cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.qjq2bvqm7
title: Data from: Effects of light quality on colonization of tomato roots by arbuscular mycorrhizal fungus (AMF) and implications for growth and defense

description: Beneficial soil microbes can enhance plant growth and defense, but the
 extent to which this occurs depends on the availability of resources, such
 as water and nutrients. However, relatively little is known about the role
 of light quality, which is altered during shading, resulting in a low red:
 far-red ratio (R:FR) of light. We examined how low R:FR light influences
 arbuscular mycorrhizal fungus (AMF)-mediated changes in plant growth and
 defense using Solanum lycopersicum (tomato) and the insect
 herbivore Chrysodeixis chalcites. We also examined effects on
 third trophic level interactions with the parasitoid Cotesia
 marginiventris. Under low R:FR light, non-mycorrhizal plants activated the
 shade avoidance syndrome (SAS), resulting in enhanced biomass production.
 However, mycorrhizal inoculation decreased stem elongation in shaded
 plants, thus counteracting the plant’s SAS response to shading.
 Unexpectedly, activation of SAS under low R:FR light did not increase
 plant susceptibility to the herbivore in either non-mycorrhizal or
 mycorrhizal plants. AMF did not significantly affect survival or growth of
 caterpillars and parasitoids but suppressed herbivore-induced expression
 of jasmonic acid-signaled defenses genes under low R:FR light. These
 results highlight the context-dependency of AMF effects on plant growth
 and defense and the potentially adverse effects of AMF under shading.
description: Data collected: AMF colonization -
 calculated in percentage from ink-stained plant roots
 Plant Biomass - plants were oven dried and then
 weighed Plant Height - plant growth or height was
 measured in the early weeks of the growth after AMF inoculation using a
 measuring scale that measured the shoot length
 Primary metabolite/chemical analysis - Carbon and Nitrogen ratio
 was analysed using Element analyzer, plant total phosphorus was analysed
 using ICP - dried plant material was used Relative
 gene expression - RNA was extracted from flash-frozen leaf material and
 qPCR was performed. Relative expression was calculated using the delta
 delta CT method. Caterpillar bioassay - weight of
 caterpillar feeding on plant was measured every 3rd day for 2 weeks. This
 data was then used for calculating relative growth rate. Mortality (if a
 caterpillar survived or died) was also noted. Caterpillar survival was
 analysed using survival analysis. All data
 was analysed using R studio
description: Microsoft Excel
DOI: 10.5061/dryad.p8cz8w9vp
title: Dataset for: The biogeography of extant lungfishes traces the breakup of Gondwana

description: Aim: Lungfishes are one of the two surviving clades from the once
 diverse grade of lobe-finned fishes leading to tetrapods. This classic
 living fossil lineage, which is the living sister to four-limbed
 terrestrial vertebrates, appeared approximately 425 million years ago and
 rapidly diversified. However, the evolution of lungfishes after their
 initial radiation is poorly understood, and whether their present
 distribution tracks ancient geographic change is a classic problem in
 biogeography. Location: Global Taxon: Lungfishes
 (Dipnoi) Methods: Here, we combine mitogenomic, nuclear gene, and
 fossil data to reconstruct the timing of lungfish diversification, and
 integrate fossil species in a Bayesian tip-dating approach to
 quantitatively test hypotheses of lungfish historical biogeography and
 divergence times. We sample all major living and extinct lungfish
 lineages, including three of the four species of African lungfishes
 (Protopterus spp.), the Australian lungfish Neoceratodus forsteri, the
 South American lungfish Lepidosiren paradoxa, and 13 fossils representing
 extinct lineages from across the globe. Results: Our results
 demonstrate that the divergences of the three major living lungfish clades
 closely recapitulate the stepwise fragmentation of the Gondwana during the
 Mesozoic. All of our model-based biogeographic reconstructions support a
 Gondwanan vicariance model for the origins of the present distribution of
 lungfish lineages. Conclusions: In turn, lungfishes provide an
 excellent example of how the integration of fossil data may drastically
 change support for historical biogeographic hypotheses previously
 discounted by molecular data and are one of the few living animal lineages
 that record incredibly ancient geographic changes in their phylogeny.
description: DNA sequence data were downloaded from NCBI's Genbank and
 aligned by eye and using MUSCLE. Please see the files attached for the
 Genbank ID's. The morphological dataset is from Kemp et al.
 (2017). 
description: PartitionFinder v. 2.1.1. (Lanfear et al. 2017)
 IQ-TREE(Nguyen et al. 2015) BEAST 2.6.6.
 (Bouckaert et al., 2019) Tracer 1.7.1(Rambaut et al.
 2018)
DOI: 10.5061/dryad.xsj3tx9ks
title: Spikiness and animacy as potential organising principles of human ventral visual cortex

description: Considerable research has been devoted to understanding the fundamental
 organising principles of the ventral visual pathway. A recent study
 revealed a series of 3–4 topographical maps arranged along the macaque
 inferotemporal (IT) cortex. The maps articulated a two-dimensional space
 based on the spikiness and animacy of visual objects, with
 ‘inanimate-spiky’ and 'inanimate-stubby’ regions of the maps
 constituting two previously unidentified cortical networks. The goal of
 our study was to determine whether a similar functional organisation might
 exist in human IT. To address this question, we presented the same object
 stimuli and images from ‘classic’ object categories (bodies, faces,
 houses) to humans while recording fMRI activity at 7 Tesla. Contrasts
 designed to reveal the spikiness-animacy object space evoked extensive
 significant activation across human IT. However, unlike the macaque, we
 did not observe a clear sequence of complete maps, and selectivity for the
 spikiness-animacy space was deeply and mutually entangled with
 category-selectivity. Instead, we observed multiple new stimulus
 preferences in category-selective regions, including functional
 sub-structure related to object spikiness in scene-selective cortex. Taken
 together, these findings highlight spikiness as a promising organising
 principle of human IT and provide new insights into the role of
 category-selective regions in visual object processing.
description: This dataset contains anatomical and functional MRI data from 10
 human subjects. All neuroimaging data are included in their raw form.
 Additionally, anatomical data have been preprocessed and parcellated using
 FreeSurfer (Dale et al. 1999; Fischl et al. 1999), specifically, using the
 recon-all function. Region of interest masks were created from the Harvard
 Oxford Cortical Structural Atlas or taken from a probabilistic retinotopic
 atlas (Wang et al., 2015) and are in standard MNI152 2mm space. 
description: Directory structure has been compressed into a single .zip file
 and can be unpacked using the native compression software included in most
 operating systems.
DOI: 10.17871/try.115
title: Photosynthetic Gas Exchange of an Urban Coastal Wetland Plant Species

description: This dataset contains photosynthetic trait measurements collected from dominant plant species in a tropical urban coastal wetland. The data include standardized measurements of leaf-level gas exchange obtained using a portable infrared gas analyzer (CIRAS3, PP Systems, Amesbury, MA, USA). Light conditions were controlled with the PLC3.
Taxonomic coverage: Plants
Field list: Species, Plant growth form, Soil Type, Latitude, Longitude, Altitude, Exposition, Plant maturity, Leaf age, Canopy position, Date, Soil salinity top 10 cm, Phreatic water salinity, Phreatic Water Level, Dry mass, Area, SLA, An, Leaf chamber area, Ci, CO2 Reference, Transpiration ( E ), gs, External PAR (PARe), PARi, Patm, RH, Ambient Air Temperature, Temp cuvette, Temp leaf, VPD, WUE, A/gs, Leaf N, Leaf C, C/N (ratio), An by mass, PNUE, Leaf Mass per Area (LMA),
 Comment
DOI: 10.5061/dryad.brv15dvdk
title: Ancient bears provide insights into Pleistocene ice age refugia in Southeast Alaska

description: During the Late Pleistocene, major parts of North America were
 periodically covered by ice sheets. However, there are still questions
 about whether ice-free refugia were present in the Alexander Archipelago
 along the Southeast (SE) Alaska coast during the Last Glacial Maximum
 (LGM). Numerous subfossils have been recovered from caves in SE Alaska,
 including American black (Ursus americanus) and brown (U. arctos) bears,
 which today are found in the Alexander Archipelago but are genetically
 distinct from mainland bear populations. Hence, these bear species offer
 an ideal system to investigate long-term occupation, potential refugial
 survival, and lineage turnover. Here we present genetic analyses based on
 99 new complete mitochondrial genomes from ancient and modern brown and
 black bears spanning the last ~45,000 years. Black bears form two SE
 Alaskan subclades that diverged &gt;100,00 years ago, one preglacial
 and one postglacial. All postglacial ancient brown bears are closely
 related to modern brown bears  in the archipelago, while a single
 preglacial brown bear is found in a distantly related clade. A hiatus in
 the bear subfossil record around the LGM and the deep split of their pre-
 and post-glacial subclades fail to support a hypothesis of continuous
 occupancy in SE Alaska throughout the LGM for either species. Our results
 are consistent with an absence of refugia along the SE Alaska coast but
 indicate that vegetation quickly expanded after deglaciation, allowing
 bears to recolonize the area after a short-lived LGM peak.
DOI: 10.25338/b8c934
title: Dispersal, habitat filtering, and eco-evolutionary dynamics as drivers of local and global wetland viral biogeography

description: Wetlands store 20–30% of the world's soil carbon, and identifying the
 microbial controls on these carbon reserves is essential to predicting
 feedbacks to climate change. Although viral infections likely play
 important roles in wetland ecosystem dynamics, we lack a basic
 understanding of wetland viral ecology. Here 63 viral size-fraction
 metagenomes (viromes) and paired total metagenomes were generated from
 three time points in 2021 at seven fresh- and saltwater wetlands in the
 California Bodega Marine Reserve. We recovered 12,826 viral population
 genomic sequences (vOTUs), 4.4% of which were also detected at the same
 field site two years prior, indicating a small degree of population
 stability or recurrence. Viral communities differed most significantly
 across the seven wetland sites and were also structured by habitat (plant
 community composition and salinity). Read mapping to a new version of our
 reference database, PIGEONv2.0 (now with 515,763 vOTUs), revealed 196
 vOTUs present over large geographic distances, often reflecting shared
 habitat characteristics. Wetland vOTU microdiversity was significantly
 lower locally than globally and lower within than between time points,
 indicating greater divergence with increasing spatiotemporal distance.
 Viruses tended to have broad predicted host ranges via CRISPR spacer
 linkages to metagenome-assembled genomes (whether this reflects true
 biology remains to be seen), and increased SNP frequencies in
 CRISPR-targeted major tail protein genes suggest viral eco-evolutionary
 dynamics, potentially in response to both immune targeting and to changes
 in host cell receptors involved in viral attachment. Together, these
 results highlight the importance of dispersal, environmental selection,
 and eco-evolutionary dynamics as drivers of local and global wetland viral
 biogeography.
description: This zip package includes:  1) All vOTUs from
 the Bodega Bay experiment, predicted from viromes, recovered in one or
 multiple samples. 2) All vOTUs in the Phages and
 Integrated Genomes Encapsidated Or Not v2.0 (PIGEONv2.0)
 database.  3) A table with habitat origins for each of
 the vOTUs in the PIGEON database and the publication the contig came
 from. 4) MAGs from the Bodega Bay experiment total soil
 metagenomes.
DOI: 10.5061/dryad.prr4xgxrd
title: Auditory region circulation in Lagomorpha: the internal carotid artery pattern revisited

description: The internal carotid artery (ICA) is one of the major vessels in the
 cranial circulation. Characters concerning the ICA, such as its course in
 the auditory region, have been employed frequently in phylogenetic
 analyses of mammals, including extinct taxa. In lagomorphs, however, our
 knowledge on vascular features of the auditory region has been based
 predominantly on living species, mostly on the European rabbit. We present
 the first survey on 11 out of 12 extant genera and key fossil taxa such as
 stem lagomorphs and early crown representatives (Archaeolagus and
 Prolagus). The ICA pattern shows a modified transpromontorial course in
 stem taxa (Litolagus, Megalagus and Palaeolagus) and Archaeolagus, which
 we propose as the ancestral character state for Lagomorpha, similar to
 that for the earliest rodents, plesiadapids and scandentians. The ICA
 pattern in leporids is perbullar but shows structural similarities to stem
 taxa, whereas the extrabullar ICA course in Ochotona is apparently a
 highly derived condition. Prolagus shows a mixed character state between
 leporids and Ochotona in its ICA route. The persistence of the
 transpromontorial ICA course and similarities in the carotid canal
 structure among stem taxa and crown leporids support morphological
 conservatism in Lagomorpha, in contrast to their sister clade Rodentia.
description: The auditory region of seven fossil and 29 extant lagomorph
 specimens has been studied, using the µCT scans and virtual 3D
 reconstructions performed in Avizo 9.0.1 (Thermo Fischer Scientific
 1995–2019) and VG Studio MAX 2.2 (Volume Graphics GmbH, Heidelberg,
 Germany) software. Detailed information on the species sample and scan
 parameters are given in Table S1 (Ruf et al. 2023).
description: The data files can be open with any program supporting .mpg files
 (e.g., Windows Media Player).
DOI: 10.5061/dryad.9p8cz8wmm
title: Predatory interactions of Gorareduvius with and without resin

description: Gorareduvius sp. (proposed name G.
 gajarrangarang is under revision) assassin bugs collect a sticky
 resin from spinifex grass (Triodia spp) in Australia. We
 evaluated whether this resin conveys a predatory advantage to the assassin
 bugs, by staging predatory interactions in the field, under controlled
 conditions. Assassin bugs were sequentially exposed to two types of prey
 (ants and flies), and while being equipped with or deprived of resin. This
 was a repeated measures design that controlled for individual predatory
 ability, in which the order of the trials was randomized. The predatory
 interactions yielded four different types of data, which were analyzed
 separately, as detailed below. 
description: Data were collected in the laboratory, which was basically a
 shaded tent in a campsite in the field. Each assassin bug experienced a
 total of 4 conditions (repeated measures analysis). The four conditions
 are the result of 2 prey items (ant or fly) experienced by the assassin
 bug (predator) one at a time in an arena, for 65 minutes. The predator
 could be equipped with resin (its body covered with resin) or depleted of
 resin (the resin covering its body was removed with cotton pads). The
 combination of these factors produced 4 conditions in total.
 The first analysis considers the outcome of the trial (two
 possibilities only: the assassin bug captured the prey item or not) within
 the given time frame. For this, only trials in which the assassin bug had
 at least 10 opportunities for attack (i.e., the prey item came within
 range of attack) were included. Also, only trials in which the assassin
 bugs attempted at least once to capture the prey item were included.
 Sometimes these conditions were not met or the assassin bug was not
 motivated throughout the whole hunt, but nevertheless, these trials hold
 important data on capture attempts by the assassin bug (e.g., a trial in
 which the prey came close only 5 times and the assassin bug attempted to
 capture it on two occasions). Hence, we did a second analysis that
 considered each capture attempt (each attack from the assassin bug)
 separately. Again, this was a repeated measures analysis that grouped
 observations by bug_id. The second analysis considers all individual
 attacks separately and thus has more information than the one included in
 the first analysis.  Data were noted by hand while
 watching the interactions directly or after watching them on video
 recordings. These data were later transferred to a spreadsheet. 
description: All datasets are Excel spreadsheets (comma-separated values, csv)
 files.
DOI: 10.5061/dryad.95x69p8q0
title: A high-quality, long-read genome assembly of the whitelined sphinx moth (Lepidoptera: Sphingidae: Hyles lineata)

description: The sphinx moth genus Hyles comprises 29 described species inhabiting all
 continents except Antarctica. The genus diverged relatively recently (40 –
 25 mya), arising in the Americas and rapidly establishing a cosmopolitan
 distribution. The whitelined sphinx moth, Hyles lineata, represents the
 oldest extant lineage of this group and is one of the most widespread and
 abundant sphinx moths in North America. Hyles lineata exhibits the large
 body size and adept flight control characteristic of the sphinx moth
 family (Sphingidae), but is unique in displaying extreme larval color
 variation and broad host plant use. These traits, in combination with its
 broad distribution and high relative abundance within its range, have made
 H. lineata a strong model organism for studying phenotypic plasticity,
 plant-herbivore interactions, physiological ecology, and flight control.
 Despite being one of the most well-studied sphinx moths, little data
 exists on genetic variation or regulation of gene expression. Here we
 report a high-quality draft genome showing high contiguity (N50 of 14.2
 Mb) and completeness (98.2% of Lepidoptera BUSCO genes), an important
 first characterization to facilitate such studies. We also annotate the
 core melanin synthesis pathway genes and confirm that they have high
 sequence conservation with other moths and are most similar to those of
 another, well-characterized sphinx moth, the tobacco hornworm (Manduca
 sexta).
description: These data were collected as part of the assembly and structural
 annotation of the whitelined sphinx moth, Hyles lineata, genome (NCBI
 BioProject PRJNA944629). The readme.md file describes all of the files
 included here. DNA for this study was isolated from a male pupal Hyles
 lineata and sequenced using a PacBio Sequel IIe at the University of
 Florida ICBR facility (RRID: SCR_019152). The genome was assembled using
 HiFiasm (RRID:SCR_021069). Structural annotation was performed using
 BRAKER 2 with RNA-seq data from an adult female, an adult male, and a
 late-instar larvae. Melanin synthesis pathway genes were identified from
 the structural annotation using sequences from the domestic silkworm
 (Bombyx mori) and compared with putative
 homologs from another sphinx moth, the tobacco hornworm
 (Manduca
 sexta), and two more
 distantly related moths: the cotton bollworm (<em>Helicoverpa
 armigera</em>) and the striped rice stemborer (<em>Chilo
 suppressalis</em>), along with <em>B. mori</em> (used to
 identify sequences) and the well-characterized vinegar fly
 (<em>Drosophila melanogaster</em>).
DOI: 10.5061/dryad.fqz612jww
title: Data from: Two forms of asynchronous release with distinctive spatiotemporal dynamics in central synapses

description: Asynchronous release is a ubiquitous form of neurotransmitter release that
 persists for tens to hundreds of milliseconds after an action potential.
 How asynchronous release is organized and regulated at the synaptic active
 zone (AZ) remains debatable. Using nanoscale-precision imaging of
 individual release events in rat hippocampal synapses, we observed two
 spatially distinct subpopulations of asynchronous events, ~75% of which
 occurred inside the AZ and with a bias towards the AZ center, while ~25%
 occurred outside of the functionally defined AZ, i.e., ectopically. The
 two asynchronous event subpopulations also differed from each other in
 temporal properties, with ectopic events occurring at significantly longer
 time intervals from synchronous events than the asynchronous events inside
 the AZ. Both forms of asynchronous release did not, to a large extent,
 utilize the same release sites as synchronous events. The two asynchronous
 event subpopulations also differ from synchronous events in some aspects
 of exo-endocytosis coupling, particularly in the contribution from the
 fast calcium-dependent endocytosis. These results identify two
 subpopulations of asynchronous release events with distinctive
 organization and spatiotemporal dynamics.
DOI: 10.5061/dryad.s1rn8pkcq
title: Data from: Climate change consequences for differential adult survival and the mating system of a temperate breeding shorebird

description: Managing for the effects of climate change on species whose
 populations are currently imperiled requires detailed knowledge
 of the relationship between their demographic rates and climate
 variables. We sought this information for the West Coast breeding
 population of snowy plover (Charadrius nivosus), which was
 federally listed as threatened in 1993 due to substantial declines in the
 numbers of plovers breeding along the coast and in the number of sites
 occupied for breeding. Snowy plovers employ a serially polygamous breeding
 system in which the male typically tends chicks to independence. This
 unusual breeding system is favored by male-biased sex ratios in local
 populations. As part of a multi-species study of the effect of climate
 change on population growth, we used mark-capture models to examine
 climate drivers of adult survival for 1,219 snowy plovers banded at
 Monterey Bay over 38 years and known to overwinter on the surrounding
 north-central California outer coast. Non-climate variables, including sex
 and unmeasured annual mortality risks (e.g., predator abundance) were the
 primary factors affecting adult survival. However, there is evidence that
 cold weather, particularly extended cold snaps with daily low temperatures
 below 2˚C and daily high temperatures below 10˚C, decreases overwinter
 survival. Exceptionally cold winters had a particularly strong effect on
 adult female plovers, contributing to the male-biased adult sex ratios.
 Future winter climate on the north-central California coast is projected
 to be generally warmer with fewer and shorter cold snaps. Reduced
 mortality from cold winter weather may mitigate other threats faced by
 plovers, such as anthropogenically enhanced predator populations, habitat
 loss, and accelerated sea level rise, while altering the adult sex ratio
 and potentially shifting the evolutionary landscape maintaining the
 plover’s unusual breeding system.
description: Data were year-round wildlife observations of individually-marked
 Snowy Plovers, collected from coastal habitat at central California sites,
 from Sonoma to Monterey Counties.  Observers were primarily persons
 employed to monitor Snowy Plovers during the breeding and non-breeding
 seasons.  Some sightings of these marked birds were contributed by
 experienced and trained volunteer observers.  Data were managed and
 summarized in Excel, including the creation of input histories for
 processing by the program MARK for analyzing mark-recapture
 data.
description: Data are submitted in Excel (CVS format), with no other softward
 required to access them.