cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.591q3
title: Data from: Microfluidic PCR-based target enrichment: a case study in two rapid radiations of Commiphora (Burseraceae) from Madagascar

description: Developing effective and cost-efficient multilocus nuclear datasets for
 angiosperm species is a continuing challenge to the systematics community.
 Here we describe the development and validation of a novel set of 91
 nuclear markers for PCR-based target enrichment. Using microfluidic PCR
 and Illumina MiSeq, we generated nuclear, subgenomic libraries for 96
 species simultaneously and sequenced them for a total cost of ca. $6000
 USD. Approximately half of these costs include reusable reagents (primers,
 barcodes, and custom sequencing primers) and taxon sampling could be
 increased by an order of magnitude to maximize sequencing depth
 efficiency. The principle benefit of microfluidic PCR over alternative
 target enrichment strategies is that it bypasses costly library
 preparation. After sequencing, we evaluated the ability of the loci to
 resolve species level relationships within two recently radiated lineages
 of endemic Madagascan Commiphora Jacq. (Burseraceae) species. Our results
 demonstrate that 1) effective nuclear markers can be designed for
 non-model angiosperm taxa from these publicly available datasets; 2) that
 microfluidic PCR amplification followed by high throughput sequencing can
 produce highly complete taxon by locus sequence data matrices with minimal
 resource investment; and 3) that these numerous nuclear phylogenomic
 markers can improve our understanding of phylogenetic relationships within
 Commiphora. We provide a synopsis of ongoing activities to enhance this
 microfluidic PCR-based target enrichment strategy through more broad
 primer assays, multiplexing, and increased efficiency of sequencing depth.
description: ALLCONCATConcatenation of all 44 loci used for phylogenetic analysis in this study.99CONCATConcatenated alignment of the third dataset, including all loci shared by at least 99% of sampled taxa. Total of 20 loci.75CONCATConcatenated alignment of the second dataset, including all loci shared by at least 75% of sampled taxa. Total of 41 loci.AT5G15680AT4G21770AT4G18810BAT3G46220AT1G77550AAT2G22370BAT2G44660BAT3G10400AT3G26580RAT3G21540RAT2G40760AT1G77930AAT1G76450FAT4G37510AT1G31780_F_RAT1G59990_F_RAT4G29590_F_RAT1G10860AT1G21840RAT1G65030AT1G76450RAT2G03667AT2G04620AT2G04740AT2G05120AT2G05320AT2G17265AT2G20330AT2G20790AT2G31890AT2G31890AAT2G44660AAT2G44760AT2G46100AT3G01380FAT3G04650FAT3G04650RAT3G14910AT3G21540FAT3G22660AT3G54460AT4G00560FAT4G14605AT4G19900AT4G31770AT5G04910AT5G52180AT3G29130RAT3G29130FAT3G01380RAT2G36740AT2G21710FAT1G77550BAT1G65070CutAdapt_TrimScript_MiSeq2015This is the batch script used for quality trimming and adapter trimming from raw sequence data produced by MiSeq in this study.
DOI: 10.5061/dryad.vj3p9
title: Data from: The rpb2 gene represents a viable alternative molecular marker for the analysis of environmental fungal communities

description: Although the commonly used internal transcribed spacer region of rDNA
 (ITS) is well suited for taxonomic identification of fungi, the
 information on the relative abundance of taxa and diversity is negatively
 affected by the multicopy nature of rDNA and the existence of ITS
 paralogues. Moreover, due to high variability, ITS sequences cannot be
 used for phylogenetic analyses of unrelated taxa. The part of single-copy
 gene encoding the second largest subunit of RNA polymerase II (rpb2) was
 thus compared with first spacer of ITS as an alternative marker for the
 analysis of fungal communities in spruce forest topsoil, and their
 applicability was tested on a comprehensive mock community. In soil, rpb2
 exhibited broad taxonomic coverage of the entire fungal tree of life
 including basal fungal lineages. The gene exhibited sufficient variation
 for the use in phylogenetic analyses and taxonomic assignments, although
 it amplifies also paralogues. The fungal taxon spectra obtained with rbp2
 region and ITS1 corresponded, but sequence abundance differed widely,
 especially in the basal lineages. The proportions of OTU counts and read
 counts of major fungal groups were close to the reality when rpb2 was used
 as a molecular marker while they were strongly biased towards the
 Basidiomycota when using the ITS primers ITS1/ITS4. Although the taxonomic
 placement of rbp2 sequences is currently more difficult than that of the
 ITS sequences, its discriminative power, quantitative representation of
 community composition and suitability for phylogenetic analyses represent
 significant advantages.
description: MOCK_ITSSequence data from the mock comunity for the fungal ITS region.MOCK_rpb2Sequence data from the mock comunity for for the rpb2 gene.OTU_tablesOTU tables for the fungal ITS region and for the rpb2 gene.tree_data_Figure2Aligned fasta file as an input for the phylogeny tree in Figure 2.tree_data_Figure2Phylogeny tree from Figure 2 in NEXUS multiple alignment format.tree_data_Figure2Phylogeny tree from Figure 2 in Newick tree format.
DOI: 10.5061/dryad.c6688
title: Data from: Macroecological patterns of archaeal ammonia oxidizers in the Atlantic Ocean

description: Macroecological patterns are found in animals and plants, but also in
 micro-organisms. Macroecological and biogeographic distribution patterns
 in marine Archaea, however, have not been studied yet. Ammonia-oxidizing
 Archaea (AOA) show a bipolar distribution (i.e. similar communities in the
 northernmost and the southernmost locations, separated by distinct
 communities in the tropical and gyral regions) throughout the Atlantic,
 detectable from epipelagic to upper bathypelagic layers (&lt;2000 m
 depth). This tentatively suggests an influence of the epipelagic
 conditions of organic matter production on bathypelagic AOA communities.
 The AOA communities below 2000 m depth showed a less pronounced
 biogeographic distribution pattern than the upper 2000 m water column.
 Overall, AOA in the surface and deep Atlantic waters exhibit
 distance–decay relationships and follow the Rapoport rule in a similar way
 as bacterial communities and macroorganisms. This indicates a major role
 of environmental conditions in shaping the community composition and
 assembly (species sorting) and no, or only weak limits for dispersal in
 the oceanic thaumarchaeal communities. However, there is indication of a
 different strength of these relationships between AOA and Bacteria, linked
 to the intrinsic differences between these two domains.
description: OTUS
 pyrosequencingExcel table with the AOA
 OTUs abundance obtained from pyrosequencing. Sheet 1: forward sequenced,
 Sheet 2: reverse sequenced. Label indicates the name of the sample. Region
 and depth are also indicatedGPS
 coordinatesExcel table with the
 Cruise number, Station number during the cruise, cast, code for the
 station, sampling date, GPS coordinates, and final station number through
 the transectT-RFLP
 data
DOI: 10.5061/dryad.21qs5
title: Data from: Falling with style: bats perform complex aerial rotations by adjusting wing inertia

description: The remarkable maneuverability of flying animals results from precise
 movements of their highly specialized wings. Bats have evolved an
 impressive capacity to control their flight, in large part due to their
 ability to modulate wing shape, area, and angle of attack through many
 independently controlled joints. Bat wings, however, also contain many
 bones and relatively large muscles, and thus the ratio of bats’ wing mass
 to their body mass is larger than it is for all other extant flyers.
 Although the inertia in bat wings would typically be associated with
 decreased aerial maneuverability, we show that bat maneuvers challenge
 this notion. We use a model-based tracking algorithm to measure the wing
 and body kinematics of bats performing complex aerial rotations. Using a
 minimal model of a bat with only six degrees of kinematic freedom, we show
 that bats can perform body rolls by selectively retracting one wing during
 the flapping cycle. We also show that this maneuver does not rely on
 aerodynamic forces, and furthermore that a fruit fly, with nearly massless
 wings, would not exhibit this effect. Similar results are shown for a
 pitching maneuver. Finally, we combine high-resolution kinematics of wing
 and body movements during landing and falling maneuvers with a
 52-degree-of-freedom dynamical model of a bat to show that modulation of
 wing inertia plays the dominant role in reorienting the bat during landing
 and falling maneuvers, with minimal contribution from aerodynamic forces.
 Bats can, therefore, use their wings as multifunctional organs, capable of
 sophisticated aerodynamic and inertial dynamics not previously observed in
 other flying animals. This may also have implications for the control of
 aerial robotic vehicles.
description: tracked_dataZip file containing the tracked data from each of the landing and falling sequences analyzedEulerAnglesMeasured and Simulated Euler angles as a function of time for all 12 trials discussed in the manuscriptminimal_simulationMATLAB codes to perform minimal model simulationsfull_simulationPython codes to perform full model simulations
DOI: 10.5061/dryad.1bm8c
title: Data from: Fixation biases towards the index finger in almost-natural grasping

description: We use visual information to guide our grasping movements. When grasping
 an object with a precision grip, the two digits need to reach two
 different positions more or less simultaneously, but the eyes can only be
 directed to one position at a time. Several studies that have examined eye
 movements in grasping have found that people tend to direct their gaze
 near where their index finger will contact the object. Here we aimed at
 better understanding why people do so by asking participants to lift an
 object off a horizontal surface. They were to grasp the object with a
 precision grip while movements of their hand, eye and head were recorded.
 We confirmed that people tend to look closer to positions that a digit
 needs to reach more accurately. Moreover, we show that where they look as
 they reach for the object depends on where they were looking before,
 presumably because they try to minimize the time during which the eyes are
 moving so fast that no new visual information is acquired. Most
 importantly, we confirmed that people have a bias to direct gaze towards
 the index finger’s contact point rather than towards that of the thumb. In
 our study, this cannot be explained by the index finger contacting the
 object before the thumb. Instead, it appears to be because the index
 finger moves to a position that is hidden behind the object that is
 grasped, probably making this the place at which one is most likely to
 encounter unexpected problems that would benefit from visual guidance.
 However, this cannot explain the bias that was found in previous studies,
 where neither contact point was hidden, so it cannot be the only
 explanation for the bias.
description: All data files by all
 participants in all experimentsE* describes the
 experiment number, S* describes the participant number. Each file is a
 trial, except of the file with the name "stimlist" in which
 there is information about which condition was presented in each trial.
 More detailed information about what exactly is contained in the data and
 stimlist files is provided in the "readme"
 file.All
 data.zip
DOI: 10.5061/dryad.15237
title: Data from: Protein expression parallels thermal tolerance and ecologic changes in the diversification of a diving beetle species complex

description: Physiological changes associated with evolutionary and ecological
 processes such as diversification, range expansion or speciation are still
 incompletely understood, especially for non-model species. Here we study
 differences in protein expression in response to temperature in a western
 Mediterranean diving beetle species complex, using two-dimensional
 differential gel electrophoresis with one Moroccan and one Iberian
 population each of Agabus ramblae and Agabus brunneus. We identified
 proteins with significant expression differences after thermal treatments
 comparing them with a reference EST library generated from one of the
 species of the complex (A. ramblae). The colonisation during the Middle
 Pleistocene of the Iberian peninsula by A. ramblae, where maximum
 temperatures and seasonality are lower than in the ancestral north African
 range, was associated with changes in the response to 27 °C in proteins
 related to energy metabolism. The subsequent speciation of A. brunneus
 from within populations of Iberian A. ramblae was associated with changes
 in the expression of several stress-related proteins (mostly chaperons)
 when exposed to 4 °C. These changes are in agreement with the known
 tolerance to lower temperatures of A. brunneus, which occupies a larger
 geographical area with a wider range of climatic conditions. In both
 cases, protein expression changes paralleled the evolution of thermal
 tolerance and the climatic conditions experienced by the species. However,
 although the colonisation of the Iberian peninsula did not result in
 morphological change, the speciation process of A. brunneus within Iberia
 involved genetic isolation and substantial differences in male genitalia
 and body size and shape.
description: TableS1Table S1. Standardized volumes of the 563 spots common to all experiments for all treatments. Highlighted in green, spots which proteins have been identified (see Tables 2,3). RT: room temperature treatment (control). Biological replicas: r1, 2, 3.6569_documents_from_Agabus_454Fasta file with the contigs of the whole transcriptome of combined specimens of Agabus ramblae (Coleoptera, Dytiscidae) after being subjected for 12h to three temperature treatments: 4ºC, control (room temperature) and 27ºC.
DOI: 10.5061/dryad.hm5k9
title: Data from: Evaluating distributional shifts in home range estimates

description: A variety of methods are commonly used to quantify animal home ranges
 using location data acquired with telemetry. High-volume location data
 from global positioning system (GPS) technology provide researchers the
 opportunity to identify various intensities of use within home ranges,
 typically quantified through utilization distributions (UDs). However, the
 wide range of variability evident within UDs constructed with modern home
 range estimators is often overlooked or ignored during home range
 comparisons, and challenges may arise when summarizing distributional
 shifts among multiple UDs. We describe an approach to gain additional
 insight into home range changes by comparing UDs across isopleths and
 summarizing comparisons into meaningful results. To demonstrate the
 efficacy of this approach, we used GPS location data from 16 bighorn sheep
 (Ovis canadensis) to identify distributional changes before and after
 habitat alterations, and we discuss advantages in its application when
 comparing home range size, overlap, and joint-space use. We found a
 consistent increase in bighorn sheep home range size when measured across
 home range levels, but that home range overlap and similarity values
 decreased when examined at increasing core levels. Our results highlight
 the benefit of conducting multiscale assessments when comparing
 distributions, and we encourage researchers to expand comparative home
 range analyses to gain a more comprehensive evaluation of distributional
 changes and to evaluate comparisons across home range levels.
description: R Code for multi-level
 UD comparative measuresUDCodeArchive.RPaired comparison results in .csv formatIndexdata.csvBighorn #3 prefire BBMMbh3preBighorn #3 postfire BBMMbh3postBighorn #4 prefire BBMMbh4preBighorn #4 postfire BBMMbh4postBighorn #7 prefire BBMMbh7preBighorn #7 postfire BBMMbh7postBighorn #8 prefire BBMMbh8preBighorn #8 postfire BBMMbh8postBighorn #9 prefire BBMMbh9preBighorn #9 postfire BBMMbh9postBighorn #10 prefire BBMMbh10preBighorn #10 postfire BBMMbh10postBighorn #12 prefire BBMMbh12preBighorn #12 postfire BBMMbh12postBighorn #14 prefire BBMMbh14preBighorn #14 postfire BBMMbh14postBighorn #18 prefire BBMMbh18preBighorn #18 postfire BBMMbh18postBighorn #19 prefire BBMMbh19preBighorn #19 postfire BBMMbh19postBighorn #22 prefire BBMMbh22preBighorn #22 postfire BBMMbh22postBighorn #25 prefire BBMMbh25preBighorn #25 postfire BBMMbh25postBighorn #26 prefire BBMMbh26preBighorn #26 postfire BBMMbh26postBighorn #27 prefire BBMMbh27preBighorn #27 postfire BBMMbh27postBighorn #33 prefire BBMMbh33preBighorn #33 postfire BBMMbh33postBighorn #34 prefire BBMMbh34preBighorn #34 postfire BBMMbh34post
DOI: 10.18167/dvn1/79mu0r
title: Kaw Forest Censuses

description: Data from tree census in Kaw permanent forest plots, CIRAD, French Guiana in the &lt;a href="https://umr-ecofog.cirad.fr/organisation/dispositifs-experimentaux/guyafor-reseau-de-parcelles-forestieres"&gt;Guyafor network&lt;/a&gt;; &lt;a href="https://doi.org/10.18167/DVN1/B8FHHA"&gt;Guyafor Data Dictionary&lt;/a&gt;
DOI: 10.15468/dl.h73rpu
title: Occurrence Download

description: A dataset containing 3741 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Teleogryllus emma"
 ]
}

 The dataset includes 3741 records from 74 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001652-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.evju97
title: Occurrence Download

description: A dataset containing 779 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Papilio crino"
 ]
}

 The dataset includes 779 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001651-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.128p6
title: Data from: Antitropicality and convergent evolution: a case study of Permian neospiriferine brachiopods

description: Antitropical distribution is a biogeographical pattern characterized by
 natural occurrences of the same species or members of the same clade in
 the middle- or middle-to-high-latitudinal habitats of both hemispheres,
 either on land or in marine environments, without appearing in the
 intervening tropical environments. For most of the noted examples of
 Permian antitropical distribution, particularly in marine invertebrates,
 the causes of disjunctions have been mainly linked to either dispersal or
 vicariance models. Little attention has been paid to other possible
 mechanisms. This study investigated the antitropicality of some Permian
 neospiriferine brachiopods through detailed taxonomic revision, comparison
 of palaeobiogeographical distribution, and a phylogenetic analysis.
 Several species, previously assigned to Kaninospirifer, are here
 reassigned to other genera, especially to Fasciculatia in the northern
 hemisphere and to Quadrospira in the southern hemisphere during the
 Permian. Both Kaninospirifer and Fasciculatia appear to have been
 restricted to north-western Pangea and north-eastern Asia during the
 Permian, but there is no robust evidence to suggest their presence in the
 southern hemisphere to which Imperiospira and Quadrospira were confined.
 In spite of the distributional separation between the two pairs of
 neospiriferine genera in the Permian palaeobiogeographical regime, they
 share considerable numbers of morphological characters, such as a large
 shell, subdued fasciculation, and reduction of ventral adminicula.
 Notwithstanding these morphological similarities, our phylogenetic
 reconstruction of the neospiriferines does not support a close
 relationship between these genera. This therefore must indicate that these
 similar morphological features were independently acquired, probably with
 these taxa living in spatially separate but ecologically compatible
 environmental conditions in the mid-latitudinal area of each hemisphere
 during the Permian. We regard this as an example of convergent evolution.
description: Appendix S1. Localities
 of Kaninospirifer, Fasciculatia, Imperiospira, and Quadrospira with their
 current- and palaeo-coordinatesAppendixS1_Current-andPalaeo-Coordinates.xlsxAppendix S2. Full serial sections of Fasciculatia striatoparadoxaAppendixS2_FullSerialSectionsOfFasciculatiaStriatoparadoxa.pdf
DOI: 10.5061/dryad.42p5n
title: Data from: Irrational time allocation in decision-making

description: Time is an extremely valuable resource but little is known about the
 efficiency of time allocation in decision making. Empirical evidence
 suggests that in many ecologically relevant situations, decision
 difficulty and the relative reward from making a correct choice, compared
 to an incorrect one, are inversely linked, implying that it is optimal to
 use relatively less time for difficult choice problems. This applies, in
 particular, to value-based choices, in which the relative reward from
 choosing the higher-valued item shrinks as the values of the other options
 get closer to the best option and are thus more difficult to discriminate.
 Here, we experimentally show that people behave sub-optimally in such
 contexts. They do not respond to incentives that favor the allocation of
 time to choice problems in which the relative reward for choosing the best
 option is high; instead they spend too much time on problems in which the
 reward difference between the options is low. We demonstrate this by
 showing that it is possible to improve subjects’ time allocation with a
 simple intervention that cuts them off when their decisions take too long.
 Thus we provide a novel form of evidence that organisms systematically
 spend their valuable time in an inefficient way, and simultaneously offer
 a potential solution to the problem.
description: Study 1
 datakrajbich_data_study1.xlsStudy 2 dataCollected at Princeton University.study_2_data.xlsx
DOI: 10.15468/dl.peke9z
title: Occurrence Download

description: A dataset containing 387 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Helarctos malayanus",
 "Year 2010-2026"
 ]
}

 The dataset includes 387 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001653-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.