cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.b25r538
title: Tortoises develop and overcome position biases in a reversal learning task

description: The capability of animals to alter their behaviour to novel or familiar
 stimuli, or behavioural flexibility, is strongly associated with their
 ability to learn in novel environments. Reptiles are capable of learning
 complex tasks, and offer a unique opportunity to study the relationship
 between visual proficiency and behavioural flexibility. The focus of this
 study was to investigate the behavioural flexibility of red-footed
 tortoises and their ability to perform reversal learning. Reversal
 learning involves first learning a visual discrimination, after which the
 previously rewarded cue is reversed and then subjects perform the visual
 task with new reward contingencies. Red-footed tortoises were required to
 learn the visual cues within a Y-maze, a complex task that required
 coordination. Once subjects learned the visual discrimination, tortoises
 were required to successfully learn 4 reversals. Compared to acquisition
 learning, tortoises required significantly more trials to reach criterion
 (80% correct) in the first reversal, indicating the difficulty of
 unlearning the positive stimulus initially presented in acquisition.
 Nevertheless, subsequent reversals required similar number of sessions as
 the initial acquisition stage, demonstrating that reversal learning
 improves up to a point. All subjects tested developed a turning bias
 within the Y-maze that was absent prior to the acquisition task, but were
 able to exhibit reversal learning despite this persistent turning bias.
 The results herein demonstrate that red-footed tortoises exhibit
 behavioural flexibility in a learning task requiring coordination between
 visual cues and maze navigation. Improving performance while
 simultaneously overcoming a persistent turning bias provides us greater
 insights into the advanced cognitive abilities of tortoises.
description: Tortoise_Reversal_Learning_Data
DOI: 10.5061/dryad.35cp405
title: Data from: Genetic analyses in Lake Malawi cichlids identify new roles for Fgf signaling in scale shape variation

description: Elasmoid scales are the most common epithelial appendage among
 vertebrates, however an understanding of the genetic mechanisms that
 underlie variation in scale shape is lacking. Using an F2 mapping
 cross between morphologically distinct cichlid species, we identified
 &gt;40 QTL for scale shape at different body positions. We show that
 while certain regions of the genome regulate variation in multiple scales,
 most are specific to scales at distinct positions. This suggests a degree
 of regional modularity in scale development. We also identified a single
 QTL for variation in scale shape disparity across the body. Finally, we
 screened a QTL hotspot for candidate loci, and identified the Fgf
 receptor fgfr1b as a prime target. Quantitative rtPCR
 and small molecule manipulation support a role for Fgf signaling in
 shaping cichlid scales. While Fgfs have previously been implicated in
 scale loss, these data reveal new roles for the pathway in scale shape
 variation.
description: Parental_F2_Residuals_dataraw data for scale shape measures for parental species and a subset of F2 hybrids.LFxTRC_F2_scale_pheno_dataF2 phenotypes for QTL mapping. Genotypic data are under a different DOI.F2_scale1-6raw landmark data for all F2 hybrids in TPS format.LF_TRC_parental_scale1-6raw landmark data for parental scales in TPS format.SU5402_treatmentraw phenotypic data for scales post small molecule treatment.Cichlid_Scale_qPCR_DataqPCR data used to compare scale types between and within species.Parental_F2_sex_SLSex and standard length of fish used in this studyparental_F2scale_numberScale number in the fish used in this study.
DOI: 10.5061/dryad.q563k23
title: Data from: The effect of parasite infection on the recombination rate of the yellow fever mosquito Aedes aegyti

description: Sexual reproduction and meiotic recombination generate new genetic
 combinations and may thereby help an individual infected by a parasite to
 protect its offspring from being infected. While this idea is often used
 to understand the evolutionary forces underlying the maintenance of sex
 and recombination, it also suggests that infected individuals should
 increase plastically their rate of recombination. We tested the latter
 idea with the mosquito Aedes aegypti and asked whether females infected by
 the microsporidian Vavraia culicis were more likely to have recombinant
 offspring than uninfected females. To measure the rate of recombination
 over a chromosome we analysed combinations of microsatellites on
 chromosome 3 in infected and uninfected females, in the (uninfected) males
 they copulated with and in their offspring. As predicted, the infected
 females were more likely to have recombinant offspring than the uninfected
 ones. These results show the ability of a female to diversify her
 offspring in response to parasitic infection by plastically increasing her
 recombination rate.
description: <strong>PlosOne_rec_data.xlsx</strong>
 - Recombination - Columns
 description
 <strong>Plos_microsat.xlsx</strong>
 - Raw data microsatellites
DOI: 10.5061/dryad.7wm37pvnh
title: Data from: Microhabitat complexity influences fear acquisition in fathead minnows

description: Habitat varies in structure, with animals often preferring a certain
 degree of microhabitat complexity that facilitates fitness-related
 activities such as predator avoidance. Environments with high predation
 risk can induce elevated baseline fear and neophobia in prey, but whether
 microhabitat complexity influences the acquisition of neophobia has yet to
 be reported. Here, we tested whether exposure to predation risk induces
 different levels of fear in microhabitats that differed in complexity. We
 exposed fathead minnows, Pimephales promelas, to predation risk repeatedly
 (12 times over 4 days) in the form of damage-released chemical alarm cues
 (compared to a water control) in tanks with vertical plant structure
 distributed either throughout the tank (complex habitat) or clumped
 together (simple habitat). Then, we tested minnows before and after
 exposure to a novel odor in tanks with either the same microhabitat
 complexity (i.e., familiar habitats) or in tanks with novel habitat that
 had different substrate structure but no vertical structure. Minnows in
 the complex habitat showed less overall movement one day after the
 background risk period, whereas individuals in the simple habitat showed
 reduced movement regardless of prior risk exposure. We observed stronger
 effects in the novel habitat, where background risk in both simple and
 complex habitats caused neophobia. However, individuals from the simple
 background habitat showed higher baseline fear behaviors. Hence, for
 minnows, low microhabitat complexity appears to lead to elevated fear
 which remains even after a habitat change.
DOI: 10.5061/dryad.6np02kb
title: Pinopsin evolved as the ancestral dim-light visual opsin in vertebrates

description: Pinopsin is the opsin most closely related to vertebrate visual pigments
 on the phylogenetic tree. This opsin has been discovered among many
 vertebrates, except mammals and teleosts, and was thought to exclusively
 function in their brain for extraocular photoreception. Here, we show the
 possibility that pinopsin also contributes to scotopic vision in some
 vertebrate species. Pinopsin is distributed in the retina of non-teleost
 fishes and frogs, especially in their rod photoreceptor cells, in addition
 to their brain. Moreover, the retinal chromophore of pinopsin exhibits a
 thermal isomerization rate considerably lower than those of cone visual
 pigments, but comparable to that of rhodopsin. Therefore, pinopsin can
 function as a rhodopsin-like visual pigment in the retinas of these lower
 vertebrates. Since pinopsin diversified before the branching of rhodopsin
 on the phylogenetic tree, two-step adaptation to scotopic vision would
 have occurred through the independent acquisition of pinopsin and
 rhodopsin by the vertebrate lineage.
description: TIF files for Figure 2 and Figure S3
DOI: 10.5061/dryad.573n5tb3g
title: When natal dispersal ends: using satellite telemetry to quantify territory settlement in a long-lived raptor

description: Breeding territory settlement, as the end point of natal (juvenile)
 dispersal, is a key juncture in the life history and population dynamics
 of long-lived raptors. It spatially identifies natal dispersal distance
 and temporally identifies first recruitment to a breeding population. Its
 determination can be confused by similar temporary settlement behaviour
 during dispersal or by post-occupation territorial birds’ excursions.
 Satellite telemetry provides potentially for a method to ascertain
 location and date of territory settlement without field observer
 limitations. Prior field-observer estimates are likely biased towards
 older ages. Telemetry has previously ascertained first territory
 settlement, but not via a quantified repeatable measure based solely on
 telemetric records. Our primary goal was to derive analytical rules, via
 an algorithm based on satellite telemetric data to determine when a
 dispersing Golden Eagle Aquila chrysaetos had settled on (occupied) a
 prospective breeding territory, using 83 birds tagged as nestlings in
 Scotland.  Our algorithm derived median record locations during a
 night, also compared median values over a longer time span, and processed
 records to confirm the spatial and temporal stability that was expected
 when a territory was occupied. All 17 birds deemed as algorithmically
 settled were confirmed by visual plot checks. Field work further validated
 territory occupation in all 14 of the 17 territories where field
 observations were possible; confirming egg-laying and chick-rearing in
 some instances. Many tagged birds were not deemed algorithmically to have
 settled on a territory, despite comparable or greater age. As a research
 tool, any current telemetric method is skewed away from older settlement
 ages due to technological lifespans which will hopefully improve. These
 files provide 16 example datasets as shapefiles: eight for birds deemed to
 have settled on a territory and eight deemed not to have settled on a
 territory. Due to required confidentiality on locations of nest sites
 actual coordinates have been geometrically processed to mask their true
 locations but the scaling is unaffected.
DOI: 10.5061/dryad.m8p3q04
title: Data from: Parallel changes in gut microbiome composition and function during colonization, local adaptation and ecological speciation

description: The processes of local adaptation and ecological speciation are often
 strongly shaped by biotic interactions such as competition and predation.
 One of the strongest lines of evidence that biotic interactions drive
 evolution comes from repeated divergence of lineages in association with
 repeated changes in the community of interacting species. Yet, relatively
 little is known about the repeatability of changes in gut microbial
 communities and their role in adaptation and divergence of host
 populations in nature. Here we utilize three cases of rapid, parallel
 adaptation and speciation in freshwater threespine stickleback to test for
 parallel changes in associated gut microbiomes. We find that features of
 the gut microbial communities have shifted repeatedly in the same
 direction in association with parallel divergence and speciation of
 stickleback hosts. These results suggest that changes to gut microbiomes
 can occur rapidly and predictably in conjunction with host evolution, and
 that host-microbe interactions might play an important role in host
 adaptation and diversification.
description: Relative_abundance_of_function
 Relative_abundance_pathogenic_bacteria_families
 StickleMB_ProcB_NMDS_180612
 table.from_biom_nochloro
 Core_microbiome
DOI: 10.5061/dryad.g05g074
title: Data from: A method to generate multi-locus barcodes of pinned insect specimens using MiSeq

description: For molecular insect identification, amplicon sequencing methods are
 recommended because they offer a cost effective approach for targeting
 small sets of informative genes from multiple samples. In this context,
 high-throughput multilocus amplicon sequencing has been achieved using the
 MiSeq Illumina sequencing platform. However, this approach generates short
 gene fragments of less than 500 bp, which then have to be overlapped using
 bioinformatics to achieve longer sequence lengths. This increases the risk
 of generating chimeric sequences or leads to the formation of incomplete
 loci. Here, we propose a modified nested amplicon sequencing method for
 targeting multiple loci from pinned insect specimens using the MiSeq
 Illumina platform. The modification exists in using a three-step nested
 PCR approach targeting near full length loci in the initial PCR and
 subsequently amplifying short fragments between 300 and 350 bp for
 high-throughput sequencing using Illumina chemistry. Using this method, we
 generated 407 barcode-compliant sequences for three loci from 98 of 138
 pinned specimens. This method worked best for pinned specimens aged
 between 0 - 5 years, with a limit of 10 years for pinned and 14 years for
 ethanol preserved specimens. Hence, our method overcomes some of the
 challenges of amplicon sequencing using short read Next Generation
 Sequencing and improves possibilities to create high quality multilocus
 barcodes from insect collections.
description: GenBank blast search
 results for the consensus sequences generated in this study
 Folder contains
 GenBank blast search results for consensus sequences of 3 genes Cytochrome
 Oxidase 1 (5' and 3'), Elongation Factor 1 alpha (2nd copy) and
 Wingless gene. The consensus sequences are named in the format; Species
 name_sample name_number of reads used to assemble the consensus sequence.
 The datasets can be viewed using the Geneious software
 program. 
 NestedAmpliconSeqAnalysis-scripts Scripts for inferring consensus gene sequences of NGS data generated using A novel Nested Amplicon Sequencing Approach. Also deposited in Github under this link; https://github.com/UofABioinformaticsHub  
description: DNA was extracted from legs of pinned and ethanol preserved
 specimens and amplified using a modified nested PCR approach in order to
 allow sequencing on the illumina MiSeq platform. The raw sequence data
 generated was processed using custom scripts and the consesus sequences
 analysed as described in the manuscript including blast searching against
 the GenBank database accessed through the Geneious software program (v
 8.1.3).
DOI: 10.5061/dryad.jt1kt04
title: Data from: Predicting combined effects of land use and climate change on river and stream salinity

description: Agricultural, industrial, and urban development have all contributed to
 increased salinity in streams and rivers, but the likely effects of future
 development and climate change are unknown. I developed two empirical
 models to estimate how these combined effects might affect salinity by the
 end of this century. The first model predicts natural background from
 static (e.g., geology and soils) and dynamic (i.e., climate and
 vegetation) environmental factors and explained 78% of the variation in
 EC. I then compared the estimated background EC to current measurements at
 2001 sites chosen probabilistically from all conterminous US streams. EC
 was more than 50% greater at 34% of these sites. The second model predicts
 deviation of EC from natural background as function of human land use and
 environmental factors and explained 60% of the variation in deviation from
 natural background. I then predicted the effects of climate and land use
 change on EC at end of the century by replacing dynamic variables with
 published projections of future conditions based on the A2 emissions
 scenario. By end of century, the median EC increase 0.319 mS cm-1 to 0.524
 mS cm-1 with over 50% of streams having &gt; 50% increases in EC and
 35% more than doubling their EC. Most of the change is due to development,
 with climate change accounting for less than 10% of the increase. In
 extreme cases, increased salinity may make water unsuitable for human use,
 but widespread moderate increases are likely a greater threat to stream
 ecosystems due to the elimination of low EC habitats.
description: Reference EC
 observations & predictorsSpecific electrical
 conductivity observations and associated predictors for minimal disturbed
 reference sites in the US. See table S1 for sources of data and table 1
 for description of predictors.EC_ClimLU10.csvCurrent EC & Predictors for NRSASpecific electrical conductivity observations and associated current (2008-2010) predictors for the USEPA National Rivers and Stream Assessment (NRSA).WsNRSA_EC_ClimLU.csvFuture NRSA PredictorsFuture (2100) predictors for the USEPA National Rivers and Stream Assessment (NRSA) for predicting future EC.WsNRSA_EC_ClimLU2100.csvNRSA EC predictionsModel predictions of current natural background and future EC.NRSA_PredEC27JUL.csv
DOI: 10.5061/dryad.rd06sn7
title: When more is not merrier: using wild population dynamics to understand the effect of density on ex situ seahorse mating behaviors

description: Seahorses are one of the most iconic examples of a monogamous species in
 the animal kingdom. Documenting monogamous behaviors of seahorses have
 proven to be quite complicated to study in the wild because of their low
 population densities and cryptic habits. Another challenge involves
 interpreting these behaviors in captivity because recreating realistic
 densities of wild populations in the laboratory can be difficult due to
 their patchy distributions. This study investigates the relationship
 between stocking density and mating and competitive behavior from the
 context of the field biology of the dwarf seahorse, Hippocampus zosterae
 (Jordan & Gilbert). Animals were housed in 38 liter tanks at a
 range of densities and sex ratios (from 2-8 animals per tank), and their
 reproductive and other social behaviors were monitored from tank
 introduction through copulation. At low tank densities and even sex ratios
 but comparatively high field densities, activity level in trials was low.
 A higher level of males in tanks across all densities increased
 competition, activity levels, and aggression leading to partial egg
 transfers and failed pregnancies, resulting in lower reproductive success.
 Across seahorse species, mean and maximum wild densities were consistently
 lower than those used in captive breeding, with adult sex ratios that were
 significantly female biased. However, significant variation exists in wild
 seahorse densities across species, with higher densities detected in
 focal/mark recapture studies and on artificial habitat structures than
 reported with belt transect sampling techniques. Interchange of knowledge
 gained in both captive and wild contexts will allow us to better
 understand the biology of this genus, and improve reproduction in
 captivity. Interpreting captive reproductive behaviors of seahorses within
 various densities reported from natural populations will help us predict
 the impact of conservation efforts and increase the likelihood of
 long-term persistence of populations for this threatened genus.
description: Masonjones &
 Rose, behavioral data Paper is both a
 behavioral study and a meta-analysis of existing literature. Attached
 files are for the behavioral component of the study, with the tables in
 the paper providing the data used in the meta-analysis
DOI: 10.5061/dryad.t4j13fm
title: Data from: Critical slowing down associated with critical transition and risk of collapse in cryptocurrency

description: The year 2017 saw the rise and fall of the crypto-currency market,
 followed by high variability in the price of all crypto-currencies. In
 this work, we study the abrupt transition in
 crypto-currency residuals, which
 is associated with the critical transition (the phenomenon of critical slowing down) or the stochastic transition phenomena. We find that, regardless of the specific crypto-currency or rolling window size, the autocorrelation always fluctuates around a high value, while the standard deviation increases monotonically. Therefore, while the autocorrelation does not display signals of critical slowing down, the standard deviation can be used to anticipate critical or stochastic transitions. In particular, we have detected two sudden jumps in the standard deviation, in the second quarter of 2017 and at the beginning of 2018, which could have served as early warning signals of two majors price collapses that have happened in the following periods.  We finally propose a mean-field phenomenological model for the price of crypto-currency to show how the use of the standard deviation of the residuals is a better leading indicator of the collapse in price than the time series’ autocorrelation. Our findings represent a first step towards a better diagnostic of the risk of critical transition in the price and/or volume of crypto-currencies.
description: CryptocurrencyDatThis file contains the data of cryptocurrency. The daily (close) prices of cryptocurrencies are downloaded from the Website Coin Market Cap. We just consider the most important cryptocurrencies that were active in the period from Jan 1st 2016 to Mar 31st 2018. These cryptocurrencies include Bitcoin (BTC), Ripple (XPR), Litecoin (LTC), Stellar (XLM) and NEM (XEM) and DASH (DASH).CodeAvailabilityThis file is the whole Mathematica code to analyze the critical slowing down associated with critical transition and risk of collapse in cryptocurrency.
DOI: 10.5061/dryad.c2p0qj6
title: Data from: Chancelloriid sclerites from the Dyeran–Delamaran (lower–middle Cambrian) boundary interval of the Pioche–Caliente region, Nevada, USA

description: Chancelloriids are a poorly understood group of phylogenetically
 problematic Cambrian metazoans; complete specimens show they were sessile,
 radially symmetric, club-shaped organisms covered with sclerites in the
 form of rosettes of spines. While isolated sclerites are common components
 of Cambrian shelly assemblages, they have been relatively little studied.
 We describe chancelloriid sclerites from a series of nine sections
 spanning the upper Dyeran (uppermost traditional ‘lower’ Cambrian of
 Laurentia) to lower Delamaran (lowermost traditional ‘middle’ Cambrian)
 stages from the Pioche–Caliente region of east-central Nevada, USA.
 Samples were collected from the Combined Metals, Comet Shale, and Susan
 Duster Limestone members of the Pioche Formation on a bed-by-bed basis;
 acid maceration yielded more than 2000 sclerites. Based on careful
 examination of these sclerites and statistical analyses of co-occurring
 sclerite types, we distinguish six species, five of them new, and each
 with a restricted stratigraphic range. Chancelloria impar Moore sp. nov.
 is the dominant species in most upper Dyeran samples. Archiasterella
 cometensis Moore sp. nov. and A. auriculata Moore sp. nov. are rare in the
 upper Dyeran but widespread in the lowest Delamaran; A. uncinata Moore sp.
 nov. and C. lilioides Moore sp. nov. replace these in younger samples. A.
 auriculata is noteworthy for sharing features with both Archiasterella and
 Chancelloria, two of the more common chancelloriid genera. These results
 provide further support for the taxonomic tractability and
 biostratigraphic utility of chancelloriid sclerites; large collections
 from single horizons allow intraspecific variability to be assessed and
 species to be distinguished.
description: Chancelloriid occurrence
 data from Pioche Formation Spreadsheet with
 complete list of macerated samples from the Pioche Formation with
 chancelloriid occurrence data. Appendix.xls
 
 Occurrence
 data List of macerated
 samples with chancelloriid occurrence data. occurrence data.csv
 
  
 
 Specimen
 list List of chancelloriid
 specimens as a key to the supplemental image files.   
 Supplementary
 images