cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.c866t1gb1
title: Alloteropsis semialata as a study system for C4 evolution in grasses

description: Background Numerous groups of plants have adapted to CO2 limitations by
 independently evolving C4 photosynthesis. This trait relies on concerted
 changes in anatomy and biochemistry to concentrate CO2 within the leaf and
 thereby boost productivity in tropical conditions. The ecological and
 economical importance of C4 photosynthesis has motivated intense research,
 often relying on comparisons between distantly related C4 and non-C4
 plants. The photosynthetic type is fixed in most species, with the notable
 exception of the grass Alloteropsis semialata. This species includes
 populations exhibiting the ancestral C3 state in southern Africa,
 intermediate C3+C4 populations in the Zambezian region and C4 populations
 spread around the paleotropics.   Scope We compile here
 the knowledge on the distribution and history of Alloteropsis as a whole
 and discuss how this has furthered our understanding of C4 evolution. We
 further generate a chromosome-level reference genome for a C3 individual
 and compare the genomic architecture to that of a C4 accession. 
 Conclusions Alloteropsis semialata represents one of the best systems to
 investigate the evolution of C4 photosynthesis as the genetic and
 phenotypic variation provides a fertile ground for comparative and
 population-level studies. Initial comparative genomics show the C3 and C4
 genomes are highly syntenic and have undergone a modest amount of gene
 duplication and translocation since the different photosynthetic groups
 divided. The background knowledge and publicly available genomic resources
 make Alloteropsis semialata a great model for further comparative analyses
 of photosynthetic diversification.
description: Please see manuscript for full details of methods.
DOI: 10.5061/dryad.kwh70rz7j
title: Timing of hydrologic anomalies direct impacts on migration traits in a flood pulse fishery system

description: 1. Understanding adaptive reservoir management strategies that balance
 ecological outcomes with other objectives necessitates properly
 articulated environmental objectives. Aside from flood pulse
 extent-related metrics, residual-based descriptors provide robust
 descriptions of fish assemblage structure and harvest. 2. We proposed a
 model framework based on spectral analysis of hydrologic variation and the
 Multivariate AutoRegressive State Space (MARSS) model to statistically
 quantify the effect sizes of hydrologic variation impacts on total fish
 catch and functional group (migration types) fish harvest and applied it
 to 17 years of fish harvest data from the Lower Mekong River Basin (LMB).
 3. Our findings suggest that duration and timing of hydrologic anomalies
 matter as much as their magnitude. Anomaly droughts coupled with strong
 pulse can benefit species if timed correctly. Longitudinal migrators were
 more sensitive to anomalous floods and droughts than other migratory
 species. Fish catch projections using effect sizes derived from historical
 data revealed that a well-timed and protracted flood followed by a
 powerful flood pulse would be advantageous to the fishery, but a flood
 delay could negate such benefits. 4. Our results add to a growing body of
 research that suggests ecological flows can be engineered. For most dams,
 the rule curve describing reservoir releases and resulting downstream
 hydrograph is designed in an ecological vacuum in which the objectives are
 to maximize human services—power production, flood control or navigation.
 Our work demonstrates that hydrograph can be designed to manage aspects of
 functional biodiversity directly. Though the exact shape of our hydrograph
 may not apply to other engineered river systems, we suggest that the
 approach can be applied generally, and globally both to developed and
 developing river basins. Specifically, a functional biodiversity rule
 curve could be optimized as an additional objective function in a
 multi-objective optimization framework. Our methodology provides a
 quantitative method for deriving an ecological flow for this larger
 tradeoff analysis.
description: Data used in this analysis were from commercial fishing sampling
 activity and were provided by Mekong River Commission and the Inland
 Fisheries Research and Development Institute (IFReDI) of Cambodia. For
 detailed processing procedure, refer to the Methods section in the main
 article and Supplemental lnformation.
description: Data are uploaded in CSV format and can be opened with the
 open-source R free software environment as the article analysis was
 done.
DOI: 10.6078/d1q71k
title: Data from: Fencing amplifies individual differences in movement with implications on survival for two migratory ungulates

description: Fences have recently been recognized as one of the most prominent linear
 infrastructures on earth. As animals traverse fenced landscapes, they
 adjust movement behaviors to optimize resource access while minimizing
 energetic costs of coping with fences. Examining individual responses is
 key for connecting localized fence effects with population dynamics. We
 investigated the multi-scale effects of fencing on animal movements, space
 use, and survival of 61 pronghorn and 96 mule deer on a gradient of fence
 density in Wyoming, USA.   Taking advantage of the
 recently developed Barrier Behavior Analysis, we classified individual
 movement responses upon encountering fences (i.e. barrier behaviors). We
 adopted the reaction norm framework to jointly quantify individual
 plasticity and behavioral types of barrier behaviors, as well as behavior
 syndromes between barrier behaviors and animal space use. We also assessed
 whether barrier behaviors affect individual survival.  
 Our results highlighted a high level individual plasticity encompassing
 differences in the degree and the direction of barrier behaviors for both
 pronghorn and mule deer. Additionally, these individual differences were
 greater at higher fence densities. For mule deer, fence density determined
 the correlation between barrier behaviors and space use, and was
 negatively associated with individual survival. Yet, these relationships
 were not statistically significant for pronghorn.   By
 integrating approaches from movement ecology and behavioral ecology with
 the emerging field of fence ecology, this study provides new evidence that
 an extraordinarily widespread linear infrastructure uniquely impacts
 animals at the individual level. Managing landscape for lower fence
 densities may help prevent irreversible behavioral shifts for wide-ranging
 animals in fenced landscapes.
DOI: 10.5061/dryad.dv41ns22p
title: Data from: Loss of flockmates weakens winter site fidelity in golden-crowned sparrows (Zonotrichia atricapilla)

description: Animal social interactions have an intrinsic spatial basis—individuals
 must be close in space to interact, whether directly (e.g., co-occurrence,
 allo-grooming) or indirectly (e.g., interact with latrines or with
 parasites at communal nests). This presents a dilemma when determining
 causality: do individuals interact socially because they happen to share
 space, or do they share space because they are socially linked? We present
 a method that uses demographic turnover events as a natural experiment to
 investigate the links between social associations and space use in the
 context of inter-annual winter site fidelity in a migratory bird. We
 previously found that golden-crowned sparrows (Zonotrichia atricapilla)
 show consistent flocking relationships across years, and that familiarity
 between individuals influences the dynamics of social competition over
 resources. Using long-term data on winter social and spatial behavior
 across 10 years, we show that (i) sparrows exhibit inter-annual fidelity
 to winter home ranges on the scale of tens of meters and (ii) the
 precision of inter-annual spatial fidelity increases with age, but (iii)
 this fidelity is weakened when sparrows lose social partners from the
 previous year. Furthermore, the effect of social partner loss on spatial
 fidelity was higher for older birds, suggesting that social fidelity may
 play an increasingly important role on spatial behavior across the
 lifetime of this migratory bird. Our study provides evidence that social
 relationships can influence spatial fidelity, and shows the potential of
 long-term studies for disentangling the relationship between social and
 spatial behavior.
description: Flocks of golden-crowned sparrows were observed during the winter
 (October-March) from 2009-2019 at the University of California Santa Cruz
 Arboretum in Santa Cruz, California. Birds were captured using potter
 traps, fitted with unique combinations of color bands, and DNA samples
 were collected to identify sex. Flocks were followed on foot through the
 Arboretum and individual flock memberships and locations were recorded on
 a 10mx10m grid cell overlay on a map of the study site. 
 Dominance interactions were observed for golden-crowned sparrows
 at seed piles throughout the arboretum. This data was collected separately
 from flock observations. The included dominance data has been filtered to
 exclude the individual behavioral observations that were not used in this
 analysis.  Banding and attribute files were filtered to
 exclude morphological and behavioral data not included in this
 analysis.
description: There are four files for download, one of which is a rdat file
 that containing 32 dataframe objects in R. The text files are saved as
 non-propietary comma separated files, and all analysis was completed in
 the open-source software, Rstudio. Rstudio is required to open, edit, and
 run code scripts that are included as R files.
DOI: 10.5281/zenodo.18401576
title: Multimodal signal perception in ants: evidence for lateralization in electrophysiological responses from legs and antennae

description: Data associated with:

Multimodal signal perception in ants: evidence for lateralization in electrophysiological responses from legs and antennae

The raw electrophysiological recordings used in this study are not included in this repository but are available from the authors upon request.
DOI: 10.5281/zenodo.18401575
title: Multimodal signal perception in ants: evidence for lateralization in electrophysiological responses from legs and antennae

description: Data associated with:

Multimodal signal perception in ants: evidence for lateralization in electrophysiological responses from legs and antennae

The raw electrophysiological recordings used in this study are not included in this repository but are available from the authors upon request.
DOI: 10.15468/dl.g5f8zz
title: Occurrence Download

description: A dataset containing 16 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Etmopterus samadiae"
 ]
}

 The dataset includes 16 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003404-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.7m0cfxpzj
title: From high masked to high realized genetic load in inbred Scandinavian wolves

description: When new mutations arise at functional sites they are more likely
 to impair than improve fitness. If not removed by purifying
 selection, such deleterious mutations will generate a genetic load that
 can have negative fitness effects in small populations and increase the
 risk of extinction. This is relevant for the highly inbred Scandinavian
 wolf (Canis lupus) population, founded by only three wolves in the 1980s
 and suffering from inbreeding depression. We used functional annotation
 and evolutionary conservation scores to study deleterious variation in a
 total of 209 genomes from both the Scandinavian and neighboring wolf
 populations in northern Europe. The masked load (deleterious mutations in
 heterozygote state) was highest in Russia and Finland with deleterious
 alleles segregating at lower frequency than neutral variation. Genetic
 drift in the Scandinavian population led to the loss of ancestral alleles,
 fixation of deleterious variants and a significant increase in the
 per-individual realized load (deleterious mutations in homozygote state;
 an increase by 45% in protein-coding genes) over five generations of
 inbreeding. Arrival of immigrants gave a temporary genetic rescue effect
 with ancestral alleles re-entering the population and thereby shifting
 deleterious alleles from homozygous into heterozygote genotypes. However,
 in the absence of permanent connectivity to Finnish and Russian
 populations, inbreeding has then again led to the exposure of deleterious
 mutations. These observations provide genome-wide insight into the
 magnitude of genetic load and genetic rescue at the molecular level, and
 in relation to population history. They emphasize the importance of
 securing gene flow in the management of endangered populations.
DOI: 10.5061/dryad.w3r2280vb
title: Data from: First report of silicified wood from a late Pennsylvanian intramontane wetland of the Pyrenees: systematic affinities and paleoecological implications

description: The first anatomically preserved wood specimens of an upland Carboniferous
 flora from the Iberian Peninsula are reported from the Erillcastell Basin
 (Eastern Pyrenees, Catalonia, Spain). Two taxa are described, a
 calamitacean Equisetale (Arthropitys sp.) and a Cordaitale (Dadoxylon
 sp.). The Arthropitys specimen shows fusiform multiseriate rays composed
 of square parenchyma cells with conspicuous uniseriate or multiseriate
 simple pits. These pits are located near the transverse walls and
 occasionally in the tangential walls. The tracheids vary in lumen size,
 with scalariform-bordered pits on their radial walls and multiseriate pits
 in their cross-field areas. The Dadoxylon specimen commonly has uniseriate
 fusiform rays. The tracheids are long, with a square shape in transverse
 section. Their radial walls bear araucarian pitting with a uni- to
 triseriate arrangement. The pits are circular with a spindle-shaped
 aperture. Comparison of the Erillcastell specimens with coeval species
 from Europe indicates that they could belong to new species. The good
 preservation of the new fossil wood yields significant palaeoenvironmental
 information. The lack of marked growth rings in both specimens and the
 presence of tyloses in Dadoxylon suggest that the climate in the
 intramontane basins of the Pyrenees was slightly seasonal towards the end
 of the Carboniferous. This contrasts with the marked seasonality of coeval
 lowland basins. Such upland habitats may have enhanced the survival of
 plants adapted to humid conditions in a global context of increasing
 aridity.
description: Two specimens preserved in
 silica from the late Pennsylvanian were found in Erillcastell. Ten thin
 sections about 30 µm thick were prepared in the transverse, radial, and
 tangential planes. They are stored in the Museu de Ciències Naturals de
 Barcelona with the collection numbers MGB90407.1-MGB90407.3;
 MGB90408.1-MGB90408.7. The
 slides were photographed with a Keyence VHX-7000 digital
 microscope. The
 measurements were taken for each wood character using the free software
 “ImageJ” (https://imagej.net/Welcome).
DOI: 10.5061/dryad.v6wwpzh0p
title: TreeFlow: Probabilistic programming and automatic differentiation for phylogenetics

description: Probabilistic programming frameworks are powerful tools for statistical
 modelling and inference. They are not immediately generalisable to
 phylogenetic problems due to the particular computational properties of
 the phylogenetic tree object. TreeFlow is a software library for
 probabilistic programming and automatic differentiation with phylogenetic
 trees. It implements inference algorithms for phylogenetic tree times and
 model parameters, given a tree topology. We demonstrate how TreeFlow can
 be used to quickly implement and assess new models. We also show that it
 provides reasonable performance for gradient-based inference algorithms
 compared to specialized computational libraries for phylogenetics.
description: Carnivores sequence alignment accessed from benchmark in BEAST examples H3N2 sequence alignment taken from Vaughan TG, Kühnert D, Popinga A, Welch D, Drummond AJ. Efficient Bayesian inference under the structured coalescent. Bioinformatics. 2014 Aug 15;30(16):2272-9. doi: 10.1093/bioinformatics/btu201
description: Data processing pipeline can be found at https://github.com/christiaanjs/treeflow-paper Tree topologies inferred using RAxML 8.2.12 Tree topologies are rooted using LSD 0.2 BEAST analyses are performed using BEAST 2.6.7 Variational inference analyses are performed using TreeFlow 0.0.1beta Sequences have been removed H3N2 BEAST XML as a result of license conflicts. This complete version of this file is generated by the above pipeline.
DOI: 10.5061/dryad.f1vhhmh1d
title: Data from: Androgen-armoured amazons – reversed sex roles in coucals are associated with testosterone in females but not males

description: In some species, sexual selection is stronger in females than males. In
 classically polyandrous birds, for instance, females compete for mating
 opportunities and males care for offspring. Sex steroids such as
 testosterone have been suggested to regulate the behaviours of
 ‘role-reversed’ females and males, but comparative studies did not find
 evidence for a role of testosterone in relation to sex roles. However, the
 large variability of hormone measurements across laboratories may prevent
 detecting subtle differences in hormone levels. To circumvent this caveat,
 I compared sex steroid concentrations of females and males of two closely
 related and cohabiting species with different mating systems, the
 classically polyandrous black coucal (Centropus grillii) and the
 monogamous white-browed coucal (C. superciliosus). Baseline and
 GnRH-induced testosterone concentrations  were twice as high in
 female black coucals than  female white-browed coucals, and the
 low pre-breeding progesterone concentrations of female black coucals were
 consistent with progesterone’s modulatory role during agonistic
 interactions in this species. Baseline and GnRH-induced testosterone and
 progesterone concentrations did not differ between males of both species.
 This study provides first evidence that elevated testosterone is
 associated with sex-role reversed traits in females, whereas low levels of
 testosterone may not be necessary to facilitate sex-role reversal in
 males.
description: For details on the methodology see main manuscript
DOI: 10.5061/dryad.1c59zw401
title: Spectral images on shallow graves and reference plots

description: When a person goes missing and a crime is suspected, police forces may
 scout for clandestine graves in certain areas in which the victim is
 suspected to have been buried. Such clandestine graves are often shallow
 and may affect the vegetation on top and around the grave for prolonged
 periods of time. Search efforts by visual means are only effective in
 detecting the effects of graves on vegetation when the effects are very
 pronounced. However, it is hypothesized that even when a visual observer
 cannot discern the effect from natually occurring variance, the spectral
 characteristics of the vegetation may still be sufficiently different to
 be able to be picked up through chemometric methods. This study aimed to
 explore if and how spectral imaging could be used to discriminate between
 the vegetation growing on shallow graves and on nearby reference plots.
 Data were acquired in the visible/near-infrared (Vis-NIR, 400–900 nm) and
 short-wave infrared (SWIR, 1000–1700 nm) with mobile spectral imaging
 set-ups and used to train and validate spectral classification
 models. 
description: For the duration of this project, we had access
 to the forensic human burial site of the Amsterdam University Medical
 Center. Regular visits were made to the burial site with mobile
 high-resolution spectral camera set-ups (featuring imec Snapscan VNIR and
 SWIR). During each visit, an older grave (~2-3 years) was fully imaged, as
 well as an adjacent reference plot where no body was buried. Both the
 grave and the reference plot were imaged in a mosaic-like manner, with
 some limited overlap between adjacent tiles. In January 2022, a new body
 was donated and buried in another part of the burial site. Also here, an
 adjacent reference plot was identified, but this time the plot was
 burrowed in a similar fashion as the grave. From February until May,
 monthly data acquisition runs were executed, during which both the older
 and the fresh grave, as well as the two reference plots, were fully imaged
 using Vis-NIR (400–900 nm)
 and SWIR (1000–1700 nm)
 spectral cameras. Small Spectralon white references (99%
 nominal reflectance) were kept in the field of view to be able to make
 proper corrections to the variable lighting. All files in the dataset start with
 a date (YYYY-DD-MM) and wavelength range (VNIR and SWIR). File names then
 continue with a designation <em>graf</em> (grave) or
 <em>referentie</em> (reference plot) and either carry the
 subsequent designation <em>oud</em> (old) or not. Therefore,
 in file names <em>graf_oud</em> refers to the older grave,
 while <em>referentie_oud</em> refers to the reference plot
 adjacent to the older grave. Files without the <em>oud</em>
 designation were recorded on the newer grave or the reference plot
 adjacent to it. 
description: Spectral images and the
 corresponding metadata can be read with the <em>spectral</em>
 python library.
DOI: 10.5061/dryad.rfj6q57fc
title: Flora and basins of Angarida

description: Devonian plants in Siberia present protracted pioneer succession. Research
 into the survivourship dynamics of early plant communities upon the
 palaeocontinent Angarida have demonstrated that transgression and
 volcanogenic nutrient influx were key to the survival of colonising
 plants. Taxic proportions show that migrating taxa entered Angarida from
 the southwest, Kuznetsk and Minusinsk basins, dispersing across the
 continent in waves through central areas northwards. The patterns of
 dispersal are consistent throughout the Devonian. Increased nutrient load
 from the active pulses of the Viluy-Yakutsk Large Igneous Province,
 biogeomorphic ecosystem engineering, and the increased biomass of
 Angaridan plants are assisted by Late Devonian transgression. These
 cumulative factors can be linked to the Late Devonian marine extinctions
 observed in Siberia.
description: Collection through literature review and fieldwork by Akulov and
 Mashchuk. Processed through Microsoft Excel and
 Rstudio. 
description: Microsoft Excel.