cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.q5g33
title: Data from: Molecular phylogeny of the highly diversified catfish subfamily Loricariinae (Siluriformes, Loricariidae) reveals incongruences with morphological classification

description: The Loricariinae belong to the Neotropical mailed catfish family
 Loricariidae, the most species-rich catfish family. Among loricariids,
 members of the Loricariinae are united by a long and flattened caudal
 peduncle and the absence of an adipose fin. Despite numerous studies of
 the Loricariidae, there is no comprehensive phylogeny of this
 morphologically highly diversified subfamily. To fill this gap, we present
 a molecular phylogeny of this group, including 350 representatives, based
 on the analysis of mitochondrial and nuclear genes (8426 positions). The
 resulting phylogeny indicates that Loricariinae are distributed into two
 sister tribes: Harttiini and Loricariini. The Harttiini tribe, as
 classically defined, constitutes a paraphyletic assemblage and is here
 restricted to the three genera Harttia, Cteniloricaria, and Harttiella.
 Two subtribes are distinguished within Loricariini: Farlowellina and
 Loricariina. Within Farlowellina, the nominal genus formed a paraphyletic
 group, as did Sturisoma and Sturisomatichthys. Within Loricariina,
 Loricaria, Crossoloricaria, and Apistoloricaria are also paraphyletic. To
 solve these issues, and given the lack of clear morphological diagnostic
 features, we propose here to synonymize several genera (Quiritixys with
 Harttia; East Andean members of Crossoloricaria, and Apistoloricaria with
 Rhadinoloricaria; Ixinandria, Hemiloricaria, Fonchiiichthys, and Leliella
 with Rineloricaria), to restrict others (Crossoloricaria, and
 Sturisomatichthys to the West Andean members, and Sturisoma to the East
 Andean species), and to revalidate the genus Proloricaria.
description: Loricariinae rtn4 GBdef
 SFMAlignment of f-rtn4r
 maker for 321 loricariids. Data are as deposited in
 GenBank.
DOI: 10.5061/dryad.qd73b
title: Data from: From steps to home range formation: species-specific movement upscaling among sympatric ungulates

description: Animals move to interact with the environment in order to find food
 resources and cover. Intrinsic characteristics affecting feeding and
 antipredatory strategies likely shape variation in movement patterns and
 home range formation between individuals, populations and species.
 Browsing herbivores selectively forage on patchily distributed resources
 in areas with more canopy cover, whereas mixed feeders and grazers feed on
 more open grasslands and tend to aggregate as an antipredatory strategy.
 We therefore predicted that at small temporal scales, browsers will show
 greater net displacements (i.e. typical of searching patterns) than mixed
 feeders or grazers; but at larger temporal scales, we expect the opposite
 pattern, since gregarious species will need to use larger areas to feed
 the whole herd. We also predicted that the feeding/antipredatory strategy
 will determine the behavioural responses to other environmental factors.
 To test this, we compared spatial movement patterns at multiple scales
 (from 20-min intervals to annual home ranges) of three sympatric,
 similar-sized, alpine ungulates which differ in their
 feeding/antipredatory strategy: roe deer (solitary browsers), mouflon
 (gregarious grazers) and chamois (intermediate feeders in smaller groups).
 We used location data from GPS-collared females of the three species in
 the French Alps. As predicted, we found that multi-scale spatial patterns
 depended on the feeding/antipredatory strategy. Browsers foraged within
 smaller range areas, searching back and forth. Mixed feeders and,
 especially, grazers covered larger areas, presumably to satisfy herd
 needs. The feeding/antipredatory strategies also determined the
 interspecific variability in behavioural responses to factors such as
 maternal status, weather, habitat type or human disturbance, supporting
 our hypothesis. Exploring interspecific variability, we showed how
 movement behaviour and home range formation vary substantially, even among
 species within the same guild. This mechanism might be important to
 maintain intra-guild multi-species associations and increase biodiversity,
 through contributing to niche segregation and, thus, coexistence.
description: Ungulate movement and
 range area data for DryadMovement ecology and
 range area data for roe deer, chamois and mouflon. These data come
 originally form GPS loggers but was summarized at different time intervals
 (from 20 minute intervals to annual range areas) before
 analyses.movement and range area data
 for Dryad.xls
DOI: 10.5061/dryad.gh4k7
title: Data from: Crowdsourced geometric morphometrics enable rapid large-scale collection and analysis of phenotypic data

description: 1. Advances in genomics and informatics have enabled the production of
 large phylogenetic trees. However, the ability to collect large phenotypic
 datasets has not kept pace. 2. Here, we present a method to quickly and
 accurately gather morphometric data using crowdsourced image-based
 landmarking. 3. We find that crowdsourced workers perform similarly to
 experienced morphologists on the same digitization tasks. We also
 demonstrate the speed and accuracy of our method on seven families of
 ray-finned fishes (Actinopterygii). 4. Crowdsourcing will enable the
 collection of morphological data across vast radiations of organisms, and
 can facilitate richer inference on the macroevolutionary processes that
 shape phenotypic diversity across the tree of life.
description: Crowdsourced
 morphometrics dataThis zip file contains
 geometric morphometric landmark data collected by Mechanical Turk workers,
 as well as BAMM input and output files.dryad_data.zip
DOI: 10.5061/dryad.4fb1m
title: Data from: Distribution patterns of microbial communities in ultramafic landscape: a metagenetic approach highlights the strong relationships between diversity and environmental traits

description: Microbial species richness and assemblages across ultramafic ecosystems
 were investigated to assess the relationship between their distributional
 patterns and environmental traits. The structure of microorganism
 communities in the Koniambo massif, New Caledonia, was investigated using
 a metagenetic approach correlated with edaphic and floristic factors.
 Vegetation cover and soil properties significantly shaped the large
 phylogenetic distribution of operational taxonomic unit within microbial
 populations, with a mean per habitat of 3.477 (±317) for bacteria and 712
 (±43) for fungi. Using variance partitioning, we showed that the effect of
 aboveground vegetation was the most significant descriptor for both
 bacterial and fungal communities. The floristic significant predictors
 explained 43% of the variation for both the bacterial and fungal community
 structures, while the edaphic significant predictors explained only 32%
 and 31% of these variations, respectively. These results confirm the
 previous hypothesis that the distribution of microorganisms was more
 structured by the vegetation cover rather than the edaphic characteristics
 and that microbial diversity is not limited in ultramafic ecosystems.
description: OTU table for bacteria
 (MEC-15-0975)OTU table for
 bacteria.xlsxOTU table for fungi
 (MEC-15-0975)OTU table for
 fungi.xlsxFlore abundance matrix
 (MEC-15-0975)Flore abundance
 matrix.xlsxPhysicoChemical data
 (MEC-15-0975)PhysicoChemical
 data.xlsx
DOI: 10.5061/dryad.bn410
title: Data from: A single microphone noise reduction algorithm based on the detection and reconstruction of spectro-temporal features

description: Animals throughout the animal kingdom excel at extracting individual
 sounds from competing background sounds, yet current state-of-the-art
 signal processing algorithms struggle to process speech in the presence of
 even modest background noise. Recent psychophysical experiments in humans
 and electrophysiological recordings in animal models suggest that the
 brain is adapted to process sounds within the restricted domain of
 spectro-temporal modulations found in natural sounds. Here, we describe a
 novel single microphone noise reduction algorithm called spectro-temporal
 detection–reconstruction (STDR) that relies on an artificial neural
 network trained to detect, extract and reconstruct the spectro-temporal
 features found in speech. STDR can significantly reduce the level of the
 background noise while preserving the foreground speech quality and
 improving estimates of speech intelligibility. In addition, by leveraging
 the strong temporal correlations present in speech, the STDR algorithm can
 also operate on predictions of upcoming speech features, retaining similar
 performance levels while minimizing inherent throughput delays. STDR
 performs better than a competing state-of-the-art algorithm for a wide
 range of signal-to-noise ratios and has the potential for real-time
 applications such as hearing aids and automatic speech recognition.
description: CSV files of all paper
 dataThe data provided below
 should be enough to reproduce the primary data figures in the paper. They
 are organized in the order in which they appear in the paper. Each CSV
 file contains 11 columns: - Algorithm: The name of the algorithm being
 tested - Number: Stimulus ID - SNR: Input SNR (dB) of the stimulus -
 Composite Signal: Composite estimate of speech distortion - Composite
 Background: Composite estimate of background intrusiveness - Composite
 Overall: Composite estimate of overall quality - STOI: Short-time
 objective intelligibility - LLR: Log-likelihood ratio - Segmental SNR:
 Output segmental SNR (dB) - PESQ: Perceptual estimate of sound quality -
 WSS: Weighted spectral slope Figure 5 - 1_speakers_speech_shaped_noise.csv
 - 16_speakers_speech_shaped_noise.csv Figure 7 - 1_speakers_babble.csv -
 16_speakers_babble.csv Figure 8 - delays_babble.csv -
 delays_speech_shaped_noise.csv Supplementary Figure 2 -
 16_speakers_cafe.csv - 16_speakers_car.csv - 16_speakers_home.csv -
 16_speakers_largetrain_babble.csv -
 16_speakers_largetrain_speech_shaped_noise.csv -
 16_speakers_reverberant.csv - 16_speakers_street.csv Supplementary Figure
 3 - all_speakers_airport.csv - all_speakers_birds.csv -
 all_speakers_machine.csv - all_speakers_ocean.csv -
 all_speakers_pinknoise.csv - all_speakers_rain.csv -
 all_speakers_rainforest.csv - all_speakers_station.csv -
 all_speakers_theater.csv - all_speakers_train.csv -
 all_speakers_whitenoise.csv - all_speakers_wind.csvdata_csv_files.zip
DOI: 10.5061/dryad.4cc5m
title: Data from: Integrated radar and lidar analysis reveals extensive loss of remaining intact forest on Sumatra 2007–2010

description: Forests with high above ground biomass (AGB), including those growing on
 peat swamps, have historically not been thought suitable for biomass
 mapping and change detection using Synthetic Aperture Radar (SAR).
 However, by integrating L-band (λ = 0.23 m) SAR with lidar data from the
 ALOS and ICESat earth-observing satellites respectively, and 56 forest
 plots, we were able to create a forest biomass and change map for a 10.7
 Mha section of eastern Sumatra that still contains high AGB peat swamp
 forest. Using a time series of SAR data we estimated changes in both
 forest area and AGB. We estimate that there were 274 ± 68 Tg AGB remaining
 in natural forest (≥ 20 m height) in the study area in 2007, with this
 stock reducing by approximately 11.4% over the subsequent 3 years. A total
 of 137.4 kha of the study area were deforested between 2007 and 2010; an
 average rate of 3.8% yr−1. The ability to attribute forest loss to
 different initial biomass values allows for far more effective monitoring
 and baseline modelling for avoided deforestation projects than
 traditional, optical-based remote sensing. Furthermore, given SAR's
 ability to penetrate the smoke and cloud which normally obscure land cover
 change in this region, SAR-based forest monitoring can be relied on to
 provide frequent imagery. This study demonstrates that even at L-band,
 which typically saturates at medium biomass levels (ca. 150 Mg ha−1), it
 is possible to make reliable estimates of not just the area but the carbon
 emissions resulting from land use change.
description: Collins and Mitchard -
 Above ground forest biomass estimated for 2007This GeoTiff file
 provides estimate of per-pixel above ground biomass (AGB) for a section of
 Sumatra in 2007. Only those pixels with forest of height greater or equal
 to 20m in 2007 were included. The maximum AGB estimated per pixel is 236.5
 Mg ha^-1. The minimum per pixel biomass is 0 Mg ha^-1. The projection is
 UTM48S. The pixel size is ~100m x 100m.Collins and Mitchard Estimated
 AGB Sumatra 2007 - DataDryad.tifCollins and Mitchard
 Sumatra Deforestation 2007-10 coded -DataDryadThis GeoTiff map shows:
 *areas of forest of height greater or equal to 20m in 2007 that is stable
 over time (coded as 0). *Areas of forest of the above definition, but that
 we lost between 2007-8 (coded as 1). *Areas of forest of the above
 definition, but that were deforested between 2008-9 (coded as 2). *Areas
 of forest of the above definition, but that but that were deforested
 between 2009-10 (coded as 3). *Pixels which did not contain forest of
 height greater or equal to 20m in 2007 are excluded from the analysis
 (coded as 'no data').
DOI: 10.5061/dryad.4h40n
title: Data from: Terrestrial arthropods of Steel Creek, Buffalo National River, Arkansas. I. Select beetles (Coleoptera: Buprestidae, Carabidae, Cerambycidae, Curculionoidea excluding Scolytinae)

description: Background: The Ozark Mountains are a region with high endemism and
 biodiversity, yet few invertebrate inventories have been made and few
 sites extensively studied. We surveyed a site near Steel Creek Campground,
 along the Buffalo National River in Arkansas, using twelve trap types –
 Malaise traps, canopy traps (upper and lower collector), Lindgren
 multifunnel traps (black, green, and purple), pan traps (blue, purple,
 red, white, and yellow), and pitfall traps – and Berlese-Tullgren
 extraction for eight and half months. New information: We provide
 collection records of beetle species belonging to eight families collected
 at the site. Thirty one species represent new state records: (Buprestidae)
 Actenodes acornis, Agrilus cephalicus, Agrilus ohioensis, Agrilus
 paracelti, Taphrocerus nicolayi; (Carabidae) Agonum punctiforme, Synuchus
 impunctatus; (Curculionidae) Acalles clavatus, Acalles minutissimus,
 Acoptus suturalis, Anthonomus juniperinus, Anametis granulata, Idiostethus
 subcalvus, Eudociminus mannerheimii, Madarellus undulatus, Magdalis
 armicollis, Magdalis barbita, Mecinus pascuorum, Myrmex chevrolatii,
 Myrmex myrmex, Nicentrus lecontei, Otiorhynchus rugosostriatus,
 Piazorhinus pictus, Phyllotrox ferrugineus, Plocamus hispidulus,
 Pseudobaris nigrina, Pseudopentarthrum simplex, Rhinoncus pericarpius,
 Sitona lineatus, Stenoscelis brevis, Tomolips quericola. Additionally,
 three endemic carabids, two of which are known only from the type series,
 were collected.
description: Terrestrial arthropods
 of Steel Creek - ColeopteraThe beetles included
 within this data set were collected at Steel Creek, Buffalo National
 River, Newton County, Arkansas between April and December 2013 using a
 variety of collecting techniques. The spreadsheet uses Darwin Core
 headings, which are defined in the ReadMe file.Beetles - Darwin
 Core.xls
DOI: 10.5061/dryad.55q0s
title: Data from: Cryptic species or inadequate taxonomy? implementation of 2D geometric morphometrics based on integumental organs as landmarks for delimitation and description of copepod taxa

description: Discovery of cryptic species using molecular tools has become common in
 many animal groups but it is rarely accompanied by morphological revision,
 creating ongoing problems in taxonomy and conservation. In copepods,
 cryptic species have been discovered in most groups where fast-evolving
 molecular markers were employed. In this study at Yeelirrie in Western
 Australia we investigate a subterranean species complex belonging to the
 harpacticoid genus Schizopera Sars, 1905, using both the barcoding
 mitochondrial COI gene and landmark-based two-dimensional geometric
 morphometrics. Integumental organs (sensilla and pores) are used as
 landmarks for the first time in any crustacean group. Complete congruence
 between DNA-based species delimitation and relative position of
 integumental organs in two independent morphological structures suggests
 the existence of three distinct evolutionary units. We describe two of
 them as new species, employing a condensed taxonomic format appropriate
 for cryptic species. We argue that many supposedly cryptic species might
 not be cryptic if researchers focus on analyzing morphological structures
 with multivariate tools that explicitly take into account geometry of the
 phenotype. A perceived supremacy of molecular methods in detecting cryptic
 species is in our view a consequence of disparity of investment and
 unexploited recent advancements in morphometrics among taxonomists. Our
 study shows that morphometric data alone could be used to find diagnostic
 morphological traits and gives hope to anyone studying small animals with
 a hard integument or shell, especially opening the door to assessing
 fossil diversity and rich museum collections. We expect that simultaneous
 use of molecular tools with geometry-oriented morphometrics may yield
 faster formal description of species. Decrypted species in this study are
 a good example for urgency of formal descriptions, as they display
 short-range endemism in small groundwater calcrete aquifers in a
 paleochannel, where their conservation may be threatened by proposed
 mining.
description: SUPPLEMENTARY
 MATERIALmtCOI Alignment
 SchizoperaMEGA sequence
 alignmentraw_coordinates_CephalothoraxLandmark coordinates for Cephalothoraxraw_coordinates_GenitalSomiteLandmark coordinates for Genital double-somiteSUPPLEMENTARY TABLES AND FIGURESSUPPLEMENTARY TABLES AND FIGURES
DOI: 10.5281/zenodo.18386741
title: Data for Hydrodynamic exposure and intraspecific functional trait variation in the brown seaweed Fucus serratus

description: This repository contains the raw data and R scripts supporting the analyses presented in the research note “Hydrodynamic exposure and intraspecific functional trait variation in the brown seaweed Fucus serratus” (Rustas et al., Aquatic Botany).

The dataset comprises individual-level measurements of morphological, mechanical, and biochemical functional traits of Fucus serratus collected across a gradient of hydrodynamic exposure on rocky shores on the Swedish west coast. Traits include thallus morphology, dry matter content, blade toughness, attachment investment, epiphyte load, and photosynthetic pigment concentrations, along with associated metadata on site, exposure category, and depth.

The accompanying R scripts reproduce all data processing, statistical analyses, and figures reported in the manuscript. Together, these materials enable full reproducibility of the results and facilitate reuse of the data for comparative or trait-based studies of macroalgae.
DOI: 10.5281/zenodo.18386740
title: Data for Hydrodynamic exposure and intraspecific functional trait variation in the brown seaweed Fucus serratus

description: This repository contains the raw data and R scripts supporting the analyses presented in the research note “Hydrodynamic exposure and intraspecific functional trait variation in the brown seaweed Fucus serratus” (Rustas et al., Aquatic Botany).

The dataset comprises individual-level measurements of morphological, mechanical, and biochemical functional traits of Fucus serratus collected across a gradient of hydrodynamic exposure on rocky shores on the Swedish west coast. Traits include thallus morphology, dry matter content, blade toughness, attachment investment, epiphyte load, and photosynthetic pigment concentrations, along with associated metadata on site, exposure category, and depth.

The accompanying R scripts reproduce all data processing, statistical analyses, and figures reported in the manuscript. Together, these materials enable full reproducibility of the results and facilitate reuse of the data for comparative or trait-based studies of macroalgae.
DOI: 10.5061/dryad.cc6c0
title: Data from: Relationship between the sequencing and timing of vocal motor elements in birdsong

description: Accurate coordination of the sequencing and timing of motor gestures is
 important for the performance of complex and evolutionarily relevant
 behaviors. However, the degree to which motor sequencing and timing are
 related remains largely unknown. Birdsong is a communicative behavior that
 consists of discrete vocal motor elements (‘syllables’) that are sequenced
 and timed in a precise manner. To reveal the relationship between syllable
 sequencing and timing, we analyzed how variation in the probability of
 syllable transitions at branch points, nodes in song with variable
 sequencing across renditions, correlated with variation in the duration of
 silent gaps between syllable transitions (‘gap durations’) for adult
 Bengalese finch song. We observed a significant negative relationship
 between transition probability and gap duration: more prevalent
 transitions were produced with shorter gap durations. We then assessed the
 degree to which long-term age-dependent changes and acute
 context-dependent changes to syllable sequencing and timing followed this
 inverse relationship. Age- but not context-dependent changes to syllable
 sequencing and timing were inversely related. On average, gap durations at
 branch points decreased with age, and the magnitude of this decrease was
 greater for transitions that increased in prevalence than for transitions
 that decreased in prevalence. In contrast, there was no systematic
 relationship between acute context-dependent changes to syllable
 sequencing and timing. Gap durations at branch points decreased when birds
 produced female-directed courtship song compared to when they produced
 undirected song, and the magnitude of this decrease was not related to the
 direction and magnitude of changes to transition probabilities. These
 analyses suggest that neural mechanisms that regulate syllable sequencing
 could similarly control syllable timing but also highlight mechanisms that
 can independently regulate syllable sequencing and timing.
description: Matheson_Sakata_DataSpreadsheet containing identified branch points and their measured transition probabilities, durations of silent intervals (gaps), and syllable amplitudes. Includes recordings as young (~6 months) and older (~23 months) adults and across social contexts.