cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1rn8pk0v3
title: From nature reserve to mosaic management: improving matrix survival, not permeability, benefits regional populations under habitat loss and fragmentation

description: Although matrix improvement in fragmented landscapes is a promising
 conservation measure, matrix permeability (willingness of an organism to
 enter the matrix) and movement survival in the matrix are usually
 aggregated. Consequently, it is unknown which matrix property needs to be
 improved. It also remains unclear whether matrix upgrading from dispersal
 passage to providing reproduction opportunities has large conservation
 benefits and whether there are interactive effects between habitat and
 matrix management. We examined matrix effects on regional populations
 across a gradient of habitat loss and fragmentation using simulation
 experiments that integrated demographic processes and movement modeling
 based on circuit theory. We separately modified the levels of matrix
 permeability and movement survival to evaluate their individual effects.
 We also altered the amount and configuration of not only habitat but also
 improved matrix to assess their effects on population vital rates (size,
 survival and density). In binary landscapes comprising habitat and
 unimproved matrix, matrix movement survival had larger effects on
 population vital rates than matrix permeability. Increasing movement
 survival increased vital rates, yet, increasing matrix permeability
 decreased vital rates. Increased permeability required corresponding
 increased movement survival to offset potential negative population
 outcomes. When subsets of the matrix functioning as dispersal passage only
 (where no reproduction opportunities existed) were improved, increasing
 matrix permeability but holding movement survival constant reduced all
 vital rates, especially with increasing habitat fragmentation. In
 contrast, when movement survival increased, vital rates increased given
 strong habitat fragmentation. The benefits of upgrading dispersal passage
 to provide reproduction opportunities for population survival were
 greatest when habitat amount was moderate. We also found synergetic
 effects between amounts of habitat and improved matrix, and the benefits
 of matrix improvement were promoted when improvement was achieved in a
 spatially aggregated manner. Synthesis and applications: Matrix
 improvement and connectivity modeling aimed at increasing movement
 survival will likely bring larger conservation benefits than those for
 improving permeability alone. Buffering and connecting habitat remnants
 with improved matrix could provide benefits as long as movement survival
 is increased. Simultaneous implementation of habitat management and matrix
 improvement would yield synergistic conservation benefits.
description: We deposit the source code of our developed model and raw data
 yielded by simulation experiments.
DOI: 10.5061/dryad.vhhmgqntv
title: Data from: Metabolism drives demography in an experimental field test

description: Metabolism should drive demography by determining the rates of both
 biological work and resource demand. Long-standing ‘rules’ for how
 metabolism should covary with demography permeate biology, from predicting
 the impacts of climate change to managing fisheries. Evidence for these
 rules is almost exclusively indirect and in the form of among-species
 comparisons, while direct evidence is exceptionally rare. In a
 manipulative field experiment on a sessile marine invertebrate, we created
 experimental populations that varied systematically in population size
 (density) and metabolic rate, but not body size. We then tested key
 theoretical predictions regarding relationships between metabolism and
 demography by parameterising population models with lifetime performance
 data from our field experiment. We found populations with higher
 metabolisms had greater intrinsic rates of increase and lower carrying
 capacities, in qualitative accordance with classic theory, but we also
 found important departures from theory. In particular, carrying capacity
 declined less steeply than predicted, such that energy use at equilibrium
 increased with metabolic rate, violating the long-standing axiom of energy
 equivalence. Theory holds that energy equivalence emerges because resource
 supply is assumed to be independent of metabolic rate. We find this
 assumption to be violated under real world conditions – with potentially
 far-reaching consequences for the management of biological systems.
description: We created experimental populations that differed in their mean
 metabolic rates (MeanMR) at two different densities and then followed the
 survival, growth, onset of reproduction and fecundity (reproductive
 output) of each individual within a given population by checking colony
 absence/presence and counting the number of bifurcations (colony size) and
 the number of ovicells (external offspring bearing brood chambers; every
 ovicell contains a single larva) every two weeks over a period of six
 months (a total of 11 censuses). We then used the collected field data to
 parameterise integral projection models (IPMs) to investigate the effects
 of metabolic rate on population demography.
DOI: 10.5061/dryad.0vt4b8h0j
title: Data from: Isotopic niches of tropical birds reduced by anthropogenic impacts: A 100-year perspective

description: The intensification of land use changes in tropical forests during the
 20th century, mainly caused by deforestation for agricultural uses, had an
 overwhelming influence on bird assemblages. However, how these historical
 anthropogenic changes have impacted the habitat use and diet of tropical
 birds is poorly known. Stable isotope analysis (δ13C and δ15N) can be
 useful in this regard since it provides information not only on the
 habitat and food resource use but also insights on the dietary niche of
 species. Here, we aimed to evaluate whether centenary anthropogenic
 impacts, mainly caused by changes in landscape composition, have affected
 the resource and habitat use and isotopic niche width of Neotropical birds
 in a region that comprises two biodiversity hotspots — the Atlantic Forest
 and Cerrado in southeastern Brazil. We found that the niche width of all
 bird guilds (frugivore, granivore, insectivore, nectarivore, and omnivore)
 was largely reduced (28–70%) from the twentieth century until recently.
 This niche width reduction was likely associated with historical
 anthropogenic impacts (e.g., fragmentation, forest loss and change in
 agricultural practices), which are responsible for the decrease in the
 availability of habitat and food resources. Moreover, the mean values of
 δ15N decreased over the years in all bird guilds, which might be
 attributed to the expansion of agricultural areas and the increase in the
 use of synthetic nitrogen-based fertilizers. All the analyzed species,
 even though some of them are diet and habitat generalists, were strongly
 influenced by centenary anthropogenic actions. Our results show the
 consequences of human-induced changes in land use on the diet and habitat
 use of tropical birds that persist in fragmented landscapes, which might
 compromise their long-term survival, and provide useful information to the
 conservation strategies of bird assemblages in modern landscapes.
DOI: 10.5061/dryad.7d7wm37vv
title: Sexual selection and sexual size dimorphism in animals

description: Sexual selection is often considered as a critical evolutionary force
 promoting sexual size dimorphism (SSD) in animals. However, empirical
 evidence for a positive relationship between sexual selection on males and
 male-biased SSD received mixed support depending on the studied taxonomic
 group and on the method used to quantify sexual selection. Here, we
 present a meta-analytic approach accounting for phylogenetic
 non-independence to test how standardized metrics of the opportunity and
 strength of pre-copulatory sexual selection relate to SSD across a broad
 range of animal taxa comprising up to 95 effect sizes from 59 species. We
 found that SSD based on length measurements was correlated with the sex
 difference in the opportunity for sexual selection but showed a weak and
 statistically non-significant relationship with the sex difference in the
 Bateman gradient. These findings suggest that pre-copulatory sexual
 selection plays a limited role for the evolution of sexual size dimorphism
 in a broad phylogenetic context.
description: The dataset comprises 1) a data file
 (Janicke_&_Fromonteil_2021_DataTable.txt), which includes effect
 sizes and estimates of sexual size dimorphism and 2) a phylogenetic tree
 in NEWICK format used to account for phylogenetic
 non-independence.
DOI: 10.15468/dl.42ym79
title: Occurrence Download

description: A dataset containing 724 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cirrochroa thais"
 ]
}

 The dataset includes 724 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002910-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.hx3ffbgf7
title: STR data from: Temporal analysis shows relaxed genetic erosion following improved stocking practices in a subarctic transnational brown trout population

description: Maintaining standing genetic variation is a challenge in human-dominated
 landscapes. We used genetic (i.e., 16 short tandem repeats) and
 morphological (i.e., length and weight) measurements of 593 contemporary
 and historical brown trout (Salmo trutta) samples to study fine-scale and
 short-term impacts of different management practices. These had changed
 from traditional breeding practices, using the same broodstock for several
 years, to modern breeding practices, including annual broodstock
 replacement, in the transnational subarctic Pasvik River. Using population
 genetic structure analyses (i.e., Bayesian assignment tests, DAPCs, and
 PCAs), four historical genetic clusters (E2001A-D), likely representing
 family lineages resulting from different crosses, were found in zone E.
 These groups were characterized by consistently lower genetic diversity,
 higher within-group relatedness, lower effective population size, and
 significantly smaller body size than contemporary stocked (E2001E) and
 wild fish (E2001F). However, even current breeding practices are
 insufficient to prevent genetic diversity loss and morphological changes
 as demonstrated by on average smaller body sizes and recent genetic
 bottleneck signatures in the modern breeding stock compared to wild fish.
 Conservation management must evaluate breeding protocols for stocking
 programs and assess if these can preserve remaining natural genetic
 diversity and morphology in brown trout for long-term preservation of
 freshwater fauna.
DOI: 10.5061/dryad.6q573n601
title: Data from: Prey encounters and spatial memory influence use of foraging patches in a marine central place forager

description: Given the patchiness and long-term predictability of marine resources,
 memory of high-quality foraging grounds is expected to provide fitness
 advantages for central place foragers. However, it remains challenging to
 characterise how marine predators integrate memory with recent prey
 encounters to adjust fine-scale movement and use of foraging patches.
 Here, we used two months of movement data from harbour seals (Phoca
 vitulina) to quantify the repeatability in foraging patches as a proxy for
 memory. We then integrated these data into analyses of fine-scale movement
 and underwater behaviour to test how both spatial memory and prey
 encounter rates influenced the seals’ Area Restricted Search (ARS)
 behaviour. Specifically, we used one month’s GPS data from 29 individuals
 to build spatial memory maps of searched areas, and archived accelerometry
 data from a subset of five individuals to detect prey catch attempts, a
 proxy for prey encounters. Individuals were highly consistent in the areas
 they visited over two consecutive months. Hidden Markov Models showed that
 both spatial memory and prey encounters increased the probability of seals
 initiating ARS. These results provide evidence that predators use memory
 to adjust their fine scale movement and this ability should be accounted
 for in movement models.
description: The data consist of 18 files and include the datasets and data
 packages required to repeat the analyses. Files from 1 to 7 represent raw
 data necessary to start the analysis. Within the output folder, files from
 8 to 18 are processed outputs generated from the R codes. Outputs are
 provided so that all the R codes can be run starting from any
 point.<br>The R codes to be used with this datasets can be found
 here. A full description of each datasets is provided in the Readme.txt file: 1. pv64-2017_seal_summary.txt 2. pv64-2017_trip_summaries.txt 3. pv64-2017_gps_data_with_haulout_&_trip_info.txt 4. pv64-2017_dive.txt 5. Accelerometer_data.zip 6. Moray_Firth_1km_grid_shapefile.zip 7. Coastline_UTM30.zip Within the Output folder: 8. Dive batches dataset - 2017.txt 9. Model 1 - initial parameters selection output.txt 10. Model 1 - HMM dive batches classified.txt 11. April memory raster maps (folder) -&gt;  individual seal raster maps in .tiff format 12. Accelerometer memory raster maps (folder) -&gt; individual seal raster maps in .tiff format 13. Model 2 - initial parameters selection output.txt 14. Raw accelerometer data per trip (folder) -&gt; individual subfolder for each seal with one .txt file per trip 15. Prey encounters - cluster analysis axis thresholds.txt 16 Processed accelerometer parameters (folder) -&gt; individual .txt for each seal 17. Dive batches dataset - Acceleormeter.txt 18. Model 3 - initial parameters selection output.txt
DOI: 10.5061/dryad.ffbg79cvr
title: Between a rock and a hard polytomy: phylogenomics of the rock-dwelling mbuna cichlids of Lake Malawi

description: Whole genome sequences are beginning to revolutionise our understanding of
 phylogenetic relationships. Yet, even whole genome sequences can fail to
 resolve the evolutionary history of the most rapidly radiating lineages,
 where incomplete lineage sorting, standing genetic variation,
 introgression, and other factors obscure the phylogenetic history of the
 group. To overcome such challenges, one emerging strategy is to integrate
 results across different methods. Most such approaches have been
 implemented on reduced representation genomic datasets, but whole genomes
 should provide the maximum possible evidence approach. Here, we test the
 ability of SNPs extracted from whole genome resequencing data, implemented
 in an integrative genomic approach, to resolve key nodes in the phylogeny
 of the mbuna, rock-dwelling cichlid fishes of Lake Malaŵi, which epitomise
 the phylogenetic intractability that often accompanies explosive lineage
 diversification. This monophyletic radiation has diversified at an
 unparalleled rate into several hundred species in less than two million
 years. Using an array of phylogenomic methods, we consistently recovered
 four major clades of mbuna, but a large basal polytomy among them.
 Although introgression between clades apparently contributed to the
 challenge of phylogenetic reconstruction, reduction of the dataset to
 non-introgressed sites still did not help to resolve the basal polytomy.
 On the other hand, relationships among six congeneric species pairs were
 resolved without ambiguity, even in one case where existing data led us to
 predict that resolution would be difficult. We conclude that the bursts of
 diversification at the earliest stages of the mbuna radiation may be
 phylogenetically unresolvable, but other regions of the tree are
 phylogenetically clearly supported. Integration of multiple phylogenomic
 approaches will continue to increase confidence in relationships inferred
 from these and other whole-genome datasets.
DOI: 10.5061/dryad.v15dv41wm
title: Data from: Developmental origins of the crocodylian skull table and platyrostral face

description: The dorsoventrally flattened skull typifies extant Crocodylia perhaps more
 than any other anatomical feature and is generally considered an
 adaptation for semi-aquatic feeding. Although the evolutionary origins
 have been extensively studied, the developmental origins of craniofacial
 flattening have yet to be explored. To understand how the skull table and
 platyrostral snout develop, we quantified embryonic development and
 post-hatching growth (ontogeny) of the crocodylian skull in lateral view
 using geometric morphometrics. Our dataset (n=103) includes all but one
 extant genus and all of the major ecomorphs, including the extremely
 slender-snouted Gavialis and Tomistoma. Our analysis reveals that the
 embryonic development of the flattened skull is remarkably similar across
 ecomorphs, including the presence of a conserved initial embryonic skull
 shape, similar to prior analysis of dorsal snout shape. Although
 differences during post-hatching ontogeny of the snout are recovered among
 ecomorphs the embryonic patterns are not distinct, revealing an important
 shift in developmental rate near hatching. In particular, the flattened
 skull table is achieved by the end of embryonic development with no
 changes after hatching. Further, the rotation of skull roof and facial
 bones during development is critical for the stereotypical flatness of the
 crocodylian skull. Our results suggest selection on hatchling performance
 and constraints on embryonic skull shape may have been important in this
 pattern of developmental conservation. The appearance of aspects of
 cranial flatness among Jurassic stem crocodylians suggests key aspects of
 these cranial developmental patterns may have been conserved for over 200
 million years.
description: Extant Crocodylian Lateral Skull Landmarks A
 ZIP file containing a folder of text files with the landmark positions for
 all specimens included in the analysis.
 TwoCurves_Landmarking_Final.zip Covariates
 spreadsheet CSV file containing covariate data
 associated with each specimen.
 Croc_Lateral_Skull_Ontogeny_Covariates.csv
 List of CT scan parameters Table with scan
 parameters for all CT scans included in this analysis.
 Crocodylian_Embryo_CTScans_SI.csv
DOI: 10.5061/dryad.x95x69pjq
title: Data from: Social and physical environment independently affect oviposition decisions in Drosophila

description: In response to environmental stimuli, including variation in the presence
 of conspecifics, genotypes show highly plastic responses in behavioral and
 physiological traits influencing reproduction. Although extensively
 documented in males, such female responses are rather less studied. We
 expect females to be highly responsive to environmental variation and to
 differentially allocate resources to increase offspring fitness, given the
 major contribution of mothers to offspring number, size, and developmental
 conditions. Using Drosophila melanogaster, we (a) manipulate exposure to
 conspecific females, which mothers could use to anticipate the number of
 potential mates and larval density, and; (b) test how this interacts with
 the spatial distribution of potential oviposition sites, with females from
 higher densities expected to prefer clustered resources that can support a
 larger number of larvae. We found that high density females were slower to
 start copulating and reduced their copulation duration, the opposite
 effect to that observed in males. There was a parallel, perhaps related,
 effect on egg production behavior: females previously housed in groups
 laid fewer eggs than those housed in solitude. Resource patchiness also
 influenced oviposition: females preferred aggregated substrate, which
 attracted more females to lay eggs. However, we found no interaction
 between prior housing conditions and resource patchiness, indicating that
 females did not perceive the value of different resource distributions
 differently when exposed to environments that could signal expected levels
 of larval competition. We show that, although exposure to consexual
 competition changes copulatory behaviors of females, the distribution of
 oviposition resources has a greater effect on oviposition decisions.
description: The data were collected in laboratory conditions, and
 observations were taken live - as has been described in detail in
 Churchill et al. 2021 and the accompanying ReadMe file.
DOI: 10.5061/dryad.mcvdnck1x
title: Data from: Haploid gynogens facilitate disomic marker development in paleotetraploid sturgeons

description: Acipenseriformes (sturgeons and paddlefishes) are of substantial
 conservation concern, and development of genomic resources for these
 species is difficult due to past whole genome duplication. Development of
 disomic markers for polyploid organisms can be challenging due to
 difficulty in resolving alleles at a single locus from those among
 duplicated loci. In this study, we detail the development of disomic
 markers for the endangered pallid sturgeon (Scaphirhynchus albus) found in
 North America. One of the strategies for pallid sturgeon conservation is
 to stock U.S. rivers with offspring of pure pallid sturgeon, but
 introgression with the sympatric shovelnose sturgeon (S. platorynchus)
 threatens pallid sturgeon genetic integrity. Currently, 19 microsatellite
 loci are used to differentiate between both species and their hybrids, but
 the markers are insufficient to robustly identify backcrosses. We
 performed double digest restriction site-associated DNA sequencing
 (ddRADseq) on shovelnose sturgeon haploid gynogens to produce a
 reduced-representation genomic reference. Contiguous sequences that were
 heterozygous within a haploid individual were flagged as potentially
 encompassing multiple loci. Approximately 60 individuals of each species
 from two management units were sequenced, and reads were mapped to the
 haploid reference to identify single nucleotide polymorphisms (SNPs) at
 individual loci. The final dataset contained 11,082 microhaplotyped loci
 which offer at least an order of magnitude greater resolution for species
 discrimination than the current panel of 19 microsatellites. These markers
 will be used to examine a larger sample of Scaphirhynchus individuals
 throughout their ranges to determine the extent and trajectory of
 hybridization.
DOI: 10.5061/dryad.pk0p2ngp5
title: Empirical single-cell tracking and cell-fate simulation reveal dual roles of p53 in tumor suppression

description: The tumor suppressor p53 regulates various stress responses via increasing
 its cellular levels. The lowest p53 levels occur in unstressed cells;
 however, the impact of these low levels on cell integrity remains unclear.
 To address the impact, we used empirical single-cell tracking of
 p53-expressing and silenced cells, and developed a fate-simulation
 algorithm. Here we show that p53-silenced cells underwent more frequent
 cell death and cell fusion, which further induced multipolar cell division
 to generate aneuploid progeny. Those results suggest that the low levels
 of p53 in unstressed cells indeed have a role to maintain the integrity of
 a cell population. Results of a cell-fate simulation that provides a
 flexible and dynamic virtual culture space confirmed that these aneuploid
 progeny could propagate. However, p53-silenced cells were unable to
 propagate in a virtual cell population that was mainly comprised of
 p53-expressing cells, supporting the notion that p53 acts as a tumor
 suppressor. In contrast, when DNA damage responses were repeatedly induced
 in 53-expressed cells, p53-silenced cells became the major cell
 population, as the growth of p53-expressed cells was more tightly
 suppressed by the response than that of p53-silenced cells. In this
 context, the p53-mediated damage response that is supposed to suppress
 tumor formation has a pro-malignant function. The cellular
 microenvironment could thus be a major factor to determine the
 fate of cancer cells and the fate-simulation algorithm can be
 used to reveal the fate.