cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.gc1jf
title: Data from: Ecology and phylogenetic affinity of the early Cambrian tubular microfossil Megathrix longus

description: Abundant, exquisitely preserved specimens of the enigmatic tubular
 microfossil Megathrix longus are reported from the early Cambrian Yanjiahe
 Formation in the Yangtze Gorges area. Studies of their morphology and
 taphonomy reveal that the inner cross-wall of Megathrix longus is
 topographically flat, the trichome terminus is blunt and closed, and
 incomplete cross-walls are regularly intercalated between complete ones.
 The deformation of trichomes, as well as the corrugation of their
 cross-walls, are postmortem features caused by compaction, rather than
 biological features as previously interpreted. Statistical analysis
 indicates that chamber division is accomplished by the closure of
 incomplete cross-walls. This process, which contributed to trichome
 growth, is extremely similar to that of modern Oscillatoriaceae. Trichome
 fragmentation was also observed in a series of specimens, which closely
 resembles that of cyanobacteria, particularly the Oscillatoriaceae. The
 termini of Megathrix longus suggest that it was planktonic. In general,
 Megathrix longus bears a close affinity to the extant Oscillatoriaceae
 (Cyanophyta).
description: file1. Perpendicular to
 beddingThe table contains
 series of measurements for Megathrix longus in thin sections perpendicular
 to the bedding.file2. Parallel to
 beddingThe table contains
 series of measurements for Megathrix longus in thin sections parallel to
 the bedding.file3. measurements on
 selected trichomesThis table contains
 measurements on the selected trichomes with consistent diameter (67–70
 μm). From these data, we can get the positive linear correlation of
 complete cross-walls spacing and the intercalated incomplete cross-walls
 length.file3.
 Wp-F.xlsfile4. 3D morphological
 reconstructionThis file contains a
 three-dimensional model of Megathrix longus (after symmetrical cutting
 along the axis of a trichome).
DOI: 10.5061/dryad.4p7g1
title: Data from: Spotted in the news: using media reports to examine leopard distribution, depredation, and management practices outside protected areas in southern India

description: There is increasing evidence of large carnivore presence outside protected
 areas, globally. Although this spells conservation success through
 population recoveries, it makes carnivore persistence in human-use
 landscapes tenuous. The widespread distribution of leopards in certain
 regions of India typifies this problem. We obtained information on
 leopard-human interactions at a regional scale in Karnataka State, India,
 based on systematic surveys of local media reports. We applied an
 innovative occupancy modelling approach to map their distribution patterns
 and identify hotspots of livestock/human depredation. We also evaluated
 management responses like removals of ‘problem’ leopards through capture
 and translocations. Leopards occupied around 84,000 km2 or 47% of the
 State’s geographic area, outside designated national parks and wildlife
 sanctuaries. Their presence was facilitated by extent of vegetative cover-
 including irrigated croplands, rocky escarpments, and prey base in the
 form of feral and free-ranging dogs. Higher probabilities of
 livestock/human attacks by leopards were associated with similar
 ecological features as well as with capture/removals of leopards. Of the
 56 cases of leopard removals reported, 91% did not involve human attacks,
 but followed livestock predation or only leopard sightings. The lack of
 knowledge on leopard ecology in human-use areas has resulted in
 unscientific interventions, which could aggravate the problem rather than
 mitigating it. Our results establish the presence of resident, breeding
 leopards in human-use areas. We therefore propose a shift in management
 focus, from current reactive practices like removal and translocation of
 leopards, to proactive measures that ensure safety of human lives and
 livelihoods.
description: Leopard Media Reports:
 SpreadsheetsThe compressed folder
 has two excel files. (a) NewspaperRecords.xlsx includes the list of
 newspapers from where data were extracted, data, type of event and the
 location. (b) LeopardMediaReports_DetectionMatrices.xlsx has two sheets
 with detection matrices; the first sheet refers to detection/non-detection
 of all events and the second sheet includes records of non-detection (0),
 detection of presence only (1), and detection of conflict incidents
 (2).LeopardMediaReports_Spreadsheets.zip
DOI: 10.5061/dryad.tv54037
title: Data from: Novel traits, flower symmetry, and transcriptional autoregulation: new hypotheses from bioinformatic and experimental data

description: A common feature in developmental networks is the autoregulation of
 transcription factors which, in turn, positively or negatively regulate
 additional genes critical for developmental patterning. When a
 transcription factor regulates its own expression by binding to
 cis-regulatory sites in its gene, the regulation is direct transcriptional
 autoregulation (DTA). Indirect transcriptional autoregulation (ITA)
 involves regulation by proteins expressed downstream of the target
 transcription factor. We review evidence for a hypothesized role of DTA in
 the evolution and development of novel flowering plant phenotypes. We
 additionally provide new bioinformatic and experimental analyses that
 support a role for transcriptional autoregulation in the evolution of
 flower symmetry. We find that 5' upstream non-coding regions are
 significantly enriched for predicted autoregulatory sites in Lamiales
 CYCLOIDEA genes—an upstream regulator of flower monosymmetry. This
 suggests a possible correlation between autoregulation of CYCLOIDEA and
 the origin of monosymmetric flowers near the base of Lamiales, a pattern
 that may be correlated with independently derived monosymmetry across
 eudicot lineages. We find additional evidence for transcriptional
 autoregulation in the flower symmetry program, and report that Antirrhinum
 DRIF2 may undergo ITA. In light of existing data and new data presented
 here, we hypothesize how cis-acting autoregulatory sites originate, and
 find evidence that such sites (and DTA) can arise subsequent to the
 evolution of a novel phenotype.
description: Sengupta and Hileman
 data files
DOI: 10.5061/dryad.h2900
title: Data from: Patagonian Eocene Archaeopithecidae Ameghino, 1897 (Notoungulata): systematic revision, phylogeny and biostratigraphy

description: The Archaeopithecidae is a very poorly known group of native ungulates
 from the Eocene of Patagonia (Argentina), whose alpha taxonomy has
 remained obscure since Ameghino’s times. It is traditionally considered as
 a family representative of the Casamayoran (middle Eocene) South American
 Land Mammal Age and it is thought to be morphologically close to the
 notopithecids. After studying more than 200 specimens from several
 institutions, including all the type specimens, a taxonomic overestimation
 is established. Out of the six species considered originally as
 archaeopithecids, Archaeopithecus rogeri is here recognized as the only
 valid name and species; subsequent synonymies are proposed and previous
 taxonomic hypotheses discarded. This exhaustive revision has permitted
 improving the knowledge of A. rogeri and, for the first time, it has
 revealed many craniodental characters which allow amending its diagnosis
 and differentiating this taxon from other Eocene notoungulates.
 Archaeopithecus rogeri is a small-sized taxon characterized by its
 complete and rooted dentition, which is relatively higher than that of
 other contemporaneous short-crowned notoungulates and shows ontogenetic
 variation in size and morphology. The body mass range of A. rogeri
 (1.4–2.5 kg) is comparable to those of notopithecids and some small
 hegetotheriids. The phylogenetic analysis shows A. rogeri is not directly
 related to any family within Notoungulata, appearing into a polytomy, as a
 basal taxon of typotherians. The biochronological range of A. rogeri is
 adjusted to Vacan (middle Eocene) through the Barrancan subages (late
 middle Eocene); older (Riochican, late early Eocene) and younger
 (Mustersan, late Eocene) records remain to be confirmed.
description: List of characters
 utilized in the phylogenetic analysisSupplemental Data 1.
 List of characters utilized in the phylogenetic analysis. Modified from
 Vera (2016).Supplemental Data 1_Vera
 R3.docData matrix used in the
 phylogenetic analysis (modified from Vera, 2016).Supplemental Data 2.
 Data matrix used in the phylogenetic analysis (modified from Vera, 2016).
 Abbreviations: - , inapplicable character; ?, missing
 dataSupplemental Data 2_Vera
 R3.docDescriptive statistics
 for upper and lower cheek teeth of Archaeopithecus rogeri considering
 three levels of wear.Supplemental Data 3.
 Descriptive statistics for upper and lower cheek teeth of Archaeopithecus
 rogeri considering three levels of wear. SW (stage of wear) = 1, little;
 2, middle; 3, heavy (see text for details). CV (coefficient of variation)
 = 100 × (SD/mean). Measurements in mm.Supplemental Data 3_Vera
 R3.docx
DOI: 10.5061/dryad.73r1b
title: Data from: Adaptive plasticity and epigenetic variation in response to warming in an Alpine plant

description: Environmentally induced phenotypic plasticity may be a critical component
 of response to changing environments. We examined local differentiation
 and adaptive phenotypic plasticity in response to elevated temperature in
 half-sib lines collected across an elevation gradient for the alpine herb,
 Wahlenbergia ceracea. Using Amplified Fragment Length Polymorphism (AFLP),
 we found low but significant genetic differentiation between low- and
 high-elevation seedlings, and seedlings originating from low elevations
 grew faster and showed stronger temperature responses (more plasticity)
 than those from medium and high elevations. Furthermore, plasticity was
 more often adaptive for plants of low-elevation origin and maladaptive for
 plants of high elevation. With methylation sensitive-AFLP (MS-AFLP), we
 revealed an increase in epigenetic variation in response to temperature in
 low-elevation seedlings. Although we did not find significant direct
 correlations between MS-AFLP loci and phenotypes, our results demonstrate
 that adaptive plasticity in temperature response to warming varies over
 fine spatial scales and suggest the involvement of epigenetic mechanisms
 in this response.
description: Adaptive plasticity and
 epigenetic variation in Wahlenbergia ceraceaFile contains AFLP,
 MS-AFLP, trait data and plasticity indices as an excel
 workbook.nicotra wahlenbergia for
 DRYAD.xlsx
DOI: 10.5061/dryad.14cf0
title: Data from: Combinations of plant water-stress and neonicotinoids can lead to secondary outbreaks of Banks grass mite (Oligonychus pratensis Banks)

description: Spider mites, a cosmopolitan pest of agricultural and landscape plants,
 thrive under hot and dry conditions, which could become more frequent and
 extreme due to climate change. Recent work has shown that neonicotinoids,
 a widely used class of systemic insecticides that have come under scrutiny
 for non-target effects, can elevate spider mite populations. Both
 water-stress and neonicotinoids independently alter plant resistance
 against herbivores. Yet, the interaction between these two factors on
 spider mites is unclear, particularly for Banks grass mite (Oligonychus
 pratensis; BGM). We conducted a field study to examine the effects of
 water-stress (optimal irrigation = 100% estimated evapotranspiration (ET)
 replacement, water stress = 25% of the water provided to optimally
 irrigated plants) and neonicotinoid seed treatments (control,
 clothianidin, thiamethoxam) on resident mite populations in corn (Zea
 mays, hybrid KSC7112). Our field study was followed by a manipulative
 field cage study and a parallel greenhouse study, where we tested the
 effects of water-stress and neonicotinoids on BGM and plant responses. We
 found that water-stress and clothianidin consistently increased BGM
 densities, while thiamethoxam-treated plants only had this effect when
 plants were mature. Water-stress and BGM herbivory had a greater effect on
 plant defenses than neonicotinoids alone, and the combination of BGM
 herbivory with the two abiotic factors increased the concentration of
 total soluble proteins. These results suggest that spider mite outbreaks
 by combinations of changes in plant defenses and protein concentration are
 triggered by water-stress and neonicotinoids, but the severity of the
 infestations varies depending on the insecticide active ingredient.
description: Data from: Combinations
 of plant water-stress and neonicotinoids can lead to secondary outbreaks
 of Banks grass mite (Oligonychus pratensis Banks)These data are a
 collection of field and greenhouse studies conducted in northern Utah in
 2013 and 2015. A series of Excel files were used to document the responses
 of spider mites and plant phenotypes to neonicotinoid pesticides and
 drought stresses.BGMxNEONICxDROUGHT.zip
DOI: 10.5061/dryad.r4c7r
title: Data from: The genetic architecture of a complex ecological trait: host plant use in the specialist moth, Heliothis subflexa

description: We used genetic mapping to examine the genetic architecture of differences
 in host plant use between two species of noctuid moths, Heliothis
 subflexa, a specialist on Physalis spp., and its close relative, the broad
 generalist H. virescens. We introgressed H. subflexa chromosomes into the
 H. virescens background and analyzed 1,462 backcross insects. The effects
 of H. subflexa-origin chromosomes were small when measured as the percent
 variation explained in backcross populations (0.2 to 5%), but were larger
 when considered in relation to the interspecific difference explained (1.5
 to 165%). Most significant chromosomes had effects on more than one trait,
 and their effects varied between years, sexes, and genetic backgrounds.
 Different chromosomes could produce similar phenotypes, suggesting that
 the same trait might be controlled by different chromosomes in different
 backcross populations. It appears that many loci of small effect
 contribute to the use of Physalis by H. subflexa. We hypothesize that
 behavioral changes may have paved the way for physiological adaptation to
 Physalis by the generalist ancestor of H. subflexa and H. virescens.
description: Oppenheim phenotypes and
 genotypesFile includes phenotypes
 and marker genotypes of all assayed insects.Oppenheim permutation
 resultsFile contains results of
 permutation tests of marker-phenotype association for all traits discussed
 in the manuscript. Empirical significance thresholds are given in the
 file.
DOI: 10.5061/dryad.v6p96q5
title: Data from: Proximity to canopy mediates changes in the defensive chemistry and herbivore loads of an understory tropical shrub, Piper kelleyi

description: Phytochemical traits are a key component of plant defense theory. Chemical
 ecology has been biased towards studying effects of individual metabolites
 even though effective plant defenses are comprised of diverse mixtures of
 metabolites. We tested the phytochemical landscape hypothesis, positing
 that trophic interactions are contingent upon their spatial location
 across a phytochemically diverse landscape. Specifically, intraspecific
 phytochemical changes associated with vertical strata in forests were
 hypothesized to affect herbivore communities of the neotropical shrub
 Piper kelleyi Tepe (Piperaceae). Using a field experiment, we found that
 phytochemical diversity increased with canopy height, and higher levels of
 phytochemical diversity located near the canopy were characterized by
 tradeoffs between photoactive and non-photoactive biosynthetic pathways.
 For understory plants closer to the ground, phytochemical diversity
 increased as direct light transmittance decreased, and these plants were
 characterized by up to 37% reductions in herbivory. Our results suggest
 that intraspecific phytochemical diversity structures herbivore
 communities across the landscape, affecting total herbivory.
description: LCMS annotated
 peaksSpreadsheet contains
 LCMS identified and unidentified peaks. Includes relative
 concentrations.LCMS_annotated.xlsNMR Diversity & EcologicalDataSpreadsheet contains NMR diversity indices for each sample. The ecological data is included.NMR_EcologicalData.xlsx
DOI: 10.5061/dryad.k0fs1
title: Data from: Successive invasion-mediated interspecific hybridizations and population structure in the endangered cichlid Oreochromis mossambicus

description: Hybridization between invasive and native species accounts among the major
 and pernicious threats to biodiversity. The Mozambique tilapia Oreochromis
 mossambicus, a widely used freshwater aquaculture species, is especially
 imperiled by this phenomenon since it is recognized by the IUCN as an
 endangered taxon due to genetic admixture with O. niloticus an invasive
 congeneric species. The Lower Limpopo and the intermittent Changane River
 (Mozambique) drain large wetlands of potentially great importance for
 conservation of O. mossambicus, but their populations have remained
 unstudied until today. Therefore we aimed (1) to estimate the
 autochthonous diversity and population structure among genetically pure O.
 mossambicus populations to provide a baseline for the conservation
 genetics of this endangered species, (2) to quantify and describe genetic
 variation of the invasive populations and investigate the most likely
 factors influencing their spread, (3) to identify O. mossambicus
 populations unaffected by hybridization. Bayesian assignment tests based
 on 423 AFLP loci and the distribution of 36 species-specific mitochondrial
 haplotypes both indicate a low frequency of invasive and hybrid genotypes
 throughout the system, but nevertheless reveal evidence for limited
 expansion of two alien species (O. niloticus and O. andersonii) and their
 hybrids in the Lower Limpopo. O. mossambicus populations with no traces of
 hybridization are identified. They exhibit a significant genetic
 structure. This contrasts with previously published estimates and provides
 rather promising auspices for the conservation of O. mossambicus.
 Especially, parts of the Upper Changane drainage and surrounding wetlands
 are identified as refugial zones for O. mossambicus populations. They
 should therefore receive high conservation priority and could represent
 valuable candidates for the development of aquaculture strains based on
 local genetic resources.
description: AFLPdat_Archive_240313AFLP genotypes for 376 individuals and 423 loci. Sampling origin is indicated in the second column.
DOI: 10.5061/dryad.196m2
title: Data from: Breathing frequency bias in fractal analysis of heart rate variability

description: Detrended Fluctuation Analysis (DFA) is an algorithm widely used to
 determine fractal long-range correlations in physiological signals. Its
 application to heart rate variability (HRV) has proven useful in
 distinguishing healthy subjects from patients with cardiovascular disease.
 In this study we examined the effect of respiratory sinus arrhythmia (RSA)
 on the performance of DFA applied to HRV. Predictions based on a
 mathematical model were compared with those obtained from a sample of 14
 normal subjects at three breathing frequencies: 0.1 Hz, 0.2 Hz and 0.25
 Hz. Results revealed that: (1) the periodical properties of RSA produce a
 change of the correlation exponent in HRV at a scale corresponding to the
 respiratory period, (2) the short-term DFA exponent is significantly
 reduced when breathing frequency rises from 0.1 Hz to 0.2 Hz. These
 findings raise important methodological questions regarding the
 application of fractal measures to short-term HRV.
description: Heart rate
 data0007.txt
DOI: 10.5061/dryad.k66c0
title: Data from: High interannual variation in the diet of a tropical forest frugivore (Hylobates lar)

description: Frugivores must deal with seasonal changes in fruit availability and
 changes from year to year, as most species of tropical forest fruiting
 trees have considerable interannual variation in phenology and many are
 mast fruiters. We quantified seasonal and interannual changes in the fruit
 diet in a frugivore and important seed disperser, the white-handed gibbon,
 Hylobates lar, in Thailand. We used 40-day following data during April and
 May replicated in six consecutive years to study interannual variability
 in the diet, and compared it with seasonal changes measured in monthly
 samples of the same size collected in three successive years. The 40-day
 periods of following also allowed us to measure the decline in dietary
 similarity with time over a finer scale. We measured fruit diet similarity
 between replicated 5-day periods using the percentage overlap (Renkonen’s)
 index, and Jaccard’s similarity index. Seasonally, average dietary overlap
 between adjacent months was low, and similarity approached zero after four
 months. Average rate of decline in similarity exceeded 20 percent per five
 day period. Variation in fruit species in the diet between years was high,
 and was correlated with interannual variation in fruiting phenology. The
 strongest correlation occurred in the case of Nephelium melliferum, a
 highly preferred species that dominated the diet in good fruiting years.
 It is difficult to separate changes in food-species preference from
 changes in availability from year to year. We devised a relative measure
 of preference that depends on the degree to which the gibbons rely on
 prior knowledge to find sources.
description: Suwanvecho et al.Gibbon
 foods_2006-2011This file contains data
 on fruit species eaten by the gibbon study group A during April-May
 follows for the six years 2006-2011. It contains for each visit to a fruit
 source: the tree species and tree number visited, date, time and fruit
 species code; and a summary of sources, no. of visits and no. of days for
 each species. The full species names are given in a separate sheet, copied
 from the SI on line file associated with Suwanvecho et al. 2017 in
 Biotropica.