cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.0k2469h8
title: Data from: Contemporary evolution of sea urchin gamete-recognition proteins: experimental evidence of density-dependent gamete performance predicts shifts in allele frequencies over time

description: Species whose reproductive strategies evolved at one density regime might
 be poorly adapted to other regimes. Field and laboratory experiments on
 the sea urchin Strongylocentrotus franciscanus examined the influences of
 the two most common sperm bindin alleles, which differ at two amino acid
 sites, on fertilization success. In the field experiment, the
 Arginine/Glycine (RG) genotype performed best at low densities and the
 Glycine/Arginine (GR) genotype at high densities. In the lab experiment,
 the RG genotype had a higher affinity with available eggs, whereas the GR
 genotype was less likely to induce polyspermy. These sea urchins can reach
 200 years of age. The RG allele dominates in old sea urchins, whereas
 younger sea urchins have near equal RG and GR allele frequencies. A
 latitudinal cline in RG and GR genotypes is consistent with longer
 survival of sea urchins in the north and with predominance of RG genotypes
 in older individuals. The oldest sea urchins were likely conceived at low
 densities, before sea-urchin predators, like sea otters, were
 overharvested and sea urchin densities exploded off the west coast.
 Contemporary evolution of gamete-recognition proteins might allow species
 to adapt to shifts in abundances and reduces the risk of reproductive
 failure in altered populations.
description: Red urchin rapid
 evolution dryad fileData generated from lab
 and field studies. Each spreadsheet represents the data for each analysis
 presented in the paper.
DOI: 10.5061/dryad.3s057
title: Data from: Identification of four novel stu-miR169s and their target genes in Solanum tuberosum and expression profiles response to drought stress

description: Plant microRNAs are important endogenous gene regulators which regulate
 gene expression at post-transcriptional level. Previous studies have
 identified that miR169 family members regulated the NF-YA transcription
 factors which have been implicated in plant development and stress
 responses. At present, reported potato genome sequence data offered an
 opportunity for global insights into the molecular mechanisms of the
 miR169/NF-YA modules in potato. In this work, 4 novel stu-miR169 family
 members were predicted in potato based on potato genome sequence data.
 miRNA target prediction showed that mature stu-miR169 sequences have a
 bite sit on the 5 of StNF-YA genes in potato, and three of them were
 validated by RNA ligase-mediated 5′RACE (5′ RLM-RACE) assay. The result
 from investigation of the expression patterns of mature stu-miR169 and
 their predicted target genes also showed that mature stu-miR169 was
 down-regulated in response to the drought stress. There were some targeted
 StNF-YA genes that exhibited a negative expression pattern with mature
 stu-miR169 during the different periods of drought-treated samples. Taken
 together, the decreased expression of stu-miR169 might drive
 over-expression of NF-YA family members, they are related to resistances
 against drought stress.
description: Alignment of potato,
 tomato and Arabidopsis NF-YA genesAlignment used to
 produce phylogenies of the full-length amino acid sequences of all known
 potato, tomato and Arabidopsis NF-YA genes.NF-YA.aln
DOI: 10.5061/dryad.m0420
title: Data from: Isolation by resistance across a complex coral reef seascape

description: A detailed understanding of the genetic structure of populations and an
 accurate interpretation of processes driving contemporary patterns of gene
 flow are fundamental to successful spatial conservation management. The
 field of seascape genetics seeks to incorporate environmental variables
 and processes into analyses of population genetic data to improve our
 understanding of forces driving genetic divergence in the marine
 environment. Information about barriers to gene flow (such as ocean
 currents) is used to define a resistance surface to predict the spatial
 genetic structure of populations and explain deviations from the widely
 applied isolation-by-distance model. The majority of seascape approaches
 to date have been applied to linear coastal systems or at large spatial
 scales (more than 250 km), with very few applied to complex systems at
 regional spatial scales (less than 100 km). Here, we apply a seascape
 genetics approach to a peripheral population of the broadcast-spawning
 coral Acropora spicifera across the Houtman Abrolhos Islands, a
 high-latitude complex coral reef system off the central coast of Western
 Australia. We coupled population genetic data from a panel of
 microsatellite DNA markers with a biophysical dispersal model to test
 whether oceanographic processes could explain patterns of genetic
 divergence. We identified significant variation in allele frequencies over
 distances of less than 10 km, with significant differentiation occurring
 between adjacent sites but not between the most geographically distant
 ones. Recruitment probabilities between sites based on simulated larval
 dispersal were projected into a measure of resistance to connectivity that
 was significantly correlated with patterns of genetic divergence,
 demonstrating that patterns of spatial genetic structure are a function of
 restrictions to gene flow imposed by oceanographic currents. This study
 advances our understanding of the role of larval dispersal on the
 fine-scale genetic structure of coral populations across a complex island
 system and applies a methodological framework that can be tailored to suit
 a variety of marine organisms with a range of life-history
 characteristics.
description: Microsatellit genotypes
 RSPBScript for all analyses
 conducted in R. This includes migration matrices, forward projected
 matrices, and subsampling codeSeascape R
 Script.R
DOI: 10.5061/dryad.sb20c
title: Data from: Range-wide snow leopard phylogeography supports three subspecies

description: The snow leopard, Panthera uncia, is an elusive high-altitude specialist
 that inhabits vast, inaccessible habitat across Asia. We conducted the
 first range-wide genetic assessment of snow leopards based on noninvasive
 scat surveys. Thirty-three microsatellites were genotyped and a total of
 683-bp of mitochondrial DNA sequenced in 70 individuals. Snow leopards
 exhibited low genetic diversity at microsatellites (AN = 5.8, HO = 0.433,
 HE = 0.568), virtually no mtDNA variation, and underwent a bottleneck in
 the Holocene (~8,000 years ago) coinciding with increased temperatures,
 precipitation, and upward treeline shift in the Tibetan Plateau. Multiple
 analyses supported three primary genetic clusters: (1) Northern (the Altai
 region), (2) Central (core Himalaya and Tibetan Plateau), and (3) Western
 (Tian Shan, Pamir, trans-Himalaya regions). Accordingly, we recognize
 three subspecies, P. u. irbis (Northern group), P. u. uncia (Western
 group), and P. u. uncioides (Central group) based upon genetic
 distinctness, low levels of admixture, unambiguous population assignment,
 and geographic separation. The patterns of variation were consistent with
 desert-basin "barrier effects" of the Gobi isolating the
 northern subspecies (Mongolia), and the trans-Himalaya dividing the
 central (Qinghai, Tibet, Bhutan, and Nepal) and western subspecies (India,
 Pakistan, Tajikistan, and Kyrgyzstan). Hierarchical Bayesian clustering
 analysis revealed additional subdivision into a minimum of six proposed
 management units: western Mongolia, southern Mongolia, Tian Shan,
 Pamir-Himalaya, Tibet-Himalaya, and Qinghai, with spatial autocorrelation
 suggesting potential connectivity by dispersing individuals up to ~ 400
 km. We provide a foundation for global conservation of snow leopard
 subspecies, and set the stage for in-depth landscape genetics and genomic
 studies.
description: microsatellite data set,
 mainRange-wide snow leopard
 individuals from wild populations sampled noninvasively and genotyped at
 33 microsatellite lociPhyloUncia
 Loci33n70Pop3.xlsxReduced 6 microsatellite
 matrixReduced data set with 6
 microsatellite loci and 26 additional samples genotyped from
 LadakhAssign_UnciaLoci6n101pop3-final.xlsx
DOI: 10.5061/dryad.mp7v3
title: Data from: Auditory traits of "own voice"

description: People perceive their recorded voice differently from their actively
 spoken voice. The uncanny valley theory proposes that as an object
 approaches humanlike characteristics, there is an increase in the sense of
 familiarity; however, eventually a point is reached where the object
 becomes strangely similar and makes us feel uneasy. The feeling of
 discomfort experienced when people hear their recorded voice may
 correspond to the floor of the proposed uncanny valley. To overcome the
 feeling of eeriness of own-voice recordings, previous studies have
 suggested equalization of the recorded voice with various types of
 filters, such as step, bandpass, and low-pass, yet the effectiveness of
 these filters has not been evaluated. To address this, the aim of
 experiment 1 was to identify what type of voice recording was the most
 representative of one's own voice. The voice recordings were
 presented in five different conditions: unadjusted recorded voice, step
 filtered voice, bandpass filtered voice, low-pass filtered voice, and a
 voice for which the participants freely adjusted the parameters. We found
 large individual differences in the most representative own-voice filter.
 In order to consider roles of sense of agency, experiment 2 investigated
 if lip-synching would influence the rating of own voice. The result
 suggested lip-synching did not affect own voice ratings. In experiment 3,
 based on the assumption that the voices used in previous experiments
 corresponded to continuous representations of non-own voice to own voice,
 the existence of an uncanny valley was examined. Familiarity, eeriness,
 and the sense of own voice were rated. The result did not support the
 existence of an uncanny valley. Taken together, the experiments led us to
 the following conclusions: there is no general filter that can represent
 own voice for everyone, sense of agency has no effect on own voice rating,
 and the uncanny valley does not exist for own voice, specifically.
description: Own Voice Experiment
 dataEach worksheet
 corresponds to each experiment.Kimura_own_data.xlsx
DOI: 10.5061/dryad.7fv08k72
title: Data from: A new Bayesian method for fitting evolutionary models to comparative data with intraspecific variation

description: Phylogenetic comparative methods that incorporate intraspecific
 variability are relatively new and, so far, not especially widely used in
 empirical studies. In the present short article we will describe a new
 Bayesian method for fitting evolutionary models to comparative data that
 incorporates intraspecific variability. This method differs from an
 existing likelihood-based approach in that it requires no a priori
 inference about species means and variances; rather it takes phenotypic
 values from individuals and a phylogenetic tree as input, and then samples
 species means and variances, along with the parameters of the evolutionary
 model, from their joint posterior probability distribution. One of the
 most novel and intriguing attributes of this approach is that jointly
 sampling the species means with the evolutionary model parameters means
 that the model and tree can influence our estimates of species mean trait
 values, not just the reverse. In the present implementation we first apply
 this method to the most widely used evolutionary model for continuously
 valued phenotypic trait data (Brownian motion). However the general
 approach has broad applicability, which we illustrate by also fitting the
 λ model, another simple model for quantitative trait evolution on a
 phylogeny. We test our approach via simulation and by analyzing two
 empirical datasets obtained from the literature. Finally, we have
 implemented the methods described herein in a new function for the R
 statistical computing environment, and this function will be distributed
 as part of the ‘phytools’ R library.
description: Cyprinid_treeTree file used for analysis of empirical data. Tree is from Hulsey and Hollingsworth (2011; Biol. J. Linn. Soc. 103: 136-146).cyprinid_morphometric_dataMorphological data for cyprinid minnows used in empirical data analysis. Data from Hulsey and Hollingsworth (2011; Biol. J. Linn. Soc 103: 136-146).
DOI: 10.15468/dl.fpv6p9
title: Occurrence Download

description: A dataset containing 72449 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Gambusia holbrooki, Pseudophryne guentheri, Chenonetta jubata, Gallinula tenebrosa, Craspedacusta sowerbii, Plumatella rugosa)",
 "StateProvince is Western Australia",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Occurrence evidence, Material sample, Human Observation, Specimen, Machine Observation, Observation)"
 ]
}

 The dataset includes 72449 records from 40 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001050-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.8rg375s
title: Data from: Differential temporal beta-diversity patterns of native and non-native arthropod species in a fragmented native forest landscape

description: An important factor that hinders the management of non-native species is a
 general lack of information regarding the biogeography of non-natives,
 and, in particular, their rates of turnover. Here, we address this
 research gap by analysing differences in temporal beta-diversity (using
 both pairwise and multiple-time dissimilarity metrics) between native and
 non-native species, using a novel time-series dataset of arthropods
 sampled in native forest fragments in the Azores. We use a null model
 approach to determine whether temporal beta-diversity was due to
 deterministic processes or stochastic colonisation and extinction events,
 and linear modelling selection to assess the factors driving variation in
 temporal beta-diversity between plots. In accordance with our predictions,
 we found that the temporal beta-diversity was much greater for non-native
 species than for native species, and the null model analyses indicated
 that the turnover of non-native species was due to stochastic events. No
 predictor variables were found to explain the turnover of native or
 non-native species. We attribute the greater turnover of non-native
 species to source-sink processes and the close proximity of anthropogenic
 habitats to the fragmented native forest plots sampled in our study. Thus,
 our findings point to ways in which the study of turnover can be adapted
 for future applications in habitat island systems. The implications of
 this for biodiversity conservation and management are significant. The
 high rate of stochastic turnover of non-native species indicates that
 attempts to simply reduce the populations of non-native species in situ
 within native habitats may not be successful. A more efficient management
 strategy would be to interrupt source-sink dynamics by improving the harsh
 boundaries between native and adjacent anthropogenic habitats.
description: nativeSp_plotDataExcel file where each tab are the presence-absence data of native species for a given plot (nine plots in total). For each plot, the species code (MF) and year of sampling are given.ExoticSp_plotDataExcel file where each tab are the presence-absence data of non-native (Exotic) species for a given plot (nine plots in total). For each plot, the species code (MF) and year of sampling are given.
DOI: 10.5061/dryad.dm133
title: Data from: Triggerfish uses chromaticity and lightness for object segregation

description: Humans group components of visual patterns according to their colour, and
 perceive colours separately from shape. This property of human visual
 perception is the basis behind the Ishihara test for colour deficiency,
 where an observer is asked to detect a pattern made up of dots of similar
 colour with variable lightness against a background of dots made from
 different colour(s) and lightness. To find out if fish use colour for
 object segregation in a similar manner to humans, we used stimuli inspired
 by the Ishihara test. Triggerfish (Rhinecanthus aculeatus) were trained to
 detect a cross constructed from similarly coloured dots against various
 backgrounds. Fish detected this cross even when it was camouflaged using
 either achromatic or chromatic noise, but fish relied more on chromatic
 cues for shape segregation. It remains unknown whether fish may switch to
 rely primarily on achromatic cues in scenarios where target objects have
 higher achromatic contrast and lower chromatic contrast. Fish were also
 able to generalize between stimuli of different colours, suggesting that
 colour and shape are processed by fish independently.
description: Fish_choice_data_updatedRecorded fish choice data.
DOI: 10.5061/dryad.g615h
title: Data from: Hybridization following population collapse in a critically endangered antelope

description: Population declines may promote interspecific hybridization due to the
 shortage of conspecific mates (Hubb’s ‘desperation’ hypothesis), thus
 greatly increasing the risk of species extinction. Yet, confirming this
 process in the wild has proved elusive. Here we combine camera-trapping
 and molecular surveys over seven years to document demographic processes
 associated with introgressive hybridization between the critically
 endangered giant sable antelope (Hippotragus niger variani), and the
 naturally sympatric roan antelope (H. equinus). Hybrids with intermediate
 phenotypes, including backcrosses with roan, were confirmed in one of the
 two remnant giant sable populations. Hybridization followed population
 depletion of both species due to severe wartime poaching. In the absence
 of mature sable males, a mixed herd of sable females and hybrids formed
 and grew progressively over time. To prevent further hybridization and
 recover this small population, all sable females were confined to a large
 enclosure, to which sables from the other remnant population were
 translocated. Given the large scale declines in many animal populations,
 hybridization and introgression associated with the scarcity of
 conspecific mates may be an increasing cause of biodiversity conservation
 concern. In these circumstances, the early detection of hybrids should be
 a priority in the conservation management of small populations.
description: VazPinto_etal-ScientificReportsThe data file contains genotypes scored at 51 microsatellites for 57 sable and 24 roan individuals analysed together with the nine hybrids described in this work.
DOI: 10.5061/dryad.5gh7n
title: Data from: Bibliography of studies on hybrid zones of the common shrew chromosome races distributed in Russia

description: The common shrew, Sorex araneus Linnaeus, 1758, has become a model species
 for cytogenetic and evolutionary studies after discovery of extraordinary
 Robertsonian polymorphism at the within-species level. Development of
 differential staining techniques (Q-, R-and G-banding) made it possible to
 identify the chromosomal arms and their combination in racial karyotypes.
 Entering into contact with each other, the chromosomal races might form
 hybrid zones which represent a great interest for understanding of the
 process of speciation. Until recently all known hybrid zones of S. araneus
 were localized in Western Europe and only one was identified in Siberia
 (Russia) between Novosibirsk and Tomsk races (Aniskin and Lukianova 1989,
 Searle and Wójcik 1998, Polyakov et al. 2011). However, a rapidly growing
 number of reports on discovery of interracial hybrid zones of Sorex
 araneus in the European part of Russia and neighboring territories
 appeared lately. The aim of the present work is to compile the
 bibliography of all studies covering this topic regardless of the original
 language and the publishing source which hopefully could make research
 data more accessible to international scientists. It could also be a
 productive way to save current history of Sorex araneus researches in full
 context of the ISACC (International Sorex araneus Cytogenetics Committee)
 heritage (Searle et al. 2007, Zima 2008).
description: Index of interracial
 hybrid zones of Sorex araneus in RussiaIndex.docBibliographic List
DOI: 10.5061/dryad.177hn10
title: Data from: Apex predator suppression is linked to restructuring of ecosystems via multiple ecological pathways

description: Removal of apex predators can drive ecological regime shifts owing to
 compensatory positive and negative population level responses by organisms
 at lower trophic levels. Despite evidence that apex predators can
 influence ecosystems though multiple ecological pathways, most studies
 investigating apex predators’ effects on ecosystems have considered just
 one pathway in isolation. Here, we provide evidence that lethal control of
 an apex predator, the dingo (Canis dingo), drives shifts in the structure
 of Australia’s tropical-savannah ecosystems. We compared mammal
 assemblages and understorey structure at seven paired-sites. Each site
 comprised an area where people poisoned dingoes and an area without dingo
 control. The effects of dingo control on mammals scaled with body size.
 Where dingoes were poisoned, we found greater activity of herbivorous
 macropods and feral cats, a mesopredator, but sparser understorey
 vegetation and lower abundances of native rodents. Our study suggests that
 ecological cascades arising from apex predators’ suppressive effects on
 herbivores and mesopredators occur simultaneously. Concordant effects of
 dingo removal across tropical-savannah, forest and desert biomes suggest
 that dingoes once exerted ubiquitous top-down effects across Australia and
 provides support for calls that top-down forcing should be considered a
 fundamental process governing ecosystem structure.
description: DATA_SEMRaw data used for the structural equation modelling and graphsDATA_MetanalysisData used to create Meta-analysis graphs and supplementary tables