cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25338/b83s8c
title: Differentiation trajectories of the Hydra nervous system reveal transcriptional regulators of neuronal fate

description: The small freshwater cnidarian polyp Hydra vulgaris uses
 adult stem cells (interstitial stem cells) to continually replace neurons
 throughout its life. This feature, combined with the ability to image the
 entire nervous system (Badhiwala et al., 2021; Dupre &
 Yuste, 2017) and the availability of gene knockdown
 techniques (Juliano, Reich, et al., 2014; Lohmann et al., 1999;
 Vogg et al., 2022), makes Hydra a tractable model for
 studying nervous system development and regeneration at the whole-organism
 level. In this study, we use single-cell RNA sequencing and trajectory
 inference to provide a comprehensive molecular description of the adult
 nervous system. This includes the most detailed transcriptional
 characterization of the adult Hydra nervous system to
 date. We identified eleven unique neuron subtypes together with the
 transcriptional changes that occur as the interstitial stem cells
 differentiate into each subtype. Towards the goal of building gene
 regulatory networks to describe Hydra neuron
 differentiation, we identified 48 transcription factors expressed
 specifically in the Hydra nervous system, including many that are
 conserved regulators of neurogenesis in bilaterians. We also performed
 ATAC-seq on sorted neurons to uncover previously unidentified putative
 regulatory regions near neuron-specific genes. Finally, we provide
 evidence to support the existence of transdifferentiation between mature
 neuron subtypes and we identify previously unknown transition states in
 these pathways. Altogether, we provide a comprehensive transcriptional
 description of an entire adult nervous system, including differentiation
 and transdifferentiation pathways, which provides a significant advance
 toward understanding mechanisms that underlie nervous system regeneration.
description: For methods, please see supplemental material of
 BioRxiv: https://doi.org/10.1101/2023.03.15.531610
DOI: 10.5061/dryad.n2z34tn1r
title: Paraphlomis caloneura (Lamiaceae), a new species from Guangxi, China

description: Paraphlomis caloneura, a new species from Guangxi Zhuang Autonomous
 Region, China, is described and illustrated. Molecular phylogenetic
 analyses based on two nuclear robosomal DNA regions (ITS and ETS)
 and three plastid DNA markers (rpl32-trnL, rps16, and
 trnL-trnF) revealed that the new species is sister to P.
 hirsutissima. Both species are found in the limestone forests and are
 geographically close to each other, but P. caloneura can be
 easily distinguished from P. hirsutissima by its oblong or
 ovate-oblong and adaxially densely hispid laminas with broadly cuneate to
 cordate bases, densely hispid petioles, and slightly
 2-lobed margins of upper corolla lips.
DOI: 10.5061/dryad.3tx95x6m4
title: Rock pools as a source of environmental DNA for the detection of the threatened Pilbara olive python (Liasis olivaceus barroni)

description: Environmental DNA (eDNA) research is transforming biomonitoring at a
 global scale, but applicability to reptiles has been restricted because of
 their presumed low shedding rate. Consequently, eDNA may have considerable
 limitations as a biomonitoring tool in Australia where 40% of the
 terrestrial vertebrates are reptiles. However, there is a need to evaluate
 if method improvements such as targeting certain substrates, improves the
 ability to detect reptile eDNA. The Pilbara olive python (Liasis olivaceus
 barroni) is an uncommon and elusive Australian top predator with a high
 conservation priority. Like many other snake species, Pilbara olive
 pythons are challenging to monitor with traditional survey methods,
 therefore exploring an eDNA-based approach is highly relevant. The pythons
 are known to occasionally reside in rock pools. Thus, development of a
 reliable eDNA-based approach to detect the pythons in water would provide
 a needed alternative method. Here we use a previously developed
 metabarcoding assay targeting reptiles, to sequence a total of 228 water
 samples collected from 40 rock pools from six broad locations across the
 Pilbara region of Western Australia, and we confirm the presence of
 Pilbara olive python eDNA in 37 samples from 12 of those pools at three of
 the six broad sampling locations. Other vertebrate taxa, including other
 reptiles, amphibians, mammals and birds were also detected. Our documented
 ability to detect Pilbara olive python eDNA from rock pool water samples
 represents an important step towards eDNA-based precision monitoring of
 this species.
description: Please refer to the methods section of the paper.
description: The files can be opened using command line programs (e.g. less,
 vi, nano) or any text editors.
DOI: 10.5061/dryad.mpg4f4r4g
title: Brain cortical volume and area from Freesurfer's parcellation in a sample of healthy volunteers from South America

description: This dataset aims to deepen the analysis of cortical gyral and sulcal
 asymmetry of the entire cerebral cortex of healthy adult individuals by
 quantifying the gray matter content of the right and left hemispheres in a
 reference sample from South America. The subjects were sampled from
 populations scarcely represented in MRI research, which tends to be biased
 towards groups of European ancestry from Europe and North America. In
 contrast, the population under study is an admixture of Native American,
 European, and African components that contributed to a variable extent to
 their gene pool. Consequently, this study will add to expanding the
 diversity in brain morphometric data and the construction of more
 population-representative references.
description: We recruited 175 healthy adult right-handed volunteers of both sexes from the metropolitan area of Buenos Aires (Autonomous city of Buenos Aires and Florencio Varela city) and Bariloche (Argentinian Patagonia), Argentina. 3D T1 volumetric images were obtained in three high-field (3T) scanners: a) Philips Achieva scanner located at the SAMIC El Cruce Hospital (F. Varela, Buenos Aires); b) Siemens Trio scanner located at the Angel Roffo Institute (Autonomous City of Buenos Aires); c) SIGNA PET / MR 3T scanner located in INTECNUS (Bariloche, Río Negro). The parameters of the images at each sampling site were as follows: a) 3D FFE sequence, TE= 3.3 msec, TR= 2300 msec, TI= 900 msec, flip angle= 9°, FOV= 240x240x180, voxel size= 1x1x1 mm3 and 239 slices; b) MP-RAGE, TE= 2.27 msec, TR= 2000 msec, TI= 900 msec, inverted angle= 80, FOV= 250x250, voxel size= 1x1x1 mm3 and 204 slices; c) 3D SPGR (SAG) sequence with an inversion pulse, TE= 2.9 msec, TR= 7.1 msec, TI= 900 msec, flip angle= 9 °, FOV= 256x256x176, voxel size= 1x1x1 mm3 and 176 slices. All the images were processed in the same workstation (with Ubuntu 18.04), using FreeSurfer's “recon-all” algorithm (v 6.0.0.0) (http://surfer.nmr.mgh.harvard.edu), widely used in structural brain studies, and which exhibits a high precision, reliability, and validity. Then the cerebral cortex of each hemisphere was parcellated taking a probabilistic atlas as a reference, in this case, the atlas by Destrieux et al. (2010) was used. Then, in each subject’s native space, the volume and surface area of the gray matter of 74 parcels were obtained.
DOI: 10.5061/dryad.v9s4mw71c
title: Alternanthera philoxeroides haplotypes growth response to N and P

description: Interactions between invaders and resource availability may explain
 variation in their success or management efficacy. For widespread
 invaders, regional variation in plant response to nutrients can reflect
 phenotypic plasticity of the invader, genetic structure of invading
 populations, or a combination of the two. The wetland weed Alternanthera
 philoxeroides (alligatorweed) is established throughout the southeastern
 USA and California, and has high genetic diversity despite primarily
 spreading clonally. Despite its history in the USA, the role of genetic
 variation for invasion and management success is only now being uncovered.
 To better understand how nutrients and genotype may influence A.
 philoxeroides invasion, we measured the response of plants from 26 A.
 philoxeroides populations (three cp haplotypes) to combinations of
 nitrogen (4 or 200 mg/L N) and phosphorus (0.4 or 40 mg/L P). We measured
 productivity (biomass accumulation and allocation), plant architecture
 (stem diameter and thickness, branching intensity) and foliar traits
 (toughness, dry matter content, percent N, percent P). A short-term
 developmental assay was also conducted by feeding a subset of plants from
 the nutrient experiment to the biological control agent Agasicles
 hygrophila, to determine whether increased availability of N or P to its
 host influenced agent performance, as has been previously suggested. A.
 philoxeroides haplotype Ap1 was more plastic than other haplotypes in
 response to nutrient amendments, producing more than double the biomass
 from low to high N and 50-68% higher shoot:root ratio than other
 haplotypes in the high N treatment. A. philoxeroides haplotypes differed
 in 7 of 10 variables in response to increased N. We found no differences
 in short-term A. hygrophila development between haplotypes but mass was
 23% greater in high than low N treatments. This study is the first to
 explore the interplay between nutrient availability, genetic variation,
 and phenotypic plasticity in invasive characteristics of the global
 invader, A. philoxeroides.
description: Please see the README document ("README.md") and the
 accompanying article: Harms, N. E., Knight, I. A., DeRossette, A. B.,
 & Williams, D. A. (2023). Intraspecific trait plasticity to N and
 P of the wetland invader, <em>Alternanthera
 philoxeroides</em> under flooded conditions. <em>Ecology and
 Evolution</em>, 13, e9966. https://doi.org/10.1002/ece3.9966
description: Files are submitted as Excel spreadsheets.
DOI: 10.5061/dryad.n02v6wx25
title: Temporal dynamics of mother-offspring relationships in Bigg’s killer whales: opportunities for kin-directed help by post-reproductive females

description: Age-related changes in the patterns of local relatedness (kinship
 dynamics) can be a significant selective force for shaping the evolution
 of life history and social behaviour. In humans and some species of
 toothed whales, average female relatedness increases with age which can
 select for a prolonged post-reproductive lifespan in older females due to
 both the costs of reproductive conflict and the benefits of late-life
 helping of kin. Killer whales (Orcinus orca) provide a valuable system for
 exploring social dynamics related to such costs and benefits in a mammal
 with an extended post-reproductive female lifespan. We use &gt;40
 years of demographic data to investigate the opportunities for helping and
 harming in the mammal-eating Bigg’s killer whale by quantifying how
 mother-offspring social relationships change with offspring age. Our
 results suggest a high degree of male philopatry and female-biased budding
 dispersal in Bigg’s killer whales, with some variability in the dispersal
 rate for both sexes. These patterns of dispersal provide opportunities for
 late-life helping of particularly adult sons, while partly mitigating the
 costs of mother-daughter reproductive conflict. This is an important step
 towards understanding the evolution of menopause in the few species it
 occurs.
description: Demographic and association data has been collected on
 Bigg's killer whales off the West coast of Canada and the USA between
 1972 and 2020. Individuals have been identified using photo identification
 using the unique markings on the whales. For the
 analysis, the data has been combined between data collected by DFO and
 CWR. Attributes, where known, were added for each individual in the
 data. Three separate analyses were run, and for each,
 the data was formatted to either be a group-by-individual matrix or a list
 with the denominator and numerator for the simple ratio index for all
 possible dyads in each year of the data and finally a data frame where
 each row refers to the association between a mother and offspring,
 including the age and sex of the offspring.
description: RStudio
DOI: 10.5061/dryad.866t1g1vp
title: Genome-wide SNPs reveal recurrent waves of speciation in niche-pockets, in Europe’s most venomous snake

description: Within the Balkan Peninsula, topographic and climatic agents have promoted
 biodiversity and shaped the speciation history of many ectotherms. Here,
 we targeted an iconic European reptile, the nose-horned viper
 species-complex (Vipera ammodytes), and explored its spatial and temporal
 evolution. We (1) utilized genome-wide SNPs to infer genetic structure and
 build a time-calibrated species tree, and (2) applied species distribution
 modeling (SDM) with niche-divergence tests among major phylogenomic
 clades. Geographically structured genetic diversity was found. Cycles of
 recurrent isolation and expansion during glacial–interglacial periods led
 to allopatric speciation and to secondary contacts and formation of
 multiple hybrid zones throughout the Balkan Peninsula. Deep divergence is
 still detected among populations separated by old and imminent
 biogeographical barriers (e.g. Pindos Mountain Range, the Cyclades
 islands, etc.), but in most cases, speciation is incomplete. At the other
 end of the speciation continuum, we recognize two well-differentiated
 lineages, currently lacking any evidence of gene flow; one is distributed
 in the Northwestern Balkans and the other in the Southeastern Balkans,
 further expanding into Asia. Despite their split 5 Mya, there is no
 evidence of ecological divergence, as speciation probably occurred in
 niche-pockets of analogous environments. These two lineages probably
 represent different species, while V. transcaucasiana does not merit
 species status. By comparing the genomic phylogenies to an updated
 mitochondrial one, we propose an evolutionary scenario that resolves all
 mito-nuclear conflicts, according to which the history of the V. ammodytes
 species-complex was shaped by complex processes, including a major event
 of introgressive hybridization with asymmetric mitochondrial capture.
description: Please find details in the "Materials and Methods"
 section and the Supplementary material from the main paper.
description: The appropriate program to open each datafile is provided in the
 READme document and more details are available in the "Materials and
 Methods" section and the Supplementary material from the main paper.
 All datafiles, except "TREEMIX_75.gz", can be also opened in any
 text editor.
DOI: 10.5061/dryad.tdz08kq3z
title: Climatic forcing and individual heterogeneity in a resident mountain bird: legacy data reveal effects on reproductive strategies

description: Optimization of clutch size and timing of reproduction have substantial
 effects on lifetime reproductive success in vertebrates, and both
 individual quality and environmental variation may impact life history
 strategies. We tested hypotheses related to maternal investment and timing
 of reproduction, using 17 years (1978-1994) of individual-based life
 history data on willow ptarmigan (Lagopus l. lagopus, n=290 breeding
 females with n=319 breeding attempts) in central Norway. We analysed
 whether climatic variation and individual state variables (age and body
 mass) affected number of offspring and timing of reproduction, and
 individual repeatability in strategies. The results suggest that willow
 ptarmigan share a common optimal clutch size that is largely independent
 of measured individual states. While we found no clear direct weather
 effects on clutch size, higher spring temperatures advanced onset of
 breeding, and early breeding was followed by an increased number of
 offspring. Warmer springs were positively related to maternal mass, and
 mass interacted with clutch size in production of hatchlings. Finally,
 clutch size and timing of reproduction were highly repeatable within
 individuals, indicating that individual quality guided trade-offs in
 reproductive effort. Our results demonstrate how climatic forcing and
 individual heterogeneity in combination influenced life history traits in
 a resident montane keystone species.
description: The ecological data was collected in 1978-1994 in Dovre,
 Norway.
DOI: 10.5061/dryad.w9ghx3ftk
title: Leaf angle as a leaf and canopy trait: Rejuvenating its role in ecology with new technology

description: Life on Earth depends on the conversion of solar energy to chemical energy
 by plants through photosynthesis. A fundamental challenge in optimizing
 photosynthesis is to adjust leaf angles to efficiently use the intercepted
 sunlight under the constraints of heat stress, water loss, and
 competition. Despite the importance of leaf angle, until recently, we have
 lacked data and frameworks to describe and predict leaf angle dynamics and
 their impacts from leaves to the globe. We review the role of leaf angle
 in studies of ecophysiology, ecosystem ecology, and earth system science
 and highlight the essential yet understudied role of leaf angle as an
 ecological strategy to regulate plant carbon-water-energy nexus and to
 bridges leaf, canopy, and earth system processes. Using two models, we
 show that leaf angle variations have significant impacts on not only
 canopy-scale photosynthesis, energy balance, and water use efficiency but
 also light competition within forest canopy. New techniques to measure
 leaf angles are emerging, opening opportunities to understand the
 rarely-measured intraspecific, interspecific, seasonal, and interannual
 variations of leaf angles and their implications to plant biology and
 earth system science. We conclude by proposing three directions for future
 research.
description: One dataset was collected by Leica RTC360 terrestrial laser
 scanner in Puerto Rico and Virginia. The leaf angle data was derived with
 the TLSLeAF algorithm. The other results are model
 simulation results from SCOPE and ED2
DOI: 10.5061/dryad.djh9w0w4p
title: Fundamental niche narrows through larval stages of a filter-feeding marine invertebrate

description: Ontogenetic niche theory predicts that resource use should change across
 complex life histories. To date, studies of ontogenetic shifts in food
 niches have mainly focused on a few systems (e.g. fish), with less
 attention on organisms with filter-feeding larval stages (e.g. marine
 invertebrates). Recent studies suggest that filter-feeding organisms can
 select specific particles, but our understanding of whether niche theory
 applies to this group is limited. We characterised the fundamental niche
 (i.e. feeding proficiency) by examining how niche breadth changes across
 the larval stages of the filter-feeding marine polychaete Galeolaria
 caespitosa. Using a no-choice experimental design, we measured feeding
 rates of trochophore, intermediate-stage and metatrochophore larvae on the
 prey phytoplankton species: Nannochloropsis oculata, Tisochrysis lutea,
 Dunaliella tertiolecta and Rhodomonas salina, that vary 10-fold in size,
 from the smallest to the largest. We formally estimated Levins’ niche
 breadth index to determine the relative proportions of each species in the
 diet of the three larval stages and also tested how feeding rates vary
 with algal species and stage. We found that early stages eat all four
 algal species in roughly equal proportions, but niche breadth narrows
 during ontogeny, such that metatrochophores are feeding specialists
 relative to early stages. We also found that feeding rates differed across
 phytoplankton species—the medium-sized cells (Tisochrysis and Dunaliella)
 were eaten most, and the smallest species (Nannochloropsis) was eaten the
 least. Our results demonstrate that ontogenetic niche theory describes
 changes in fundamental niche in filter feeders—an important next step is
 to test whether the realized niche (i.e. preference) changes during the
 larval phase as well.
DOI: 10.5061/dryad.3j9kd51pj
title: Ostrinia population genomics: Custom scripts and synteny mapping results

description: We sampled seven Ostrinia furnacalis (Guenée) populations across 23
 degrees of latitude in China to elucidate the genetic basis of diapause
 variation and evolutionary mechanisms driving parallel clinal responses.
 Using pooled whole-genome sequencing (Pool-seq) data, population genomic
 analyses revealed hundreds of single nucleotide polymorphisms (SNP) whose
 allele frequencies covaried with mean diapause phenotypes along the cline.
 Archived on Dryad are the custom R scripts used in the population genomic
 analyses as well as the mapping of O. furnacalis scaffolds to
 Bombyx mori reference chromosomes (for visualizing population genetic
 statistics across chromosomes).
description: <strong>Data:</strong>
 scaff_chr_map.txt Tab-delimited table mapping
 Ostrinia furnacalis scaffolds (RefSeq GCF_004193835.1) to Bombyx mori
 chromosomes (Silkbase ver. Jan 2017). 
 <strong>Scripts (Zenodo)</strong>
 Written under R version 4.0.0 
 <strong>abba_alltopo.R</strong>
 R script that calculates Patterson's D
 (Durand et al., 2011; Green et al., 2010) and fd (Martin et al., 2015) in
 windows of a given number of SNPs or basepairs to detect signatures of
 introgression in all possible combinations and permutations of 4
 populations (tree topologies). Uses a modified sync file (see inline
 comments) as the input. An output file is generated for each possible tree
 topology. 
 <strong>blockjackknife.R</strong>
 R script that calculates the genome-wide average
 Patterson's D and its confidence interval and z score by block
 jackknifing from an output file generated by abba_alltopo.R
 <strong>blockjackknife.sh</strong>
 Example usage of blockjackknife.R in bash.
 <strong>dxy.R</strong> R script
 that calculates genetic divergence dxy in genomic windows of a given size
 in basepairs for all possible pairs of populations from a modified sync
 file (see inline comments). Each column in the output file is one pair of
 populations. Other scripts (e.g., pipeline, figures)
 are available upon request.