverage information, and configuration and log files used in all phylogenetic analyses.mafft-gblocks-clean-95p-complete-raxml.tar.gzPartition-finder and RAxML input/output files for ML analysis of the 95 % complete data set.mafft-gblocks-clean-95p-complete-EXABAYES.tar.gzExaBayes output files for Bayesian analysis of the 95 % complete data set.mafft-gblocks-clean-75p-complete-raxml.tar.gzPartition-finder and RAxML input/output files for ML analysis of the 75 % complete data set.mafft-gblocks-clean-75p-complete-EXABAYES.tar.gzExaBayes output files for Bayesian analysis of the 75 % complete data set.phylogenetic-analysis-steps.txtSteps used during the phylogenetic analysis. All used the PHYLUCE software package (available from: https://github.com/faircloth-lab/phyluce).analysis-steps.txtfish-uce-1k-probes.fasta.gzFasta file detailing probes targeting UCEs in Acanthomorphs.all-tre-files.tar.gzAn archive of all trees generated for the manuscript text in Newick format.
DOI: 10.5061/dryad.4gm03
title: Data from: Ecological speciation in sympatric palms: 1. Gene expression, selection and pleiotropy

description: Ecological speciation requires divergent selection, reproductive
 isolation, and a genetic mechanism to link the two. We examined the role
 of gene expression and coding sequence evolution in this process using two
 species of Howea palms that have diverged sympatrically on Lord Howe
 Island, Australia. These palms are associated with distinct soil types and
 have displaced flowering times, representing an ideal candidate for
 ecological speciation. We generated large amounts of RNA-Seq data from
 multiple individuals and tissue types collected on the island from each of
 the two species. We found that differentially expressed loci as well as
 those with divergent coding sequences between Howea species were
 associated with known ecological and phenotypic differences, including
 response to salinity, drought, pH and flowering time. From these loci we
 identified potential ‘ecological speciation genes’, and further validate
 their effect on flowering time by knocking out orthologous loci in a model
 plant species. Finally, we put forward six plausible ecological speciation
 loci, providing support for the hypothesis that pleiotropy could help to
 overcome the antagonism between selection and recombination during
 speciation with gene flow.
description: Howea_forsteriana_Trinity_transcriptomeTable_S1 - Sample statsTable_S1 - Sample statsTable_S5 - Transcriptome statsTable_S5 - Transcriptome stats
DOI: 10.5061/dryad.713v1
title: Data from: Population genomic footprints of fine-scale differentiation between habitats in Mediterranean blue tits

description: Linking population genetic variation to the spatial heterogeneity of the
 environment is of fundamental interest to evolutionary biology and
 ecology, in particular when phenotypic differences between populations are
 observed at biologically small spatial scales. Here, we applied
 restriction-site associated DNA sequencing (RAD-Seq) to test whether
 phenotypically differentiated populations of wild blue tits (Cyanistes
 caeruleus) breeding in a highly heterogeneous environment exhibit genetic
 structure related to habitat type. Using 12106 SNPs in 197 individuals
 from deciduous and evergreen oak woodlands, we applied complementary
 population genomic analyses, which revealed that genetic variation is
 influenced by both geographical distance and habitat type. A fine-scale
 genetic differentiation supported by genome- and transcriptome-wide
 analyses was found within Corsica, between two adjacent habitats where
 blue tits exhibit marked differences in breeding time while nesting less
 than 6 km apart. Using redundancy analysis (RDA), we show that genomic
 variation remains associated with habitat type when controlling for
 spatial and temporal effects. Finally, our results suggest that the
 observed patterns of genomic differentiation were not driven by a small
 proportion of highly differentiated loci, but rather emerged through a
 process such as habitat choice, which reduces gene flow between habitats
 across the entire genome. The pattern of genomic isolation-by-environment
 closely matches differentiation observed at the phenotypic level, thereby
 offering significant potential for future inference of phenotype-genotype
 associations in a heterogeneous environment.
description: Szulkin_Blue_Tit_working_dataset_MAF0.02_callrate0.9The filtered VCF file containing 12K SNPs from Continental and Corsican populations of Mediterranean blue tit. The 12K SNP VCF file can be filtered further to subsets of individuals where no family ties are present, or that contribute to the symmetrical minimal dataset (more info about these datasets can be found in the Materials & Methods section and in Supplementary Information files).szulkin_blue_tit_sample_detailsAn excel spreadsheet providing further details regarding each sequenced bird (GPS coordinates, information on birth year, population of origin, nestbox of first reproduction, nestbox coordinates and nr of reads obtained for each individual). The relationships between the different nested datasets are also provided and can be used to generate 6K and 3K datasets.List_19760_Consensus_RAD_Stacks_1_80Full list of consensus RAD tag sequences (in fasta format) that were used for blast annotations.Szulkin_Blue_Tit_raw_unfiltered_209K_SNPs_from_Stacks_maf1The raw VCF file generated with Stacks, containing 209K SNPs with a global minor allele frequency of at least 0.01. This dataset was then filtered based on quality and population genetic criteria in vcftools to produce the working dataset conatining 12 SNPs.
DOI: 10.5061/dryad.4r4j835
title: Data from: Genome sequence and population declines in the critically endangered greater bamboo lemur (Prolemur simus) and implications for conservation

description: Background: The greater bamboo lemur (Prolemur simus) is a member of the
 Family Lemuridae that is unique in their dependency on bamboo as a primary
 food source. This Critically Endangered species lives in small forest
 patches in eastern Madagascar, occupying a fraction of its historical
 range. Here we sequence the genome of the greater bamboo lemur for the
 first time, and provide genome resources for future studies of this
 species that can be applied across its distribution. Results: Following
 whole genome sequencing of five individuals we identified over 152,000
 polymorphic single nucleotide variants (SNVs), and evaluated geographic
 structuring across nearly 19k SNVs. We characterized a stronger signal
 associated with a north-south divide than across elevations for our
 limited samples. We also evaluated the demographic history of this
 species, and infer a dramatic population crash. This species had the
 largest effective population size (estimated between ~900,000 to one
 million individuals) between approximately 60,000-90,000 years before
 present (ybp), during a time in which global climate change affected
 terrestrial mammals worldwide. We also note the single sample from the
 northern portion of the extant range had the largest effective population
 size around 35,000 ybp. Conclusions: From our whole genome sequencing we
 recovered an average genomic heterozygosity of 0.0037%, comparable to
 other lemurs. Our demographic history reconstructions recovered a probable
 climate-related decline (60-90,000 ybp), followed by a second population
 decrease following human colonization, which has reduced the species to a
 census size of approximately 1,000 individuals. The historical
 distribution was likely a vast portion of Madagascar, minimally estimated
 at 44,259 km2, while the contemporary distribution is only ~1,700 km2. The
 decline in effective population size of 89-99.9% corresponded to a vast
 range retraction. Conservation management of this species is crucial to
 retain genetic diversity across the remaining isolated populations.
description: MAKER Annotation
 KIAN8.4Whole genome annotation
 from the greater bamboo lemur, Prolemur simus, from a wild-caught
 monitored individual.lemur.gff.zip
DOI: 10.5061/dryad.5fj6t
title: Data from: Diet breadth and exploitation of exotic plants shift the core microbiome of Cephaloleia, a group of tropical herbivorous beetles

description: The beetle genus Cephaloleia has evolved in association with tropical
 ginger plants and for many species their specific host plant associations
 are known. Here we show that the core microbiome of six closely related
 Costa Rican Cephaloleia species comprises only eight bacterial groups,
 including members of the Acinetobacter, Enterobacteriacea, Pseudomonas,
 Lactococcus, and Comamonas. The Acinetobacter and Enterobacteriacea
 together accounted for 35% of the total average 16S rRNA ribotypes
 recovered from all specimens. Further, microbiome diversity and community
 structure was significantly linked to beetle diet breadth, between those
 foraging on less than two plant types (specialists) versus over nine plant
 types (generalists). Moraxellaceae, Enterobacteriaceae, and
 Pseudomonadaceae were highly prevalent in specialist species, and also
 present in eggs, while Rickettsiaceae associated exclusively with
 generalist beetles. Bacteria isolated from Cephaloleia digestive systems
 had distinct capabilities and suggested a possible beneficial role in both
 digestion of plant-based compounds, including xylose, mannitol, and
 pectin, and possible detoxification, via lipases. Cephaloleia species are
 currently expanding their diets to include exotic invasive plants, yet it
 is unknown whether their microbial community plays a role in this
 transition. In this study, colonization of invasive plants was correlated
 with a dysbiosis of the microbiome, suggesting a possible relationship
 between gut bacteria and niche adaptation.
description: Cb_egg1Cp1Cp2Cp4Cp3Cp5Cdor_eggCdor3Cdor2Cdil3Cdil2Cf2Cdil1Cf1Cb1Cb3Cb2Cb8Cb7Cb5Cb4Cb_inv4Cdil_egg2Cp_inv1Cp_inv2Cdil_inv2Cdil_inv1Cdil_inv3Cf5Cf3Cf4Cb_egg2Cf6Cf7Cr2Cr3Cr1Cb_inv2Cb_inv1Cb_inv3Cdor1Cdil_egg1beetle_OTU_table_4Dryad
DOI: 10.5061/dryad.hm813
title: Data from: Microsorum × tohieaense (Polypodiaceae), a new hybrid fern from French Polynesia, with implications for the taxonomy of Microsorum

description: A new hybrid microsoroid fern, Microsorum × tohieaense (Microsorum
 commutatum × Microsorum membranifolium) from Moorea, French Polynesia is
 described based on morphology and molecular phylogenetic analysis.
 Microsorum × tohieaense can be distinguished from other French Polynesian
 Microsorum by the combination of sori that are distributed more or less in
 a single line between the costae and margins, apical pinna wider than
 lateral pinnae, and round rhizome scales with entire margins. Genetic
 evidence is also presented for the first time supporting the hybrid origin
 of Microsorum × maximum (Microsorum grossum × Microsorum punctatum), and
 possibly indicating a hybrid origin for the Hawaiian endemic Microsorum
 spectrum. The implications of hybridization for the taxonomy of
 microsoroid ferns are discussed, and a key to the microsoroid ferns of the
 Society Islands is provided.
description: Microsorum_x_tohieaense_BI_postdistThis zip file contains posterior distributions of model parameters and trees produced by MrBayes during phylogenetic analysis for Nitta et al. Microsorum × tohieaense (Polypodiaceae), a new hybrid fern from French Polynesia, with implications for the taxonomy of Microsorum.Microsorum_x_tohieaense_dryad_dataThis is a zipped archive containing data associated with Nitta et al. Microsorum × tohieaense (Polypodiaceae), a new hybrid fern from French Polynesia, with implications for the taxonomy of Microsorum. Please see the README file in each directory for a description of the data. Note that a portion of the data (posterior distributions of model parameters and trees produced during MrBayes runs) has been provided separately due its large size (ca. 2 gb).
DOI: 10.5061/dryad.4ck56
title: Data from: The effect of interaural timing on the posterior auricular muscle reflex in normal adult volunteers

description: The posterior auricular muscle (PAM) reflex to sounds has been used
 clinically to determine hearing threshold as an alternative to other
 audiological diagnostic measures such as the auditory brainstem response.
 We have shown that the PAM response is also sensitive to interaural timing
 differences in normally hearing adults. PAM responses were evoked by both
 ipsilateral/ contralateral monaural stimulation and by binaural
 stimulation. Introducing sound delays ipsilaterally or contralaterally
 decreased the PAM response amplitude and increased its latency. The PAM
 response in this study shows a qualitatively similar pattern to that seen
 by the binaural interaction component (BIC) of the auditory brainstem
 potential to binaural clicks described in previous studies, in that both:
 have their shortest latency and maximal amplitudes centered around zero
 interaural timing differences, have response latencies increase with
 increasing interaural delays up to 1.2 ms and have response amplitudes
 decrease with increasing interaural delays of up to 1.2 ms. Our data show
 that the PAM response may be useful in measuring binaural integration in
 humans non-invasively for diagnostic or research studies.
description: DataSummaryMatlab 2017B .mat data file
DOI: 10.5061/dryad.370rv
title: Data from: Courting disaster: how diversification rate affects fitness under risk

description: Life is full of risk. To deal with this uncertainty, many organisms have
 evolved bet-hedging strategies that spread risk through phenotypic
 diversification. These rates of diversification can vary by orders of
 magnitude in different species. Here we examine how key characteristics of
 risk and organismal ecology affect the fitness consequences of variation
 in diversification rate. We find that rapid diversification is strongly
 favored when the risk faced has a wide spatial extent, with a single
 disaster affecting a large fraction of the population. This advantage is
 especially great in small populations subject to frequent disaster. In
 contrast, when risk is correlated through time, slow diversification is
 favored because it allows adaptive tracking of disasters that tend to
 occur in series. Naturally-evolved diversification mechanisms in diverse
 organisms facing a broad array of environmental risks largely support
 these results. The theory presented in this paper provides a testable
 ecological hypothesis to explain the prevalence of slow stochastic
 switching among microbes and rapid, within-clutch diversification
 strategies among plants and animals.
description: Simulated data, Figure
 1aSimulated data, Figure
 1aSimulated data, Figure
 2aSimulated data, Figure
 2bSimulated data, Figure
 2cSimulated data, Figure
 3Simulated data, Figure
 4Simulated data, Figure
 S2The
 modelSimulated Data, Figure
 1bFig1b.zip