cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2jm63xsvs
title: Reproductive output and telomere dynamics following calcium supplementation in wild Tree Swallows (Tachycineta bicolor)

description: This data was the result of an experiment investigating whether
 biologically relevant differences in reproductive investment influence
 fitness in a wild bird species. We employed calcium supplementation to
 experimentally modify reproductive output in Tree Swallow mothers and
 offspring and we used telomere dynamics during the breeding season as a
 proxy for fitness. To confirm that calcium supplementation positively
 impacts reproductive parameters at our study site, we initiated a 4-year
 trial of calcium supplementation with our Tree Swallow study population.
 In the following two breeding seasons, we used calcium supplementation to
 experimentally alter reproductive output and measured telomere length in
 mothers immediately before egg-laying and shortly before fledging to
 determine the direct relationship between reproductive investment and
 telomere shortening in this species. Our study includes one
 hundred eighty-eight nests initiated and monitored over six breeding
 seasons. 
description: This study took place over six summers (2013-2018) at the
 Colorado State University Mountain Campus
 located in Larimer County, Colorado, USA (N40.5611, W105.5978). Tree
 Swallow nests were randomly assigned to either the calcium or the control
 group and females were captured at the nest. Once in hand, we banded
 females, took physiological measurements, and classified the birds into
 age categories of one-year old or greater-than-one-year based on plumage.
 Also during nest construction in 2017 and 2018, we collected between 10 µl
 and 30 µl blood samples from females. 
 Once a clutch was complete, we
 measured egg volume and clutch size. After hatching, we measured hatching
 success for each nest as the proportion of eggs in the clutch that
 hatched. In 2017 and 2018, blood samples were collected from offspring and
 mothers when offspring were 12 days old. At this time, chicks were banded,
 and physiological measurements were taken. All birds were handled and
 sampled under a Federal Bird Banding permit from the USGS Bird Banding
 Laboratory and in accordance with approved guidelines of the Institutional
 Animal Care and Use Committee of Colorado State University (Protocol # 17-7304A).
 qPCR was
 used to measure telomere length relative to the glyceraldehyde-3-phosphate
 dehydrogenase control gene. To measure change in telomere length of the mother
 during the breeding season, we calculated D, a measure of temporal
 telomere shortening adjusted for the regression to the mean.
 Telomere length measurements
 at both time-points were transformed to a log-normal scale to avoid
 negative lengths. 
description: The datasets can be opened and analyzed in R or Excel.
DOI: 10.5061/dryad.prr4xgxs9
title: Data from: Maximum stem diameter predicts liana population demography

description: Determining population demographic rates is fundamental to understanding
 differences in species life-history strategies and their capacity to
 coexist. Calculating demographic rates, however, is challenging and
 requires long-term, large-scale censuses. Body size may serve as a simple
 predictor of demographic rate; can it act as a proxy for demographic rate
 when those data are unavailable? We tested the hypothesis that maximum
 body size predicts species’ demographic rate using repeated censuses of
 the 77 most common liana species on the Barro Colorado Island, Panama
 (BCI) 50-ha plot. We found that maximum stem diameter does predict
 species’ population turnover and demography. We also found that lianas on
 BCI can grow to the enormous diameter of 635 mm, indicating that they can
 store large amounts of carbon and compete intensely with tropical canopy
 trees. This study is the first to show that maximum stem diameter can
 predict plant species’ demographic rates and that lianas can attain
 extremely large diameters. Understanding liana demography is particularly
 timely because lianas are increasing rapidly in many tropical forests, yet
 their species-level population dynamics remain chronically understudied.
 Determining per-species maximum liana diameters in additional forests will
 enable systematic comparative analyses of liana demography and potential
 influence across forest types.
description: We measured the diameter of all lianas ³ 10 mm diameter in the
 BCI plot in 2007 and again in 2017 using liana-specific census methods
 developed by Gerwing et al. (2006) and Schnitzer et al. (2008). Diameter
 measurements were taken 1.3 m along the stem from the roots using calipers
 for stems &lt; 50 mm diameter, and diameter tape for stems ³ 50 mm. If
 the stem was deformed by bulges, nodes, damage, or other defects at the
 1.3 m measurement point, we measured 50 mm below the deformity. In total,
 there were 175 liana species in the BCI 50-ha plot (Schnitzer et al.
 2021); we selected the 77 species that had 100 more individuals in the 50-
 ha plot (Appendix S1: Table S1) to calculate species population dynamics
 (measured as turnover). We defined species-specific turnover rate as the
 geometric mean of individual liana recruitment (L<sub>r</sub>)
 and mortality (L<sub>m</sub>) between the two censuses
 (Phillips & Gentry 1994):  (ln L<sub>r</sub> + ln
 L<sub>m</sub>)/2.  Both recruitment and mortality were highly
 correlated with turnover (Pearson’s r = 0.97 & 0.92,
 respectively); thus, our findings for turnover apply to its component
 parts (L<sub>r</sub> and L<sub>m</sub>).
DOI: 10.5061/dryad.905qfttrp
title: Trucks vs treks: The relative influence of motorized vs non-motorized recreation on a mammal community

description: Outdoor recreation is increasing rapidly on public lands, with potential
 consequences for wildlife communities. Recreation can induce shifts in
 wildlife activity and habitat use, but responses vary widely even within
 the same species, suggesting mitigating factors that remain poorly
 understood. Both the type of recreation – motorized or non-motorized – and
 the distance of wildlife from human disturbance may be important in
 developing a general understanding of recreation impacts on wildlife and
 making more informed management decisions. We conducted a camera-trapping
 survey in the Colville National Forest (CNF) of northeastern Washington in
 the summers of 2019 and 2020. We collected ~11,000 trap nights of
 spatially-extensive data on nine mid-large mammalian species,
 simultaneously recording the presence and activity patterns of motorized
 (primarily vehicles on roads) and non-motorized (primarily hikers on
 trails) recreation and wildlife both along trails and roads and off trails
 and roads (away from most recreation). We used diel overlap analysis, time
 lag analysis, and single-season single-species occupancy modeling to
 examine the impact of recreation on the focal species. Species temporally
 avoided recreationists either by shifting to more nocturnal hours or
 delaying return to recently-used recreation sites. Most species also
 responded spatially by altering use or intensity of use of cameras sites
 due to recreation, though both positive and negative associations with
 recreation were documented. Species’ responded to non-motorized recreation
 (e.g., hikers on trails) more often than motorized recreation (e.g.,
 vehicles on roads). Most effects of recreation extended off the trail or
 road, though in three instances the spatio-temporal response of species to
 recreation along trails/roads disappeared a short distance away from those
 features. Our work suggests that a better understanding of landscape-scale
 impacts of recreation, including fitness consequences, will require
 additional work to disentangle the effects of different types of
 recreation and estimating the effective distance at which wildlife
 responds. Moreover, these results suggest that quiet, non-consumptive
 recreation may warrant increased attention from land managers given its
 potential to influence spatiotemporal ecology of numerous species.
description: Data collected from camera traps and then post-processed to
 extract date/time and species in each photo. R packages used to manage
 data.
DOI: 10.5061/dryad.fbg79cp1n
title: Data from: Phenotypic rate and state are decoupled in response to river-to-lake transitions in cichlid fishes

description: Geographic access to isolated ecosystems is an important catalyst of
 adaptive radiation. Cichlid fishes repeatedly colonized rift, crater, and
 volcanic lakes from surrounding rivers. We test the “lake effect” on the
 phenotypic rate and state across 253 cichlid species. The rate of
 evolution was consistently higher (~10-fold) in lakes, and consistent
 across different dimensions of the phenotype. Rate shifts tended to occur
 coincident with or immediately following river-to-lake transitions,
 generally resulting in 2- to 5-fold faster rates than in the founding
 riverine lineage. By contrast, river- and lake-dwelling cichlids exhibit
 considerable overlap in phenotypes, generally with less disparity in
 lakes, but often different evolutionary optima. Taken together, these
 results suggest that lake radiations rapidly expand into niches largely
 already represented by ancestral riverine lineages, albeit in different
 frequencies. Lakes may provide ecological opportunity via ecological
 release (e.g., from predators/competitors), but need not be coupled with
 access to novel ecological niches.
DOI: 10.5061/dryad.5qfttdzc0
title: Data from: Hierarchical power control of a large-scale wind farm by using a data-driven optimization method

description: With the participation in automatic generation control (AGC), a
 large-scale wind farm should distribute the real-time AGC signal to
 numerous wind turbines (WTs). This easily leads to an expensive
 computation for a high-quality dispatch scheme, especially considering the
 wake effect among WTs. To address this problem, a hierarchical power
 control (HPC) is constructed based on the geographical layout and
 electrical connection of all the WTs. Firstly, the real-time AGC signal of
 the whole wind farm is distributed to multiple decoupled groups in
 proportion of their regulation capacities. Secondly, the AGC signal of
 each group is distributed to multiple WTs via the data-driven
 surrogate-assisted optimization, which can dramatically reduce the
 computation time with a small number of time-consuming objective
 evaluations. Besides, a high-quality dispatch scheme can be acquired by
 the efficient local search based on the dynamic surrogate. The
 effectiveness of the proposed technique is thoroughly verified with
 different AGC signals under different wind speeds and directions.
DOI: 10.5061/dryad.d7wm37q6f
title: Evaluation of recombination detection methods for viral sequencing

description: Recombination is a key evolutionary driver in shaping novel viral
 populations and lineages. When unaccounted for, recombination can impact
 evolutionary estimations, or complicate their interpretation. Therefore,
 identifying signals for recombination in sequencing data is a key
 prerequisite to further analyses. A repertoire of recombination detection
 methods have been developed over the past two decades, however, the
 prevalence of pandemic-scale viral sequencing data poses a computational
 challenge for existing methods. Here, we assessed five recombination
 detection methods (PhiPack (Profile), 3SEQ, GENECONV, VSEARCH (UCHIME),
 and gmos) to determine if any are suitable for the analysis of bulk
 sequencing data. To test the performance and scalability of these methods,
 we analysed simulated viral sequencing data across a range of sequence
 diversities, recombination frequencies, and sample sizes. Further, we
 provide a practical example for the analysis and validation of empirical
 data. We find that recombination detection methods need to be scalable,
 use an analytical approach and resolution that is suitable for the
 intended research application, and are accurate for the properties of a
 given dataset (e.g. sequence diversity and estimated recombination
 frequency). Analysis of simulated and empirical data revealed that the
 assessed methods exhibited considerable trade-offs between these criteria.
 Overall, we provide general guidelines for the validation of recombination
 detection results, the benefits and shortcomings of each assessed method,
 and future considerations for recombination detection methods for the
 assessment of large-scale viral sequencing data.
description: Simulated .fasta files by SANTA-SIM across different parameters. All file
 names follow the structure of msa_m_r_n_dual_rep.fasta with a numeric
 value following each letter. The parameters are: m = mutation rate r =
 recombination rate n = number of sequences dual = dual-infection
 probability rep = replicate The numeric indicates the parameter value it
 follows, for example, msa_m0.001_rc0.05_n100_dual1_rep2.fasta means that
 the alignment was simulated with the parameters: mutation rate = 0.001
 recombination rate = 0.05 number of sequences = 100 dual-infection
 probability = 1 replicate = 2 ## Files performance.tar.gz - alignments for
 the performance benchmark scale.tar.gz - alignments for the scalability
 benchmark
DOI: 10.5061/dryad.cvdncjt8q
title: Variable expression of cyanide detoxification and tolerance genes in cyanogenic and acyanogenic white clover (Trifolium repens L.)

description: Premise of the study: β-cyanoalanine synthase (β-CAS) and alternative
 oxidase (AOX) play important roles in the ability of plants to detoxify
 and tolerate hydrogen cyanide (HCN) stress.  These functions are
 critical for all plants, as HCN is produced at low levels during basic
 metabolic processes, but are likely to be especially important in
 cyanogenic species, which release high levels of HCN following tissue
 damage. However, their expression has not been examined in cyanogenic
 species, nor has it been compared between cyanogenic and acyanogenic
 genotypes within a species. Methods: We used a natural polymorphism for
 cyanogenesis in white clover to examine β-CAS and Aox gene expression in
 relation to cyanogenesis-associated HCN exposure.  We identified
 all β-CAS and Aox gene copies present in the genome, including members of
 the Aox1, Aox2a and Aox2d subfamilies previously reported in
 legumes.  Expression levels were compared between cyanogenic and
 acyanogenic genotypes, and under conditions of leaf tissue damage compared
 to undamaged tissue.   Key results: Results indicate that β-CAS
 and Aox2a expression are differentially elevated in cyanogenic genotypes,
 and that tissue damage is not required to induce this increased
 expression.  Aox2d, in contrast, appears to be upregulated as a
 generalized wounding response. Conclusions: These findings suggest a
 heightened constitutive role for both HCN detoxification (via elevated
 β-CAS expression) and HCN-toxicity mitigation (via elevated Aox2a
 expression) in plants that are capable of cyanogenesis.  As such,
 freezing-induced cyanide autotoxicity is unlikely to be the primary
 selective factor in the evolution of climate-associated cyanogenesis
 clines.  
description: All qPCR protocols followed MIQE guidelines, including for
 numbers of biological and technical replicates and reaction optimization
 protocols.  Gene expression level was quantified using the CFX96 Real-Time
 PCR Detection System (BIO-RAD, Hercules, California, USA). For all genes,
 reactions included 1× iTaq™ Universal SYBR<sup>®</sup> Green
 Supermix, 0.5 µM (0.3 µM for β-CAS) forward primer, 0.5 µM (0.3 µM for
 β-CAS) reverse primer and 4-10 ng cDNA in a 20 µL reaction volume. Ef1α
 was used as the reference gene. PCR conditions followed the standard SYBR®
 Green cycle in CFX96 Real-Time PCR Detection System with slight
 modifications to maximize reaction efficiency: 95°C for 30 s, then [95°C
 for 5 s, 60°C (63°C for β-CAS) for 30 s] × 40 cycles. Three technical
 replicates were applied to each cDNA of the sample. The data were analyzed
 by the ΔΔC<sub>T</sub> method with efficiency calibration in
 CFX Maestro™ Software (BIO-RAD, Hercules, California, USA) according to
 the manufacturer’s instructions.
DOI: 10.5061/dryad.tqjq2bw51
title: Data from: Centromere innovations within a mouse species

description: Mammalian centromeres direct faithful genetic inheritance and are
 typically characterized by regions of highly repetitive and rapidly
 evolving DNA. We focused on a mouse species, Mus pahari, that we found has
 evolved to house centromere-specifying CENP-A nucleosomes at the nexus of
 a satellite repeat that we identified and term p-satellite (p-sat), a
 small number of recruitment sites for CENP-B, and short stretches of
 perfect telomere repeats. One M. pahari chromosome, however, houses a
 radically divergent centromere harboring ~6 Mbp of a homogenized
 p-sat-related repeat, p-satB, that contains &gt;20,000 functional
 CENP-B boxes. There, CENP-B abundance drives accumulation of
 microtubule-binding components of the kinetochore, as well as a
 microtubule-destabilizing kinesin of the inner centromere. The balance of
 pro- and anti-microtubule-binding by the new centromere permits it to
 segregate during cell division with high fidelity alongside the older ones
 whose sequence creates a markedly different molecular composition.
description: # Centromere innovations within a mouse species ## List of scripts used :
 findKmers.py Code2_hist.m Code2_loadFile.m
 Code3_plotting_fixIncrement_1sizeClass_JDM20170206_allPlots.m
 Code2_mkdir.m Code2_parentSeq.m Code2_aligning_main_JDM_20160401.m
 Code2_FwdRevSum.m Code2_getFileNames.m
 Code1_joining_fq2sam_linux_JDMmod20190521.m findKmers.py Identifies
 instances of a Kmer sequence in a fasta file. Python version 3.8.10. Run
 from the command line as ./findKmers.py --kmers {CENP-B_box_sequences}
 --fasta {genome_assembly.fasta} --out {out.bed}/. Dependent on
 matplotlib.pyplot. Dependent on Bio.SeqIO and matplotlib.pyplot (v3.5.3).
 Code1_joining_fq2sam_linux_JDMmod20190521.m Joins fastq paired-end fastq
 reads and converts to a sam file. Plots a histogram of frequency of joined
 reads. Run from MATLAB 2017a (9.2.0.556344)
 Code2_aligning_main_JDM_20160401.m Aligns joined reads from Code1 to a
 sequence. Sequence choices are described in Code2_parentSeq.m. Run from
 MATLAB 2017a (9.2.0.556344). Dependent on Code2_hist.m, Code2_loadFile.m,
 Code2_mkdir.m, Code2_parentSeq.m, Code2_FwdRevSum.m, Code2_getFileNames.m.
 Code3_plotting_fixIncrement_1sizeClass_JDM20170206_allPlots.m Using the
 output from Code2, generates several plots of sequencing reads aligned to
 a specific sequence including nucleosome occupancy plots, midpoints plots
 and stack plots. Run from MATLAB 2017a (9.2.0.556344). See "Hasson et
 al. NSMB. 2013." for examples.
 2020-04-29-INP-consensus-align-hist-line.m Using the output from
 Code2_aligning_main_JDM_20160401.m, generates the a histogram of %
 identity of reads to the target sequence. Run from MATLAB 2017a
 (9.2.0.556344).
DOI: 10.5061/dryad.8cz8w9gx5
title: Polymorphic structure of a-type screw dislocation cores in alpha-Ti

description: The dislocation core structure has a significant role in determining the
 dominant slip plane and the magnitude of the Peierls stress for a
 dislocation. An important challenge when studying
 dislocation cores is to determine the stable and metastable core
 morphologies, and then relate these structures to the dynamics of
 the dislocations. This study introduces a method for identifying core
 structures that are metastable at zero temperature. Application
 of this method to ⟨a⟩-type screw dislocations in α-Ti (as
 described using an empirical potential) reveals a multitude of
 (meta-)stable non-planar cores.  This dataset contains
 the LAMMPS files for all the (meta-)stable morphologies of screw
 dislocation cores in α-Ti as described by Hennig's MEAM potential
 identified in this study. We identified stable core configurations for an
 ⟨a⟩-type screw dislocation under a compressive non-Schmid stress of 0,
 250, 500, 750, and 1000 MPa applied in the [1-100] direction.
description: # Polymorphic Structure of a-type Screw Dislocation Cores in alpha-Ti
 [https://doi.org/10.5061/dryad.8cz8w9gx5](https://doi.org/10.5061/dryad.8cz8w9gx5) This dataset contains LAMMPS files of (meta-)stable morphologies of screw dislocation cores in α-Ti as described by Hennig's MEAM potential. It contains the stable core configurations under a compressive non-Schmid stress of 0, 250, 500, 750, and 1000 MPa applied in the [1-100] direction. The stable core morphologies were obtained with the ESP method or with the NEB core search method. ## Description of the data and file structure Each file is named according to the core periodicity, the stress state, and the core morphology. For instance, the file 1b\_sNS\_500\_m1 is a supercell with a m1-type core that has a 1b-periodicity with a compressive non-Schmid stress of 500 MPa applied in the [1-100] direction. The file 2b\_sNS\_750\_coremu1 is a supercell with a mu1-type core that has a 2b-periodicity with a compressive non-Schmid stress of 750 MPa applied in the [1-100] direction. The reference supercells (perfect crystal in the same stress state as the dislocated cells) used to build the dislocated cells are also in this dataset, named after their stress state. 1b\_sNS\_500\_Ref is a perfect crystal under a 500 MPa compressive stress in the [1-100] direction. Each file is in a LAMMPS data format. The number of atoms, number of atom types, periodicity vectors, and corresponding mass for the atom types first appear in that order. It is followed by 4 columns containing the ID number, the type, and the coordinates (x, y, z) of each atom.
DOI: 10.5061/dryad.ns1rn8q0d
title: DNA barcoding for the assessment of marine and coastal Fish Diversity from the Coast of Mozambique

description: The ichthyological provinces of Mozambique are understudied hotspots of
 global fish diversity. In this study, we applied DNA barcoding to identify
 the composition of the fish fauna from the coast of Mozambique. A total of
 143 species belonging to 104 genera, 59 families, and 30 orders were
 identified. The overall K2P distance of the COI sequences within species
 ranged from 0.00% to 1.51%, while interspecific distances ranged from
 3.64% to 24.49%. Moreover, the study revealed 15 threatened species
 according to the IUCN Red List of Threatened Species, with elasmobranchs
 being the most represented group. Additionally, the study also uncovered
 four new species that were not previously recorded in this geographic
 area, including Boleophthalmus dussumieri, Maculabatis gerrardi,
 Hippocampus kelloggi, and Lethrinus miniatus. This study represents the
 first instance of utilizing molecular references to explore the fish fauna
 along the Mozambican coast. Our results indicate that DNA barcoding is a
 dependable technique for the identification and delineation of fish
 species in the waters of Mozambique. The DNA barcoding library established
 in this research will be an invaluable asset for advancing the
 understanding of fish diversity and guiding future conservation
 initiatives.
DOI: 10.13140/rg.2.2.19873.67681
title: شهادة الكاميرون