cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.711dc
title: Data from: Multiple loci and complete taxonomic sampling resolve the phylogeny and biogeographic history of tenrecs (Mammalia: Tenrecidae) and reveal higher speciation rates in Madagascar’s humid forests

description: The family Tenrecidae (tenrecs) is one of only four extant terrestrial
 mammal lineages to have colonized and diversified on Madagascar. Over the
 past 15 years, several studies have disagreed on relationships among major
 tenrec lineages, resulting in multiple reinterpretations of the number and
 timing of historical transoceanic dispersal events between Africa and
 Madagascar. We reconstructed the phylogeny of Tenrecidae using multiple
 loci from all recognized extant species and estimated divergence timing
 using six fossil calibrations within Afrotheria. All phylogenetic analyses
 strongly support monophyly of the Malagasy tenrecs, and our divergence
 timing analysis places their colonization of the island at 30-56 Ma. Our
 comprehensive phylogeny supports three important taxonomic revisions that
 reflect the evolutionary history of tenrecs: (1) we formally elevate the
 African otter shrews to their own family Potamogalidae, thereby rendering
 extant Tenrecidae entirely endemic to Madagascar, (2) we subsume the
 semiaquatic genus Limnogale within the shrew-tenrec genus Microgale, and
 (3) we re-elevate the two largest-bodied shrew tenrecs, Microgale dobsoni
 and M. talazaci, to the genus Nesogale Thomas 1918. Finally, we use
 recently summarized habitat data to test the hypothesis that
 diversification rates differ between humid and arid habitats on
 Madagascar, and we compare three common methods for ancestral
 biogeographic reconstruction. These analyses suggest higher speciation
 rates in humid habitats and reveal a minimum of three and more likely five
 independent transitions to arid habitats. Our results resolve the
 relationships among previously recalcitrant taxa, illuminate the timing
 and mechanisms of major biogeographic patterns in an extraordinary example
 of an island radiation, and permit the first comprehensive,
 phylogenetically consistent taxonomy of Madagascar’s tenrecs.
description: SequenceData_NexusFileNexus file containing all sequence data (11 loci, all tenrec species plus three golden mole outgroups)AllLoci_Concatenated.nexSupplementary Tables and FiguresSupplementary materials (K.M. Everson, V. Soarimalala, S.M. Goodman, & L.E. Olson, 2016)AllTogetherNow_SuppAppendices_EversonOlsonEtAl.pdf
DOI: 10.5061/dryad.20kq0
title: Data from: Mitochondrial responses to prolonged anoxia in brain of Red-eared slider turtles

description: Mitochondria are central to aerobic energy production and play a key role
 in neuronal signalling. During anoxia, however, the mitochondria of most
 vertebrates initiate deleterious cell death cascades. Nonetheless, a
 handful of vertebrate species, including some freshwater turtles, are
 remarkably tolerant of low oxygen environments and survive months of
 anoxia without apparent damage to brain tissue. This tolerance suggests
 that mitochondria in the brains of such species are adapted to withstand
 prolonged anoxia, but little is known about potential neuroprotective
 responses. In this study, we address such mechanisms by comparing
 mitochondrial function between brain tissues isolated from cold-acclimated
 red-eared slider turtles (Trachemys scripta elegans) exposed to two weeks
 of either normoxia or anoxia. We found that brain mitochondria from
 anoxia-acclimated turtles exhibited a unique phenotype of remodelling
 relative to normoxic controls, including: (i) decreased citrate synthase
 and F1FO-ATPase activity but maintained protein content, (ii) markedly
 reduced aerobic capacity, and (iii) mild uncoupling of the mitochondrial
 proton gradient. These data suggest that turtle brain mitochondria respond
 to low oxygen stress with a unique suite of changes tailored towards
 neuroprotection.
description: Oroboros data
 filesOroboros Instruments
 DatLab Data (DLD) files.
DOI: 10.5061/dryad.1vm38
title: Data from: Phenotypic covariation and morphological diversification in the ruminant skull

description: Differences among clades in their diversification patterns result from a
 combination of extrinsic and intrinsic factors. In this study I examined
 the role of intrinsic factors in the morphological diversification of
 ruminants in general, and in the differences between bovids and cervids in
 particular. Using skull morphology, which embodies many of the adaptations
 that distinguish bovids and cervids, I examined 132 of the 200 extant
 ruminant species. As a proxy for intrinsic constraints I quantified
 different aspects of the phenotypic covariation structure within species,
 and compared them with the among-species divergence patterns, using
 phylogenetic comparative methods. My results show that for most species,
 divergence is well aligned with their phenotypic covariance matrix, and
 those that are better aligned have diverged further away from their
 ancestor. Bovids have dispersed into a wider range of directions in
 morphospace than cervids, and their overall disparity is higher. This
 difference is best explained by the lower eccentricity of bovids'
 within-species covariance matrices. These results are consistent with the
 role of intrinsic constraints in determining amount, range, and direction
 of dispersion, and demonstrate that intrinsic constraints can influence
 macroevolutionary patterns even as the covariance structure evolves.
description: Data
 packageThis data package
 includes raw data, R code and other information required to reproduce all
 results in the paper. Raw data and specimen information are provided as
 both tab-limited text file and R object. Phylogenetic trees are provided
 as both R object of class "phylo" (package ape). Other
 information is provided as R objects. A detailed README file is also
 includedintMorphDiv_Artio_AmNat.zip
DOI: 10.5061/dryad.tp1cs
title: Data from: Functional diversity supports the biomass-diversity humped-back relationship in phytoplankton assemblages

description: Modelling the relationship between biomass and diversity in phytoplankton
 assemblages provides new insights into the mechanisms responsible for the
 coexistence of species, even in terrestrial ecosystems. We tested the
 biomass–diversity relationship in lake phytoplankton along a wide biomass
 gradient using functional species groups. We hypothesized that changes in
 the taxonomic diversity of the phytoplankton along a biomass gradient are
 associated with altered functional diversity. For the analyses, in total
 768 samples were collected from 30 oxbows, reservoirs and lakes in the
 Hungarian Lowland Region and analysed between 1992 and 2002. We found that
 the diversity and also the number of functional species groups showed a
 humped-back curve similar to the species richness. The changes in
 functional group composition act as a good proxy for phytoplankton species
 responses. We found that the peak of the number of strategy groups and
 their Shannon diversity was at a much lower biomass than that of species
 richness. We revealed the fine-scale effects of increasing the dominance
 of respective species or species groups with increasing biomass. This
 increase was well reflected by the changes in the functional
 characteristics: first, the species evenness; then, the Shannon diversity;
 and finally, the species richness started to decrease with increasing
 biomass. Cyanoprokaryota were positively correlated with increasing
 biomass and negatively with the increase in species richness; thus, the
 high increase both in their abundance and biomass can be responsible for
 the abruptly decreasing part of the humped-back curve. We detected a
 humped-back curve between biomass and diversity, where the peak compared
 to terrestrial plant communities tended to be towards high biomass scores,
 that is, &gt;60% instead of the 20–60% of the biomass range typical
 for terrestrial plant communities. Marked differences in the structural
 and dynamic features of phytoplankton assemblages and terrestrial plant
 communities are likely responsible for this difference.
description: Phytoplankton and
 Enviromental variables dataPhytoplankton taxa with
 individual biomass scores (768 samples, 896 species), Environmental
 variables: total nitrogen (TN; 297 samples), total phosphorus (TP; 339),
 total suspended solids (TSS; 351) and for Secchi depth (97 data). For TN
 (summarised the amount of different nitrogen forms), TP (measured by the
 acid molybdate method) and TSS (measured by the gravimetric method) the
 Hungarian national guidelines were used. The site numbering follows the
 order of Sampled Waterbodies table Supporting Information File of the
 paper.Torok-et-al-Funct-Ecol-Funct-Div.xlsx
DOI: 10.5061/dryad.357cr
title: Data from: Population variation reveals independent selection towards small body size in Chinese Debao pony

description: Body size, one of the most important quantitative traits under
 evolutionary scrutiny, varies considerably among species and among
 populations within species. Revealing the genetic basis underlying this
 variation is very important, particularly in humans where there is a close
 relationship with diseases and in domestic animals as the selective
 patterns are associated with improvements in production traits. The Debao
 pony is a horse breed with small body size that is unique to China;
 however, it is unknown whether the size-related candidate genes identified
 in Western breeds also account for the small body size of the Debao pony.
 Here, we compared individual horses from the Debao population with other
 two Chinese horse populations using SNPs identified with the Equine SNP 65
 Bead Chip. The previously reported size-related candidate gene HMGA2
 showed a significant signature for selection, consistent with its role
 observed in human populations. More interestingly, we found a candidate
 gene TBX3, which had not been observed in previous studies on horse body
 size that displayed the highest differentiation and most significant
 association, and thus likely is the dominating factor for the small
 stature of the Debao pony. Further comparison between the Debao pony and
 other breeds of horses from around the world demonstrated that TBX3 was
 selected independently in the Debao pony, suggesting that there were
 multiple origins of small stature in the horse.
description: 96_Chinese_horsewe performed a genome-wide scan on 96 individuals of three Chinese horse breeds (Debao pony, Yili horse and Mongolian horse) using Equine SNP70 BeadChip. And my genome assembly is Equus caballus EquCab2.0.Equine SNP 70 Bead Chip in Chinese horsewe performed a genome-wide scan on 96 individuals of three Chinese horse breeds (Debao pony, Yili horse and Mongolian horse) using Equine SNP70 BeadChip. And my genome assembly is Equus caballus EquCab2.096_Chinese_horse.mapSample ID and locations for 96_Chinese_horse.xlsxSample identification, sample locations and population cluster membership for all individuals.96_Chinese_horse.xlsx
DOI: 10.5061/dryad.k9v42
title: Data from: Dopamine regulates termite soldier differentiation through trophallactic behaviours

description: Caste polyphenism in social insects is regulated by social interactions
 among colony members. Trophallaxis is one of the most frequently observed
 interactions, but no studies have been conducted identifying the intrinsic
 factors involved in this behaviour and caste differentiation. Dopamine
 (DA) has multiple roles in the modulation of behaviours and physiology,
 and it produces species-specific behaviours in animals. Here, to verify
 the role of DA in termite soldier differentiation, we focused on the first
 soldier in an incipient colony of Zootermopsis nevadensis, which always
 differentiates from the oldest 3rd instar (No. 1 larva) via a presoldier.
 First, brain DA levels of the No. 1 larva at day 3 after its appearance
 were significantly higher than day 0. Second, DA synthesis gene expression
 levels were extraordinarily high in the No. 1 larva at day 0–1 after
 appearance. Finally, injection of a DA receptor antagonist into the No. 1
 larva resulted in the inhibition of presoldier differentiation.
 Behavioural observations of the antagonist or control-injected larvae
 suggested that brain DA and signalling activity regulate the frequencies
 of trophallaxis from reproductives and presoldier differentiation. Because
 trophallaxis is a social behaviour frequently observed in natural
 conditions, the role of DA should be investigated in other social insects
 with frequent trophallactic and allogrooming behaviour.
description: Supplementary
 MaterialFigure S1-S6, Table S1,
 Supplementary movie 1-3.
DOI: 10.5061/dryad.54fv5
title: Data from: Mismatch between fishway operation and timing of fish movements: a risk for cascading effects in partial migration systems

description: Habitat fragmentation is a growing problem worldwide. Particularly in
 river systems, numerous dams and weirs hamper the movement of a wide
 variety of species. With the aim to preserve connectivity for fish, many
 barriers in river systems are equipped with fishways (also called fish
 passages or fish ladders). However, few fishways provide full
 connectivity. Here we hypothesized that restricted seasonal opening times
 of fishways can importantly reduce their effectiveness by interfering with
 the timing of fish migration, for both spring- and autumn-spawning
 species. We empirically tested our hypothesis, and discuss the possible
 eco-evolutionary consequences of affected migration timing. We analyzed
 movements of two salmonid fishes, spring-spawning European grayling
 (Thymallus thymallus) and autumn-spawning brown trout (Salmo trutta), in
 Norway's two largest river systems. We compared their timing of
 upstream passage through four fishways collected over 28 years with the
 timing of fish movements in unfragmented river sections as monitored by
 radiotelemetry. Confirming our hypothesis, late opening of fishways
 delayed the migration of European grayling in spring, and early closure of
 fishways blocked migration for brown trout on their way to spawning
 locations during late autumn. We show in a theoretical framework how
 restricted opening times of fishways can induce shifts from migratory to
 resident behavior in potamodromous partial migration systems, and propose
 that this can induce density-dependent effects among fish accumulating in
 lower regions of rivers. Hence, fragmentation may not only directly affect
 the migratory individuals in the population, but may also have effects
 that cascade downstream and alter circumstances for resident fish. Fishway
 functionality is inadequate if there is a mismatch between natural fish
 movements and fishway opening times in the same river system, with
 ecological and possibly evolutionary consequences for fish populations.
description: Fishway
 dataFishway
 dataTelemetry
 dataTelemetry
 data
DOI: 10.5061/dryad.9f1p2
title: Data from: The extracellular and cytoplasmic domains of Syndecan cooperate postsynaptically to promote synapse growth at the Drosophila neuromuscular junction

description: The heparan sulfate proteoglycan (HSPG) Syndecan (Sdc) is a crucial
 regulator of synapse development and growth in both vertebrates and
 invertebrates. In Drosophila, Sdc binds via its extracellular heparan
 sulfate (HS) sidechains to the receptor protein tyrosine phosphatase LAR
 to promote the morphological growth of the neuromuscular junction (NMJ).
 To date, however, little else is known about the molecular mechanisms by
 which Sdc functions to promote synapse growth. Here we show that all
 detectable Sdc found at the NMJ is provided by the muscle, strongly
 suggesting a post-synaptic role for Sdc. We also show that both the
 cytoplasmic and extracellular domains of Sdc are required to promote
 synapse growth or to rescue Sdc loss of function. We report the results of
 a yeast two-hybrid screen using the cytoplasmic domains of Sdc as bait,
 and identify several novel candidate binding partners for the cytoplasmic
 domains of Sdc. Together, these studies provide new insight into the
 mechanism of Sdc function at the NMJ, and provide enticing future
 directions for further exploring how Sdc promotes synapse growth.
description: 24B Sdc RNAi Sdc and
 FasIIRaw image of muscle
 expressed Sdc RNAi, stained with Sdc and Fasciclin IIElav Sdc RNAi Sdc and
 FasIIRaw image of neural
 expressed Sdc RNAi, stained with Sdc and Fasciclin IISdc and FasII in
 wtRaw
 image of wild type 3rd instar larvum, stained with Sdc and Fasciclin
 II24BUASFLsdcmyc1Raw image of muscle expressed Sdc-FL, stained with HRP and anti-MycElav x UAS-Sdc mycRaw image of neural expressed Sdc-FL, stained with HRP and anti-MycCS for overexpressionRaw image of wild type larvum stained with HRP and anti-MycNormalized Bouton CountsRaw data and analyzed data on bouton counts used to generate bar graphs in Figure 224BUASFLsdcmyc1Raw image for Figure 324BUASsdcdeltaC1myc6Raw image for Figure 324BUASsdcdeltaC2myc8Raw image for Figure 324BUASsdcdeltaCytomyc14Raw image for Figure 3sdcdeltaectoRaw image for Figure 3sdctmswapRaw image for Figure 324bflsdcpbs3Raw image for Figure 424Bsdcdeltac1pbs13Raw image for Figure 424Bsdcdeltac2pbs11Raw image for Figure 424bsdcdeltacytopbs5Raw image for Figure 4sdcdeltaectoPBSRaw image for Figure 4sdctmswapPBSRaw image for Figure 4Normalized Bouton Counts ResubmissionThis file contains all the bouton counts for this manuscript.
DOI: 10.5061/dryad.26j85
title: Data from: Restricted grouper reproductive migrations support community-based management

description: Conservation commonly requires trade-offs between social and ecological
 goals. For tropical small-scale fisheries, spatial scales of socially
 appropriate management are generally small—the median no-take locally
 managed marine area (LMMA) area throughout the Pacific is less than 1 km2.
 This is of particular concern for large coral reef fishes, such as many
 species of grouper, which migrate to aggregations to spawn. Current data
 suggest that the catchment areas (i.e. total area from which individuals
 are drawn) of such aggregations are at spatial scales that preclude
 effective community-based management with no-take LMMAs. We used acoustic
 telemetry and tag-returns to examine reproductive migrations and catchment
 areas of the grouper Epinephelus fuscoguttatus at a spawning aggregation
 in Papua New Guinea. Protection of the resultant catchment area of
 approximately 16 km2 using a no-take LMMA is socially untenable here and
 throughout much of the Pacific region. However, we found that spawning
 migrations were skewed towards shorter distances. Consequently, expanding
 the current 0.2 km2 no-take LMMA to 1–2 km2 would protect approximately
 30–50% of the spawning population throughout the non-spawning season.
 Contrasting with current knowledge, our results demonstrate that species
 with moderate reproductive migrations can be managed at scales congruous
 with spatially restricted management tools.
description: Raw acoustic
 dataThis .CSV file contains
 the raw data downloaded from the acoustic array, pertaining to the
 manuscript: 'Restricted grouper reproductive migrations support
 community-based management'.WALDIE_etal_fusco_acoustic.csvAcoustic tagging dataThis .CSV file contains the data describing Epinephelus fuscoguttatus fitted with acoustic tags at the Bolsurik FSA, pertaining to the manuscript: 'Restricted grouper reproductive migrations support community-based management'.WALDIE_etal_tagging.csvVisitation and migration dataThis .CSV file contains data collated from 'Raw acoustic data', detailing arrival, departure and residence at, as well as migrations to/from, the Bolsurik FSA during the tagging study discussed in 'Restricted grouper reproductive migrations support community-based management'.WALDIE_etal_movement.csvStakeholder survey dataThis .CSV file contains data collected during stakeholder surveys, pertaining to the study discussed in 'Restricted grouper reproductive migrations support community-based management'.WALDIE_etal_stakeholdersurvey.csvData analysis R scriptThis .R file contains annotated R script to perform analyses discussed in 'Restricted grouper reproductive migrations support community-based management'.WALDIE_etal_dataanalysis.R
DOI: 10.5061/dryad.pg470
title: Data from: Assessing the performance of DNA barcoding using posterior predictive simulations

description: Accurate estimates of biodiversity are required for research in a broad
 array of biological subdisciplines including ecology, evolution,
 systematics, conservation and biodiversity science. The use of statistical
 models and genetic data, particularly DNA barcoding, has been suggested as
 an important tool for remedying the large gaps in our current
 understanding of biodiversity. However, the reliability of biodiversity
 estimates obtained using these approaches depends on how well the
 statistical models that are used describe the evolutionary process
 underlying the genetic data. In this study, we utilize data from the
 Barcode of Life Database and posterior predictive simulations to assess
 the performance of DNA barcoding under commonly used substitution models.
 We demonstrate that the success of DNA barcoding varies widely across DNA
 substitution models and that model choice has a substantial impact on the
 number of operational taxonomic units identified (changing results by
 ~4–31%). Additionally, we demonstrate that the widely followed practice of
 a priori assuming the Kimura 2-parameter model for DNA barcoding is
 statistically unjustified and should be avoided. Using both data-based and
 inference-based test statistics, we detect variation in model performance
 across taxonomic groups, clustering algorithms, genetic divergence
 thresholds and substitution models. Taken together, these results
 illustrate the importance of considering both model selection and model
 adequacy in studies quantifying biodiversity.
description: AlignmentsAlignments in nexus format of DNA barcode datasets assembled and used in this study.alignments.tar.gzPython scriptsPython scripts used in study to generate results and posterior predictive simulations. Information about usage can be found in the header of each file.python_scripts.tar.gz