cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.gqnk98shq
title: Bending and Looping of long DNA by Polycomb repressive complex 2 revealed by AFM imaging in liquid

description: Polycomb repressive complex 2 (PRC2) is a histone methyltransferase that
 methylates histone H3 at Lysine 27. PRC2 is critical for epigenetic gene
 silencing, cellular differentiation, and the formation of facultative
 heterochromatin. It can also promote or inhibit oncogenesis. Despite this
 importance, the molecular mechanisms by which PRC2 compacts chromatin are
 relatively understudied. Here, we visualized the binding of PRC2 to naked
 DNA in liquid at the single-molecule level using atomic force microscopy.
 Analysis of the resulting images showed PRC2, consisting of 5 subunits
 (EZH2, EED, SUZ12, AEBP2, and RBBP4), bound to a 2.5-kbp DNA with an
 apparent dissociation constant (KdApp) of 150 ± 12 nM. PRC2 did not show
 sequence-specific binding to a region of high GC content (76%) derived
 from a CpG island embedded in such a long DNA substrate. At higher
 concentrations, PRC2 compacted DNA by forming DNA loops typically anchored
 by two or more PRC2 molecules. Additionally, PRC2 binding led to a 3-fold
 increase in the local bending of DNA’s helical backbone and no evidence of
 DNA wrapping around the protein. We suggest that the bending and looping
 of DNA by PRC2, independent of PRC2’s methylation activity, may contribute
 to heterochromatin formation and therefore epigenetic gene silencing.
description: Polyacrilamide gel exlectrophoresis (PAGE) gels and AFM images /
 metadata.
description: AFM images organized by PRC2 moiety (catalytic, 5mer, regulatory)
 and DNA substrate type (12x601 Widom, GC island ( = GC-rich), GC poor (=
 AT-rich)).  Control data (.e.g only PRC2, only DNA, or DNA bound to the
 restriction enzyme BSP-MI) are also included. Each file
 is a .zip file, containing one or more folders with the data and a README
 describing the data and the folders.
DOI: 10.15468/dl.dejfa5
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Etmopterus caudistigmus"
 ]
}

 The dataset includes 9 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002112-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.k98sf7m35
title: Local climate determines vulnerability to camouflage mismatch in snowshoe hares

description: Aim: Phenological mismatches, when life-events become mistimed
 with optimal en- vironmental conditions, have become increasingly common
 under climate change. Population-level susceptibility to mismatches
 depends on how phenology and pheno- typic plasticity vary across a
 species’ distributional range. Here, we quantify the envi- ronmental
 drivers of colour moult phenology, phenotypic plasticity, and the extent
 of phenological mismatch in seasonal camouflage to assess vulnerability to
 mismatch in a common North American mammal. Location: North
 America. Time period: 2010–2017. Major taxa
 studied: Snowshoe hare (Lepus americanus). Methods: We
 used &gt; 5,500 by-catch photographs of snowshoe hares from 448 re-
 mote camera trap sites at three independent study areas. To quantify moult
 phenol- ogy and phenotypic plasticity, we used multinomial logistic
 regression models that incorporated geospatial and high-resolution climate
 data. We estimated occurrence of camouflage mismatch between hares’ coat
 colour and the presence and absence of snow over 7 years of monitoring.
 Results: Spatial and temporal variation in moult phenology
 depended on local climate conditions more so than on latitude. First,
 hares in colder, snowier areas moulted earlier in the fall and later in
 the spring. Next, hares exhibited phenotypic plasticity in moult phenology
 in response to annual variation in temperature and snow dura- tion,
 especially in the spring. Finally, the occurrence of camouflage mismatch
 varied in space and time; white hares on dark, snowless background
 occurred primarily during low-snow years in regions characterized by
 shallow, short-lasting snowpack. Main conclusions: Long-term
 climate and annual variation in snow and temperature determine coat colour
 moult phenology in snowshoe hares. In most areas, climate change leads to
 shorter snow seasons, but the occurrence of camouflage mismatch varies
 across the species’ range. Our results underscore the population-specific
 sus- ceptibility to climate change-induced stressors and the necessity to
 understand this variation to prioritize the populations most vulnerable
 under global environmental change.
DOI: 10.5061/dryad.p8cz8w9kr
title: Multi-scale landscape genetics of American marten at their southern range periphery

description: American marten (Martes americana) are a conservation priority in many
 forested regions of North America. Populations are fragmented at the
 southern edge of their distribution due to suboptimal habitat conditions.
 Facilitating gene flow may improve population resilience through genetic
 and demographic rescue. We used a multi-scale approach to estimate the
 relationship between genetic connectivity and landscape characteristics
 among individuals at three scales in the northeastern United States:
 regional, subregional, and local. We integrated multiple modeling
 techniques and identified top models based on consensus. Top models were
 used to parameterize resistance surfaces at each scale, and circuit theory
 was used to identify potential movement corridors. Regional gene flow was
 affected by forest cover, elevation, developed land cover, and slope. At
 subregional and local scales, effects were site-specific and included
 subsets of temperature, elevation, developed land cover, and slope.
 Developed land cover significantly affected gene flow in all sites
 examined at each scale. At finer scales, lack of variance in forest cover
 may have limited the ability to detect a relationship with gene flow. The
 effect of slope on gene flow was positive or negative depending on the
 site examined. Occupancy probability was a relatively poor predictor and
 we caution its use as a proxy for landscape resistance. Our results
 underscore the importance of replication and multi-scale approaches in
 landscape genetics. Climate warming and landscape conversion may reduce
 the genetic connectivity of marten populations in the northeastern United
 States and represent the primary challenges to marten conservation at the
 southern periphery of their range.
DOI: 10.5061/dryad.cfxpnvx2j
title: Migration-tracking integrated phylogeography supports long-distance dispersal-driven divergence for a migratory bird species in the Japanese archipelago

description: Previous phylogeographic studies of migratory bird species have not
 discriminated long-distance dispersal (LDD) from vicariant
 speciation in their diversification process. We conducted an integrative
 phylogeographic approach to test the LDD hypothesis, which predicts that a
 Japanese migratory bird subspecies diverged from a population in the
 coastal region of the East China Sea (CRECS) via LDD over the East China
 Sea (ECS). We used the Brown Shrike as a model species, and we conducted
 molecular phylogenetics, species distribution models (SDMs) and migration
 tracking. We assessed whether the LDD hypothesis is applicable to the
 divergence history of the Japanese subspecies of the Brown Shrike. The
 datasets include three zipped files, namely DataS1.zip, DataS2.zip, and
 DataS3.zip. See the READ ME (AOKI_et_al_2021_DATASET_README.txt) for how
 each of the folder and files contained in them can be used to reproduce
 our results. DataS1.zip inlcudes an xml file to conduct the BEAST
 analysis. Molecular data, which include nucleotide sequences
 obtained for cytochrome b (cytb), cytochrome oxidase c subunit I (COI),
 myoglobin intron-2 (MB) and transforming growth factor beta 2 intron-5
 (TGFb2), have been all reposited to DDBJ international nucleotide sequence
 database, and accession numbers have been already given to them. Accession
 numbers are provided in the appendix attached to the main manuscript.
 DataS2.zip includes several data that are related to produce occurrence
 data of the Brown Shrike used in the analysis and an R code to
 reproduce the SDMs. Explanatory climatic variables are all available at
 WorldClim v.1.4 (Hijmans et al., 2005), which are processed in the R code.
 DataS3.zip includes migratory route analyses using light-level geolocator
 data are available as the original light-level data and R codes.
 Sensitivity analyses were also conducted in these analyses, but their
 codes and results are seperately provided here.
description: See the READ ME (AOKI_et_al_2021_DATASET_README.txt) for how each
 of the folder and files contained in them can be used to reproduce our
 results.
DOI: 10.15468/k6ghva
title: A review of geographic variation in the monocled cobra, Naja kaouthia Lesson, 1831 (Serpentes: Elapidae) with the designation of a neotype

description: This dataset contains the digitized treatments in Plazi based on the original journal article Balchan, Neil R., Esquerré, Damien, Wogan, Guinevere O. U., Wüster, Wolfgang (2025): A review of geographic variation in the monocled cobra, Naja kaouthia Lesson, 1831 (Serpentes: Elapidae) with the designation of a neotype. Zootaxa 5717 (4): 488-516, DOI: 10.11646/zootaxa.5717.4.2, URL: https://doi.org/10.11646/zootaxa.5717.4.2AbstractThe monocled cobra (Naja kaouthia Lesson, 1831) is a medically important elapid snake with substantial geographic variation across South and Southeast Asia. Throughout its broad distribution, spanning various major ecoregions and habitat types, N. kaouthia displays a great amount of phenotypic variation. Recent taxonomic developments in the Asiatic cobras (Naja, subgenus Naja), namely the description of a new species (Naja fuxi Shi et al. 2022), have resulted in confusion regarding the affinities of non-spitting cobras across Indochina. Due to close morphological resemblances and poorly resolved phylogenetic relationships among three sympatric and/or parapatric taxa (N. atra, N. fuxi, and N. kaouthia), additional research is needed to disentangle species limits, evolutionary history, ecology, and distribution of these species from one another. A long history of taxonomic confusion and ambiguity in this group, combined with the suggestion of additional cryptic and unrecognized diversity, underscores a need for continued study of the Asiatic cobras. Consequently, we summarize information on N. kaouthia, compiling data on geographic distribution, phylogenetic relationships, phenotypic variation, venom variation, and venom spitting behavior. While distribution-wide trends do appear to be present for some characteristics (i.e., regional trends in venom spitting behavior, body coloring and patterns), they are apparently lacking or poorly defined for others (i.e., trends in venom composition). In view of future study on N. kaouthia, and accounting for the missing holotype, we designate a neotype for the species, thereby restricting the type locality to 24 Parganas, West Bengal, India, within the original ambiguous type locality of “Bengale, Inde”. Future taxonomic treatments resulting in the recognition of additional diversity within N. kaouthia will thus require that the name be maintained for snakes from the newly restricted type locality. We encourage detailed investigation on the Asiatic cobras using integrative lines of evidence combining mitochondrial, nuclear, and morphological datasets, but emphasize that nomenclatural decisions should only be made with a large body of supporting evidence.
DOI: 10.5061/dryad.tmpg4f4v5
title: Female preference and adverse developmental effects of glyphosate-based herbicides on ecologically relevant traits in Japanese quail

description: Controversial glyphosate-based herbicides (GBHs) are the most frequently
 used herbicides globally. An increasing number of studies have identified
 GBH residues in soil, water and even human food that may expose non-target
 organism including wildlife, livestock, and humans to health risks. After
 a heated debate, European Union allowed the use of GBHs to continue until
 2022, after which their risks will be re-evaluated. Thus, decision makers
 urgently need scientific evidence on GBH residues and their possible
 effects on ecosystems. An important, yet neglected, aspect is to assess
 whether animals show preference or avoidance for GBH contaminated food, as
 it can influence the likelihood of adverse health effects in wildlife.
 Here, using Japanese quails (Coturnix japonica) as our model, we show that
 females preferred GBH-contaminated food compared to control food. In
 females, exposure to GBHs caused delayed plumage development, and GBH
 residues were present in eggs, muscles and liver. These results indicate
 that female preference is not adaptive, potentially exposing non-target
 animals to greater risk of adverse effects of GBHs in natural and
 agricultural environments. Our results on tissue residues suggest that
 further studies are needed to understand the risks of such residues in the
 food chain.
DOI: 10.5061/dryad.s1rn8pk41
title: Data to accompany manuscript: Detection and tracking of cracks based on thermoelastic stress analysis

description: Thermoelastic stress analysis datasets were collected during tensile
 loading of hole-in-plate aluminium alloy specimens, at both constant
 amplitude and frequency conditions, and at variable amplitude and
 frequency conditions - based on an idealised flight cycle. Data were
 collected during initiation and propagation of a fatigue crack and
 monitored using three types of infra-red detector at different price
 points.   -------------------------- This dataset accompanies the
 manuscript: Detection and tracking of cracks based on thermoelastic stress
 analysis Middleton C. A.1, Weihrauch, M.1, Christian, W. J. R.1, Greene,
 R. J.2, and Patterson, E. A.1 1School of Engineering, University of
 Liverpool, The Quadrangle, Brownlow Hill, Liverpool, L69 3GH, U.K. 2Strain
 Solutions Ltd, Dunston Innovation Centre, Dunston Road, Chesterfield,
 Derbyshire S41 8NG, U.K. Royal Society Open Science, Accepted: 26 November
 2020    
description: Please see uploaded ReadMe file.
description: Please see uploaded ReadMe file.
DOI: 10.5061/dryad.7sqv9s4p9
title: Data from: Sympatric wren-warblers partition acoustic signal space and song perch height

description: Animals employing acoustic signals, such as birds, must effectively
 communicate over both background noise and potentially attenuating objects
 in the environment. To surmount these obstacles, animals evolve
 species-specific acoustic signals that do not overlap with sources of
 interference (such as songs of close relatives), and issue these songs
 from locations that maximize transmission. In multispecies assemblages of
 birds, the acoustic resource may thus be interspecifically partitioned
 along multiple axes, including song perch height and signal space.
 However, very few such studies have focused on open habitats, where
 differences in sound transmission patterns and limited availability of
 song perches may drive competition across multiple axes within signal
 space. Here, we demonstrate acoustic signal space partitioning in four
 sympatric species of wren-warbler (Cisticolidae, Prinia), in an Indian dry
 deciduous scrub-grassland habitat. We found that the breeding songs of the
 four species partition acoustic signal space, resulting in interspecific
 community organization. Within each species’ signal space, we uncovered
 different intraspecific patterns in note diversity. Two species
 partitioned intraspecific signal space into multiple note types, whereas
 the other two varied note repetition rate to different extents. Finally,
 we found that the four species also partition song perch heights, thus
 exhibiting acoustic niche separation along multiple axes. We hypothesize
 that divergent song perch heights may be driven by competition for higher
 singing perches or other ecological factors rather than signal
 propagation. Acoustic signal partitioning along multiple axes may
 therefore arise from a combination of diverse ecological processes.
description: Data related to the manuscript are all within these files.
 song_data and call_data MAT files contain all the song and call data used
 here. In each, P contains the species classifications and vbls contains
 the parameter names. The randomisation and shuffling stats files contain
 the mean distances from the randomised distributions as well as the
 observed. In all cases, g is P.hodgsonii, j is P. sylvatica, a is
 P.socialis and p is P.inornata. The song PC space contains the results of
 PCA, whereas the NT clusters file contains NT variables representing note
 type classifications for each species. Codes are also attached as M files
 and MATLAb live scripts. Further information is in the manuscript
 supplementary.
DOI: 10.5061/dryad.2v6wwpzhm
title: Collapse of dispersal trait diversity across a long-term chronosequence reveals a strong negative impact of frugivore extinctions on forest resilience

description: 1. Understanding how seed dispersal disruption may alter plant community
 diversity and dynamics over a large temporal scale remains a challenge.
 Here, we use a long-term chronosequence to compare changes in the richness
 and composition of different dispersal trait assemblages in communities
 established before and after human colonisation in the Mascarene
 archipelago. 2. Our study was located on Réunion on the slopes of the
 Piton de la Fournaise, one of the most active volcanoes worldwide. We
 analysed 151 vegetation surveys on lava flows dated between 1401-AD and
 1956-AD and in tropical rainforests established on older substrata. We
 defined five classes of substratum age, according to the well-known
 chronology of native frugivore defaunation: “old substrata” and [1401,
 1665[ when frugivores were abundant and diverse before permanent human
 settlement; [1665, 1800[ when large-bodied frugivore populations were
 strongly reduced; [1800, 1900[ when large-bodied frugivores went extinct
 and small-bodied frugivores were still abundant; [1900, 1956] decline in
 the population of small-bodied frugivores. Based on dispersal traits, we
 categorised 146 native woody species as anemochorous, small fleshy-fruited
 or large fleshy-fruited, i.e. plant of which fruit could not theoretically
 be dispersed by extant frugivores. 3. Changes in dispersal trait diversity
 strongly correlated with the chronology of defaunation. Species-rich
 communities settled before human colonisation were strongly dominated by
 fleshy-fruited species. Large fleshy-fruited plants in the oldest
 communities settled after human colonisation declined markedly and almost
 disappeared after 1800. The richness of small fleshy-fruited plants
 decreased less rapidly across the chronosequence, with medium levels on
 [1665, 1800[ and [1800, 1900[ lava flows and low levels on [1900, 1956]
 lava flows. Conversely, the richness of anemochorous plants remained
 unchanged. Communities settled before human colonisation had a similar
 composition. Fleshy-fruited assemblages showed strong species loss across
 the chronosequence, while anemochorous assemblages showed strong species
 turnover, which was probably due to lower dispersal limitation. 4.
 Synthesis. Our results provide the first insights into the tremendous
 impact that frugivore extinction has on plant colonisation dynamics over
 300 years. The dramatic loss of fleshy-fruited plant diversity on
 historical lava flows highlights the irreplaceable dispersal role played
 by frugivores, especially large-bodied species. The conservation of
 plant-animal mutualistic interactions is invaluable and refaunation
 efforts need to be undertaken in areas where frugivores have been
 extirpated.
DOI: 10.5061/dryad.m0cfxpp02
title: Character displacement drives floral variation in Pelargonium (Geraniaceae) communities

description: Interactions between plant community members are an underexplored driver
 of angiosperm floral variation. We investigate character displacement as a
 potential contributor to floral variation in Pelargonium communities.
 Pelargoniums all place pollen on the ventral sides of their pollinators,
 potentially leading to interspecific pollen transfer (IPT) in sympatry. We
 show that the positions of pollen placement and receipt are determined by
 anther and style exsertion lengths. Using field experiments, we
 demonstrate that heterospecific species experience high IPT if they have
 similar style lengths. In contrast, heterospecific species with greater
 style length differences experience less IPT. Using crosses, we show that
 IPT has negative consequences on seed set. In combination, these results
 suggest that character displacement in style length is likely to reduce
 IPT and increase female fitness in sympatry. Patterns of style length
 variation across twenty-nine different Pelargonium communities suggest
 that character displacement has occurred in multiple communities.
 Furthermore, analyses using a wide-ranging species pair show that style
 lengths are more different between sympatric populations than they are
 between allopatric populations. In addition to pollinators as agents of
 floral divergence, this study suggests that variation in Pelargonium
 community structure has driven style length variation through character
 displacement.Interactions between plant community members are an
 underexplored driver of angiosperm floral variation. We investigate
 character displacement as a potential contributor to floral variation in
 Pelargonium communities. Pelargoniums all place pollen on the ventral
 sides of their pollinators, potentially leading to interspecific pollen
 transfer (IPT) in sympatry. We show that the positions of pollen placement
 and receipt are determined by anther and style exsertion lengths. Using
 field experiments, we demonstrate that heterospecific species experience
 high IPT if they have similar style lengths. In contrast, heterospecific
 species with greater style length differences experience less IPT. Using
 crosses, we show that IPT has negative consequences on seed set. In
 combination, these results suggest that character displacement in style
 length is likely to reduce IPT and increase female fitness in sympatry.
 Patterns of style length variation across twenty-nine different
 Pelargonium communities suggest that character displacement has occurred
 in multiple communities. Furthermore, analyses using a wide-ranging
 species pair show that style lengths are more different between sympatric
 populations than they are between allopatric populations. In addition to
 pollinators as agents of floral divergence, this study suggests that
 variation in Pelargonium community structure has driven style length
 variation through character displacement.