cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6078/d1fb0r
title: Data from: Barrier Behavior Analysis (BaBA) reveals extensive effects of fencing on wide-ranging ungulates

description: 1. As human activities expand globally, there is a growing need to
 identify and mitigate barriers to animal movements. Fencing is a pervasive
 human modification of the landscape that can impede the movements of
 wide-ranging animals. Previous research has largely focused on whether
 fences block movements altogether, but a more nuanced understanding of
 animals’ behavioral responses to fences may be critical for examining the
 ecological consequences and prioritizing conservation interventions. 2. We
 developed a spatial- and temporal-explicit approach, Barrier Behavior
 Analysis (BaBA, available as an R package), to examine individual-level
 behaviors in response to linear barriers. BaBA classifies animal-barrier
 encounters into six behavior categories: quick cross, average movement,
 bounce, back-and-forth, trace, and trapped. We applied BaBA to
 wide-ranging female pronghorn (Antilocapra americana) and mule deer
 (Odocoileus hemionus) in an area of western Wyoming, USA with &gt;
 6,000 km of fencing. 3. We found both species were extensively affected by
 fences, with nearly 40% of fence encounters altering their normal
 movements, though pronghorn were more strongly affected than mule deer. On
 average, an individual pronghorn encountered fences 250 times a year –
 twice the encounter rate of mule deer. Pronghorn were more likely to
 bounce away from fences, whereas deer engaged in more back-and-forth,
 trace, and average movement near fences. 4. We aggregated these behavioral
 responses to demonstrate how BaBA can be used to examine species-specific
 fencing permeability and to identify problematic fence segments in order
 to guide fence modification or removal. 5. Synthesis and applications: Our
 work provides empirical evidence on how fences affect wildlife movement.
 Importantly, BaBA can be applied to other linear features (such as roads,
 railways, and pipelines) and habitat edges, enhancing our ability to
 understand and mitigate widespread barrier effects to animal movement.
description: Data files include:  1) A shapefile
 (FENCE.shp) shows fence locations in the study area as depicted in Figure
 1.  2) A  CSV file (PRONGHORN.csv) that contains 20
 pronghorn-year movement locations as depicted in Figure S1.
 3) A CSV file (MULEDEER.csv) that contains 20 mule deer-year
 movement locations as depicted in Figure S1. Code used
 to analyze these datasets can be found on GitHub: https://github.com/wx-ecology/BaBA
DOI: 10.5061/dryad.wstqjq2jv
title: The preservation potential of terrestrial biogeographic patterns

description: Extinction events in the geological past are similar to the present-day
 biodiversity crisis in that they have a pronounced biogeography, producing
 dramatic changes in the spatial distributions of species. Reconstructing
 paleobiogeographic patterns from fossils therefore allows us to examine
 the long-term processes governing the formation of regional biotas, and
 potentially helps build spatially-explicit models for future biodiversity
 loss in a potential ‘6th mass extinction’ event. However, the extent to
 which biogeographic patterns can be preserved in the fossil record is not
 well understood. Here, we perform a suite of simulations based on the
 present-day distribution of North American mammals, aimed at quantifying
 the preservation potential of beta diversity and spatial richness patterns
 over extinction events of varying intensities, and after applying a
 stepped series of taphonomic filters. We show that taphonomic biases
 related to body size are the biggest barrier to reconstructing
 biogeographic patterns over extinction events, but that these may be
 compensated for by both the small-mammal record preserved in bird
 castings, as well as range-expansion in surviving species. Overall our
 results suggest that the preservation potential of biogeographic patterns
 is surprisingly high, and thus that the fossil record represents an
 invaluable dataset recording the changing spatial distribution of biota
 over key intervals in Earth History.
description: Simulations-based study that uses the present-day distribution of
 374 mammal species across North America, and then simulates fossil
 preservation, and attempts to reconstruct diversity patterns after
 applying a stepped series of taphonomic filters.
description: All data and code required to repeat simulations provided; please
 refer to the README.txt file for detailed instructions on how to operate R
 code and reproduce figures.
DOI: 10.5061/dryad.wh70rxwm7
title: Data from: Drought and soil nutrients effects on symbiotic nitrogen fixation in seedlings from eight Neotropical legume species

description: Symbiotic nitrogen fixation is a dominant source of nitrogen to many
 terrestrial ecosystems, and thus may influence their responses to global
 change. High legume species diversity and abundance are thought to lead to
 high rates of symbiotic nitrogen fixation in Neotropical forests. However,
 how changes in water and nutrient availability will affect symbiotic
 nitrogen fixation have only recently been explored, even as droughts begin
 to increase in severity and frequency in the Neotropics.  To
 explore these effects, we grew eight species of Neotropical woody legume
 seedlings in a shadehouse for four months while manipulating soil water,
 phosphorus and molybdenum availability. Overall, drought reduced
 nodule biomass, nitrogenase activity (acetylene reduction g-1 nodule), and
 acetylene reduction per seedling by 33%, 27%, and 41%, respectively, but
 reduced seedling biomass by only 18%.  Species varied in the
 manifestation of drought effects. For example, drought reduced the
 probability that nodules formed in some species, but in others reduced the
 nitrogenase activity or acetylene reduction per seedling.  In
 contrast, the effects of phosphorus and molybdenum availability were more
 species-specific. However, fertilization did affect (both positively and
 negatively) one or more symbiotic nitrogen fixation response variables in
 two of the eight species. Our results indicate drought reduces symbiotic
 nitrogen fixation in Neotropical legume seedlings, but the mechanism of
 response may be species-specific.  Therefore, predicting the
 response of symbiotic nitrogen fixation in the Neotropics to a changing
 climate, with expected increases in drought frequency and severity, may
 require grappling with the diversity of responses among nitrogen-fixing
 legumes.
description: Acetylene reduction assay and seedling biomass data from a
 greenhouse experiment in Bahia, Brazil with seedlings from eight
 Neotropical legume species that examined the effect of drought and soil
 nutrients.
DOI: 10.5061/dryad.r7sqv9s9z
title: Phylogenetic analysis of the distribution of deadly amatoxins among the little brown mushrooms of the genus Galerina

description: Some but not all of the species of 'little brown mushrooms' in
 the genus Galerina contain deadly amatoxins at concentrations equaling
 those in the death cap, Amanita phalloides. However, Galerina's ~300
 species are notoriously difficult to identify by morphology and the
 identity of toxin-containing specimens has not been verified with DNA
 barcode sequencing. This left open the question of which Galerina species
 contain toxins and which do not. We selected specimens for toxin analysis
 using a preliminary phylogeny of the fungal DNA barcode region, the
 ribosomal internal transcribed spacer (ITS) region. Using liquid
 chromatography/mass spectrometry, we analyzed amatoxins from 70 samples of
 Galerina and close relatives, collected in western British Columbia,
 Canada. To put the presence of toxins into a phylogenetic context, we
 included the 70 samples in maximum likelihood analyses of 438 taxa, using
 ITS, RNA polymerase II second largest subunit gene (RPB2), and nuclear
 large subunit ribosomal RNA (LSU) gene sequences. We sequenced barcode DNA
 from types where possible to aid with applications of names. We detected
 amatoxins only in the 24 samples of the G. marginata s.l. complex in the
 Naucoriopsis clade. We delimited 56 putative Galerina species using
 Automatic Barcode Gap Detection software. Phylogenetic analysis showed
 moderate to strong support for Galerina infrageneric clades Naucoriopsis,
 Galerina, Tubariopsis, and Sideroides. Mycenopsis appeared paraphyletic
 and included Gymnopilus. Amatoxins were not detected in 46 samples from
 Galerina clades outside of Naucoriopsis or from outgroups. Our data show
 significant quantities of toxin in all mushrooms tested from the G.
 marginata s.l. complex. DNA barcoding revealed consistent accuracy in
 morphology-based identification of specimens to G. marginata s.l. complex.
 Prompt and careful morphological identification of ingested G. marginata
 s.l. has the potential to improve patient outcomes by leading to fast and
 appropriate treatment.
description: The dataset consists of concatenated sequences for 437 taxa, from
 the internal transcribed spacer DNA barcode region, the nuclear large
 subunit ribosomal RNA (LSU) gene and the RNA polymerase II second largest
 subunit gene (<i>RPB2</i>). The tree is a maximum likelihood
 tree from 200 search replicates with RAxML.  
 Taxon names are in the format:- 'G
 sideroides F25207 CA -TOX' where 'G sideroides' is a
 species in Galerina; F25207 is the herbarium accession number; CA is the
 two-digit code for country of collection;  and -TOX indicates that the
 specimen was assayed and lacked detectable amatoxins.
 +TOX would mean that the specimen was assayed and contained
 detectable amatoxins.  
description: This is a nexus file created in Mesquite.
DOI: 10.5061/dryad.ffbg79ct5
title: Shell shape and environmental data for five North American land snail species

description: The morphological distinctness of land snail shells is almost certainly
 related to the unique environments in which they live. Even with the
 development of genetic and epigenetic tools for understanding factors
 contributing to phenotype, much research is focused on understanding
 environmental effects on land snail shell form. Most studies focus on
 single taxa, with review articles summarizing shared patterns and
 correlations of shell response to the environment. Herein we provide a
 dataset of shell shapes and environmental data for five species of
 partially sympatric North American land snail. Data are sourced from
 museum specimens, invaluable resources for biological and biodiversity
 information. We imaged, landmarked, georeferenced, and extracted
 environmental parameters for 3,701 land snail specimens
 representing five North American land snail species: Anguispira
 alternata, Euglandina rosea, Haplotrema concavum, Mesodon
 thyroidus, and Mesomphix globosus. These specimens represent most
 of the primary dry holdings for the five species at the Florida
 Museum of Natural History, Gainesville, Florida, USA. The landmark and
 environmental data are provided in formats (TPS and CSV respectively)
 compatible with modern methods of analyzing and interpreting geometric
 morphometric data.
description: We utilized shell material from the Florida Museum of Natural
 History, Gainesville, Florida, USA mollusk collection. Specimen
 identifications and locality data on museum labels were assumed to be
 correct. Each shell was digitally photographed in apertural view. A set of
 landmarks was digitized on each shell using tpsDig2 and a slider file was
 generated for each species using tpsUtil. The positions of type III
 landmarks (=semi-landmarks) can be allowed to "slide" in order
 to minimize either Procrustes distance or bending energy during
 generalized Procrustes alignment. A set of landmark "links" for
 each species was also produced in tpsUtil to aid in visualizing
 differences between individuals and taxa. Locality
 information from the museum label accompanying each shell was captured and
 used to georeference the specimen using GEOLocate 3.22. We accepted the
 GEOLocate-generated latitude and longitude coordinates for each specimen
 without correction except in the case where a single locality string
 produced multiple possible matches. In those instances, we chose the
 locality we felt was most consistent with what was known about where the
 collector collected from and the uncertainty radius generated by
 GEOLocate. With the latitude and longitude coordinates generated by
 GEOLocate, we extracted 13 environmental values for each specimen using
 ArcGIS 10 and multiple, publicly available geographical information system
 (GIS) files.
description: Images are provided for <em>Haplotrema
 concavum</em>, <em>Mesodon thyroidus</em>,
 and <em>Mesomphix globosus</em>.
DOI: 10.5061/dryad.80gb5mkpz
title: Phosphorus release from intact soil monoliths of manure amended fields under simulated snowmelt flooding

description: Anaerobic conditions developed in soils with flooding can enhance the
 release of soil phosphorus (P) to overlying water, but little information
 is available for soils with a long history of manure application. We
 examined the P release from manure-amended soils under simulated snowmelt
 flooding. Intact monoliths from manured (solid-swine, SSM or liquid swine,
 LSM) and unamended (control) field plots were collected from Carman,
 Manitoba. Monoliths were frozen for seven days, then thawed, flooded and
 incubated at +4±1 °C. Redox potential, pH, and concentrations of dissolved
 reactive P (DRP), Ca, Mg, Fe and Mn in pore water and floodwater were
 determined weekly up to 56 days after flooding (DAF), and then at 84 DAF.
 Redox potential decreased with DAF with a greater, and more rapid,
 decrease in SSM (from initial value of ~300 mV to &lt; 0 mV by 84 DAF)
 compared to LSM and control (~100 mV by 84 DAF). Pore water and floodwater
 DRP concentrations were significantly greater in manured treatments than
 the control at all DAFs, and in SSM than LSM for most DAFs. While
 floodwater DRP concentrations remained relatively stable in the control
 treatment, concentrations in manured treatments increased substantially
 from the onset of flooding to 35-42 DAF (3-4-fold increase) and remained
 relatively stable thereafter. Significantly greater P release from SSM-
 than LSM-treated monoliths was due to greater input of P, as well as the
 higher organic matter content in SSM treated soils. These favored the
 rapid development of anaerobic conditions that further induced P release.
description: Soil monoliths were collected from replicated (4) field plots of
 three selected treatments (control, liquid swine manure and solid swine
 manure) from a long term manure field trial. Mololiths were flooded under
 simulated snowmelt condition. Porewater was extracted at 5 cm depth and
 floodwater from the overlying floodwater at weekly intervals upto 8 weeks
 and then at 12 weeks. pH and dissolved reactive P in pore water and
 floodwater were analyzed. The dissolved reactive P concentrations (mg/L)
 and pH are given for pore water and floodwater seprately for each
 replicate soil monolith for the three treatments. 
description: Details of the experiment and the analysis are provided in the
 manuscript.
DOI: 10.5061/dryad.vmcvdncrh
title: Can evolutionary theories of dispersal and senescence predict postrelease survival, dispersal, and body condition of a reintroduced threatened mammal?

description: Theories of dispersal and senescence (or ageing) predict that dispersal,
 and ongoing survival and body condition, are influenced by evolutionary
 drivers, along with intrinsic and extrinsic factors. Such theories are
 relevant to translocations of animals where high mortality, loss of body
 condition, and dispersal beyond the area of release are commonly reported.
 However, these theories have rarely been tested using data from
 translocations. We explore whether theories of dispersal and senescence,
 together with biological knowledge and management interventions, can
 predict rates of post-release dispersal, survival and change in body
 condition of a translocated endangered meso-predator, the eastern quoll
 Dasyurus viverrinus. Captive-bred quolls (n = 60) from three sanctuaries
 were translocated to an unfenced, predator-managed reserve (Booderee
 National Park) over 2 years (2018, 2019). Survival, dispersal and body
 mass were monitored via GPS / VHF tracking and targeted trapping for 45
 days post-release. We found support for the ‘social subordinate’
 hypothesis, with smaller quolls dispersing further. Consistent with
 theories of senescence and the biology of our species, survival was
 marginally greater for females, and females regained losses in body mass
 in both years following release. In contrast, males recovered body
 condition in the first but not the second release as this coincided with
 breeding. Quolls that originated from the mainland sanctuary were on
 average heavier at release and, after accounting for weight, dispersed
 further. Synthesis and applications. Using theory to test outcomes of
 wildlife translocations can provide insights into patterns across taxa and
 under different conditions, enabling useful improvements to future fauna
 translocations. This allows for better predictions to be made about the
 likelihood of success from proposed translocations, changes to planning to
 improve outcomes (e.g. modifying sex ratios, individual selection and
 release cohort), and improved animal welfare as fewer animals are
 subjected to trials.
description: Radio tracking using VHF/GPS collars to monitor survival and
 dispersal, cage trapping to monitor weight.
description: All required data are provided either here, or in the manuscript
 and supplementary material.
DOI: 10.5061/dryad.ncjsxkst1
title: YAP and TAZ maintain PROX1 expression in the developing lymphatic and lymphovenous valves in response to VEGF-C signaling

description: Lymphatic vasculature is an integral part of digestive, immune and
 circulatory systems. The homeobox transcription factor PROX1 is necessary
 for the development of lymphatic vessels, lymphatic valves (LVs) and
 lymphovenous valves (LVVs). We and others previously reported a feedback
 loop between PROX1 and Vascular Endothelial Growth Factor-C (VEGF-C)
 signaling. PROX1 promotes the expression of the VEGF-C receptor VEGFR3 in
 lymphatic endothelial cells (LECs). In turn, VEGF-C signaling maintains
 PROX1 expression in LECs. However, the mechanisms of PROX1/VEGF-C feedback
 loop remain poorly understood. Whether VEGF-C signaling is necessary for
 LV and LVV development is also unknown. Here, we report for the first time
 that VEGF-C signaling is necessary for valve morphogenesis. We have also
 discovered that the transcriptional co-activators YAP and TAZ are required
 to maintain PROX1 expression in LVs and LVVs in response to VEGF-C
 signaling. Deletion of Yap and Taz in the lymphatic vasculature of mouse
 embryos did not affect the formation of LVs or LVVs, but resulted in the
 degeneration of these structures. Our results have identified
 VEGF-C/YAP/TAZ as a critical molecular pathway in valve development.
description: Primary human lymphatic endothelial cells were treated with 20µM
 VP for 2 hours. RNA was subjected to ribosomal RNA depletion followed by
 Truseq stranded total RNA library preparation according to the
 manufacturer’s instruction (Illumina). The resulting RNA-seq libraries
 were analyzed on the Illumina HiSeq sequencing platform.
description: The entire dataset is provided.
DOI: 10.5061/dryad.9kd51c5fv
title: Phage origin of mitochondrion-localized family A DNA polymerases in kinetoplastids and diplonemids

description: Mitochondria retain their own genomes as other bacterial
 endosymbiont-derived organelles. Nevertheless, no protein for DNA
 replication and repair is encoded in any mitochondrial genomes (mtDNAs)
 assessed to date, suggesting the nucleus primarily governs the maintenance
 of mtDNA. As the proteins of diverse evolutionary origins occupy a large
 proportion of the current mitochondrial proteomes, we anticipate finding
 the same evolutionary trend in the nucleus-encoded machinery for mtDNA
 maintenance. Indeed, none of the DNA polymerases (DNAPs) in the
 mitochondrial endosymbiont, a putative α-proteobacterium, seemingly had
 been inherited by their descendants (mitochondria), as none of the known
 types of mitochondrion-localized DNAP showed a specific affinity to the
 α-proteobacterial DNAPs. Nevertheless, we currently have no concrete idea
 of how and when the known types of mitochondrion-localized DNAPs emerged.
 We here explored the origins of mitochondrion-localized DNAPs after the
 improvement of the samplings of DNAPs from bacteria and phages/viruses.
 Past studies revealed that a set of mitochondrion-localized DNAPs in
 kinetoplastids and diplonemids, namely PolIB, PolIC, PolID, PolI-Perk1/2,
 and PolI-dipl (henceforth designated collectively as “PolIBCD+”) have
 emerged from a single DNAP. In this study, we recovered an intimate
 connection between PolIBCD+ and the DNAPs found in a particular group of
 phages. Thus, the common ancestor of kinetoplastids and diplonemids most
 likely converted a laterally acquired phage DNAP into a
 mitochondrion-localized DNAP that was ancestral to PolIBCD+. The phage
 origin of PolIBCD+ hints at a potentially large contribution of proteins
 acquired via non-vertical processes to the machinery for mtDNA maintenance
 in kinetoplastids and diplonemids.
description: The files included are;
 global_famA_DNAP_ali.nxs, the nexus formatted alignment used for
 the phylogenetic tree shown in Fig. 1.
 AGC_PolIBCD_DNAP_ali.nxs, the nexus formatted alignment used for
 the phylogenetic tree shown in Fig. 2.
 global_famA_DNAP_treefile.tre, the treefile for Fig. 1. You can
 see the full taxon names in the tree。
DOI: 10.5061/dryad.vt4b8gtqm
title: CATS tag example deployment

description: Biologging tags are capable of capturing high-resolution data from cryptic
 species that spend a significant portion of their lives in remote or
 inaccessible environments, such as below the sea surface. The advancement
 of biologging technologies over the last ~30 years has lead to an
 explosion of research into the hidden lives of these elusive animals.
 Information about locomotion, feeding, migratory patterns, reproduction,
 and metabolism have all been determined using data obtained with
 biologging tags. CATS (customized animal tracking solutions) tags are one
 of the newest platforms for this type of research and integrate
 high-resolution video with a suite of inertial and environment sensors.
 For the last 5 years, we as members of the Goldbogen lab at Stanford
 University's Hopkins Marine Station have been using CATS tags to
 study the biomechanics and behavior of large baleen whale species. In the
 course of this work, we have tested and streamlined a workflow and set of
 tools to integrate multiple streams of raw sensor data into a simple data
 packet that can be used for further analyses. This dataset is an example
 CATS tag deployment for training use with the CATS toolkit.
description: This is raw inertial sensing data that was collected from a
 humpback whale on 03/20/2020.