cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.zgmsbccbs
title: Flapping Wing Aerodynamics with PRSSM

description: Flying animals resort to fast, large-degree-of-freedom motion of flapping
 wings, a key feature that distinguishes them from rotary or fixed-winged
 robotic fliers with limited motion of aerodynamic surfaces. However,
 flapping-wing aerodynamics are characterised by highly unsteady and
 three-dimensional flows difficult to model or control, and accurate
 aerodynamic force predictions often rely on expensive computational or
 experimental methods. Here, we developed a computationally efficient and
 data-driven state-space model to dynamically map wing kinematics to
 aerodynamic forces/moments. This model was trained and tested with a total
 of 548 different flapping-wing motions and surpassed the accuracy and
 generality of the existing quasi-steady models. This model used 12 states
 to capture the unsteady and nonlinear fluid effects pertinent to force
 generation without explicit information of fluid flows. We also provided a
 comprehensive assessment of the control authority of key wing kinematic
 variables and found that instantaneous aerodynamic forces/moments were
 largely predictable by the wing motion history within a half-stroke cycle.
 Furthermore, the angle of attack, normal acceleration, and pitching motion
 had the strongest effects on the aerodynamic force/moment generation. Our
 results show that flapping flight inherently offers high force control
 authority and predictability, which can be key to developing agile and
 stable aerial fliers.
description: This dataset includes the data used in the manuscript
 "State-space aerodynamic model reveals high force control authority
 and predictability in flapping flight".  The code for the PRSSM model
 and to analyze the data is provided in
 "https://github.com/yagiz-bayiz/flapping-wing-aerodynamics-prssm". See the manuscript for more details ("https://arxiv.org/abs/2103.07994").The aerodynamics data ("flapping_wing_aerodynamics.mat")  used to train and test the Probabilistic Recurrent State-Space Model (PRSSM) was generated by the dynamically scaled robotic wing designed by the BioRob-InFL lab. The data set includes all 548 trajectories used in the analysis. The measured positions, forces, and moments were denoised and post-processed by the robotic wing target PC to remove the sensor bias, buoyancy, and gravitational effects. Furthermore, the data was downsampled and organized in the postprocessing to have a 25Hz sampling time and 470 data points for each trajectory.
DOI: 10.5061/dryad.x95x69pjk
title: Metapopulation connectivity retains genetic diversity following historical bottleneck in a federally endangered seabird

description: Despite intensive management since the 1970s, recovery of the endangered
 northwestern Atlantic population of the Roseate Tern (Sterna dougallii
 dougallii) has not offset low productivity from a female-biased sex ratio,
 low adult survival, and habitat constriction. Now, &gt;90% of
 individuals breed at three sites within 200 km from Long Island, NY to
 Buzzards Bay, MA (warm-water subregion). To characterize the impact of
 historical bottlenecks, metapopulation structure, and demographic
 fluctuations on genetic variation, Roseate Terns from the warm-water
 (1870s, 1970s, 1997, 2016) and cold-water (Nova Scotia, Canada; 2018)
 subregions were genotyped at 8-16 microsatellites and two-three
 mitochondrial regions. Diversity declined in the warm-water subregion from
 the 1870s (HE= 0.44, AR= 2.86) and 1970s (HE = 0.53, AR = 3.25) to 1997
 (HE = 0.38, AR = 2.58). Genetic signatures of bottlenecks persisted in
 1997 (P = 0.001 – 0.003) and 2016 (P = &lt;0.001 – 0.005), but an
 increase in variation occurred by 2016 (HE= 0.50, AR= 2.85). Weak
 structure was detected between contemporary warm- and cold-water
 subregions (θ = 0.06) and within the warm-water subregion (θ = 0.04). Both
 demographic (= 3439-3821) and genetic (= 3040) estimates suggested
 effective population size stability over the last 100 years, despite large
 fluctuations in census size (4000 – 8662). Results suggest that 50 years
 of management (restoring habitat, preventing gull encroachment,
 controlling predators) at colony sites supported a small, stable Ne and
 maintained a hierarchical metapopulation that allowed gene flow to
 redistribute genetic variation throughout the NW Atlantic. The
 metapopulation remains highly vulnerable to stochastic events but harbors
 resiliency and redundancy through gene flow and a stable Ne. For long-term
 persistence from a genetic perspective, managers must maintain the major
 source colonies, increase availability of high-quality peripheral breeding
 sites, and protect concentrated non-breeding sites that facilitate gene
 flow.
description: Microsatellite genotypes; population genetic analyses analyzed in
 STRUCTURE, adegenet, and packages in R.
description: "ReadMe" file contains description of data files,
 scripts, and how to run analyses.
DOI: 10.5061/dryad.1ns1rn8tk
title: Maximum clade credibility (MCC) tree of Argyrodes lanyuensis from Philippines and Orchid Island Taiwan using BEAST 1.10

description: Oceanic islands are unique geographic systems that promote local
 adaptations and allopatric speciation in many of their highly endemic
 taxa. This is a common case in the Philippine Archipelago, where
 numerous unrelated taxa on islands have been inferred to have diversified
 in isolation. However, few cases have been reported in invertebrates
 especially among parasitic organisms. Here, we tested for biogeographical
 structure in novel populations of the “generalist" kleptoparasitic
 spider, Argyrodes lanyuensis Yoshida, Tso & Severinghaus, 1998 in
 the Philippines. Results showed that, in addition to Orchid Island, this
 species has a wide geographic distribution in the Philippine Archipelago.
 The estimated divergence time of this lineage using the mitochondrial
 cytochrome oxidase 1 (mt-CO1) suggests that this species diverged ca 3.12
 MYA, during the Pliocene. Two reciprocal monophyletic clades were
 elucidated in A. lanyuensis, but with limited differentiation across
 Pleistocene Aggregate Island Complex (PAIC) boundaries and modern-day
 islands. However, in our analyses of morphological variation, we
 identified two phenotypically differentiated units in males (Orchid
 Island, Taiwan+Luzon, Philippine PAIC populations versus Palawan+West
 Visayan+Mindanao PAIC populations). We infer that this species diverged in
 the southern portion of the Philippine Archipelago and only recently
 colonized Orchid Island. Our study provides new information on the
 extensive distribution of A. lanyuensis outside Orchid Island, Taiwan, but
 we documented a very limited geographically associated genetic variation.
 Our study points to behavioral phenomena such as foraging behavior as
 essential contributor to the evolutionary process of species
 diversification, in contrast to the traditionally invoked geographic
 drivers of divergence.
description: We amplified the mitochondrial cytochrome oxidase 1 and sequenced
 it. Contigs were generated from merged forward, and reverse, sequences and
 their consensus sequences were aligned using Geneious Pro 6.03. We
 reconstructed a time-calibrated phylogenetic tree using BEAST v1.10.4. We
 incorporated seven species (nine sequences in total) from GenBank as an
 outgroup. The GTR+I+G best-fit nucleotide substitution model, Yule process
 speciation tree model prior and the uncorrelated lognormal relaxed clock
 model were applied for node age time calibration. We used the
 ucld.mean=0.0112 site -1 My -1 based on the spider mitochondrial
 substitution rate estimates (Bidegaray-Batista and Arnedo 2011;
 Kuntner<i> et al.</i> 2013) with an arbitrary standard
 deviation (ucld.stdv=0.01). The MCMC parameters were fixed to 1 x 10
 <sup>9</sup> generations with tree sampling every 1 x
 10<sup>4</sup> generations. Tracer v.1.7.1 was used to
 determine burn-in  (discarded the first 10% of the trees). MCC tree was
 then generated using the program TreeAnnotator v.1.8.4.
DOI: 10.5061/dryad.mcvdnck1j
title: CT data and 3D models associated with: Palaeoneurology of the Early Cretaceous iguanodont Proa valdearinnoensis and its bearing on the parallel developments of cognitive abilities in theropod and ornithopod dinosaurs

description: Proa valdearinnoensis is a relatively large-headed and stocky
 iguanodontian dinosaur from the latest Early Cretaceous of Spain. Its
 braincase is known from three specimens. Similar to that of other
 dinosaurs, it shows a mosaic ossification pattern in which most of the
 bones seem to have fused together indistinguishably while a few bones
 (frontoparietal, basioccipital) might have remained loosely attached. The
 endocasts of the three specimens are described based on CT data and
 digital reconstructions. They show unmistakable morphological similarities
 with the endocast of closely related taxa, such as Sirindhorna khoratensis
 (which is close in age but from Thailand). This supports a high
 conservatism of the endocranial cavity. The issue of volumetric
 correspondence between endocranial cavity and brain in dinosaurs is
 analysed. Although a brain-to-endocranial cavity (BEC) index of 0.50 has
 been traditionally used, we employ instead  0.73. This is indeed
 the mid-value between the situation in adults of Alligator
 mississippiensis and Gallus gallus, which are members of the extant
 bracketing taxa of dinosaurs (Crocodilia and Aves). We thence gauge the
 level of encephalisation of Proa valdearinnoensis by the calculation of
 the Encephalisation Quotient (EQ), which remains valuable as a metric for
 assessing the degree of cognitive function in extinct taxa, especially
 those with fully ossified braincases like dinosaurs and other archosaurs.
 The EQ obtained for Proa valdearinnoensis (3.611) suggests that this
 species was significantly more encephalised than most if not all extant
 non-avian, non-mammalian amniotes. Our work adds to the growing body of
 data concerning theoretical cognitive capabilities in dinosaurs and
 supports the idea that increasing encephalisations were fostered not only
 once in theropods but also in parallel in the shorter-lived lineage of
 ornithopods. Proa valdearinnoensis was ill-equipped to respond to theropod
 dinosaurs and possibly lived in groups as a strategy to mitigate the risk
 of being predated upon. We hypothesize that group-living and protracted
 caring of juveniles in this and possibly many other iguanodontian
 ornithopods favoured a degree of encephalisation that was outstanding by
 reptile standards.
DOI: 10.5061/dryad.b2rbnzsfv
title: Limited sink but large storage: biomass dynamics in naturally developing beech (Fagus sylvatica) and oak (Quercus robur, Quercus petraea) forests of northwestern Germany

description: 1. Currently, the dynamics underlying the storage and acquisition of
 biomass, and thus carbon, in naturally developing forests are under
 debate. A better understanding of the biomass dynamics of forests is
 needed to clarify the role played by naturally developing forests in the
 mitigation of climate change. 2. Long-term monitoring data from unmanaged
 strict forest reserves (SFRs) in northwestern Germany were used to analyze
 the biomass dynamics of pure beech, mixed beech, and mixed oak forests. A
 complete balance of aboveground woody biomass (biomass) and growth,
 density-dependent and -independent mortality, as well as deadwood decay
 was derived. Density-independent mortality served as a proxy for
 disturbance severity. 3. After a time of abandonment (TSA) of 50 years,
 the average biomass ranged between 334 t ha-1 in mixed oak and 478 t ha-1
 in pure beech stands. The net change in biomass was positive in all forest
 types. Density-independent mortality and decay rates were much lower than
 the growth rates. Pure beech forests reached higher levels of biomass, a
 higher net change in biomass, and more growth than either of the mixed
 forest type. Biomass increased linearly with TSA in pure beech stands but
 followed an asymptotic course in the mixed forests. In the latter, the net
 change in biomass and growth were consistent with a unimodal development
 pattern. The development of biomass could not be explained by the aging of
 the tree communities. 4. Synthesis: We hypothesized that the observed
 biomass dynamics is a result of the interaction between resource supply
 within a limited growing space and the resource-use efficiency of the tree
 stand in conjunction with disturbances. The still-linear increase in the
 biomass of pure beech forests was assumed to reflect the high resource-use
 efficiency of beech, especially its use of light. The aboveground capacity
 of naturally developing broadleaved forests to store and acquire biomass,
 and thus carbon, is substantial. Accordingly, allowing broadleaved forests
 to develop naturally can contribute substantially to carbon storage and
 sequestration. However. our study also suggests that the aboveground
 carbon sink decreases after several decades.
DOI: 10.5061/dryad.jwstqjq90
title: Droplet digital PCR (ddPCR) as a tool for investigating dynamics of cryptic symbionts

description: Interactions among symbiotic organisms and their hosts are major drivers
 of ecological and evolutionary processes. Monitoring the infection
 patterns among natural populations and identifying factors affecting these
 interactions is critical for understanding symbiont-host relationships.
 However, many of these interactions remain understudied since the
 knowledge about the symbiont species is lacking and hinders the
 development of appropriate tools. In this study, we developed a digital
 droplet PCR (ddPCR) assay based on apicomplexan COX1 gene to detect an
 undescribed agamococcidian symbiont. We show that the method gives precise
 and reproducible results and enables detecting cryptic symbionts in low
 target concentration. We further exemplify the assay’s use to survey
 seasonally sampled natural host (Pygospio elegans) populations for
 symbiont infection dynamics. We found that symbiont prevalence differs
 spatially but does not show seasonal changes. Infection load differed
 between populations and was low in spring and significantly increased
 towards fall in all populations. We also found that the symbiont
 prevalence is affected by host length and population density. Larger hosts
 were more likely to be infected and high host densities were found to have
 lower probability of infection. The observed variations could be due to
 characteristics of both symbiont and host biology, especially the seasonal
 variation in encounter rates. Our findings show that the developed ddPCR
 assay is a robust tool for detecting undescribed symbionts that are
 otherwise difficult to quantify, enabling further insight into the impact
 cryptic symbionts have on their hosts.
description: Molecular detection of agamococcidian COX1 gene was done using
 Bio-Rad's QX200 droplet digital PCR system with QX Eva Green
 chemitsry from whole host DNA samples. Infection load is calculated in
 number of copies/ ng of host DNA, infection status is defined infected (=
 1), if more than 0 copies/ ng of host DNA is detected, and non-infected (=
 0) otherwise. Environmental data (temperature,
 salinity, and sediment characteristics), host length and density is from
 original paper: Thonig A., Knott K.E., Kesäniemi J.E., Winding Hansen B.
 & Banta G.T. 2016. Population and reproductive dynamics of the
 polychaete <i>Pygospio elegans</i> in a boreal estuary
 complex. <i>Invertebrate Biology</i>, 135(4):
 370–384.
description: Missing values are marked as NA. Environmental
 data and host density is missing from October and host length from 2
 individuals.
DOI: 10.5061/dryad.02v6wwq3j
title: Plasticity in guarding superb starlings

description: Cooperatively breeding vertebrates are common in unpredictable
 environments where the costs and benefits of providing offspring care
 fluctuate temporally. To balance these fitness outcomes, individuals of
 cooperatively breeding species often exhibit behavioral plasticity
 according to environmental conditions. Although individual variation in
 cooperative behaviors is well-studied, less is known about variation in
 plasticity of social behavior. Here, we examine the fitness benefits,
 plasticity, and repeatability of nest guarding behavior in cooperatively
 breeding superb starlings (Lamprotornis superbus). After demonstrating
 that the cumulative nest guarding performed at a nest by all breeders and
 helpers combined is a significant predictor of reproductive success, we
 model breeder and helper behavioral reaction norms to test the hypothesis
 that individuals invest more in guarding in favorable seasons with high
 rainfall. Variation in nest guarding behavior across seasons differed for
 individuals of different reproductive status: breeders showed plastic nest
 guarding behavior in response to rainfall, whereas helpers did not.
 Similarly, we found that individual breeders show repeatability and
 consistency in their nest guarding behavior while individual helpers did
 not. Thus, individuals with the potential to gain direct fitness benefits
 exhibit greater plasticity and individual-level repeatability in
 cooperative behavior.
DOI: 10.5061/dryad.4tmpg4f9w
title: Stickleback sensory morphology 2015 & 2017 measurements and analysis files

description: The peripheral sensory systems, whose morphological attributes help
 determine the acquisition of distinct types of information, provide a
 means to quantitatively compare multiple modalities of a species’ sensory
 ecology. We used morphological metrics to characterize multiple sensory
 modalities—the visual, olfactory, and mechanosensory lateral line sensory
 systems—for Gasterosteus aculeatus, the three‐spined stickleback,
 to compare how sensory systems vary in animals that evolve in different
 ecological conditions. We hypothesized that the dimensions of sensory
 organs and correlations among sensory systems vary in populations adapted
 to marine and freshwater environments, and have diverged further among
 freshwater lake-dwelling populations. Our results showed that among
 environments, fish differed in which senses are relatively elaborated or
 reduced. When controlling for body length, littoral fish had larger eyes,
 more neuromasts, and smaller olfactory tissue area than pelagic or marine
 populations. We also found differences in the direction and magnitude of
 correlations among sensory systems for populations even within the same
 habitat type. Our data suggest that populations take different
 trajectories in how visual, olfactory, and lateral line systems respond to
 their environment. For the populations we studied, sensory modalities do
 not conform in a predictable way to the ecological categories we assigned.
description: Missing values (due to unobtained collection of values for
 animals identified in the data frame) are entered in the data sheet as
 NULL.  Rows with all values missing are retained
 included in the dataframe to work with associated scripts (e.g.
 dataframespecifications.R)
DOI: 10.25349/d9vp6g
title: Pesticide Mitigation Prioritization Model (PMPM) - Environmental Release Tool and Results

description: Pesticides continue to pose a significant threat to the environment,
 endangering both aquatic and terrestrial ecosystems. However, effectively
 targeting and reducing pesticide toxicity in the environment faces several
 challenges. These challenges include evaluating toxicity over large areas,
 obtaining precise spatiotemporal data on pesticide use, assessing
 cumulative toxicity, and identifying the health and economic impacts of
 pesticide application sites. To address these challenges, we present the
 Environmental Release Tool, a sub-tool of the Pesticide Mitigation
 Prioritization Model. This tool aims to advance the understanding in these
 four areas and facilitate pesticide management by promoting collaboration
 between experts and non-experts. It employs a framework that generates
 user-friendly graphical and tabular summaries of pesticide impact
 information, contextualized within management opportunities. While the
 Pesticide Mitigation Prioritization Model can be applied across the United
 States, its utility is particularly valuable in California. This is
 because the California Department of Pesticide Regulation (CDPR) hosts the
 most comprehensive pesticide use data globally. The CDPR's Pesticide
 Use Reports (PUR) database records agricultural pesticide applications on
 a daily time step and at the scale of one square mile (2.6 square
 kilometers) per application site. Leveraging this extensive database, we
 have integrated it directly into the Pesticide Mitigation Prioritization
 Model. This integration enables us to rapidly quantify the applied
 pesticide toxicity by chemical, source, and watershed across California,
 typically within seconds to minutes.
description: Refer to PMPM_EnvironmentalRelease_UserGuide.pdf for details
 about data collection and processing.
description: Requires R and Rstudio. Refer to the Readme
 files and PMPM_EnvironmentalRelease_UserGuide.pdf for details.
DOI: 10.25338/b83p8b
title: Limnological data for Lake Tahoe seasonal and long-term clarity trend analysis report

description: This data set includes imnological data used for a report "Lake Tahoe
 Seasonal and Long-Term Clarity Trend Analysis
 Report."   The clarity of Lake Tahoe, observed
 using a Secchi disk, continues to be a sentinel metric. It is influenced
 by both physical and biological processes and has had a declining trend
 over decades of monitoring, with differences apparent between summer and
 winter patterns. The report summarized key findings of an investigation on
 Lake Tahoe water clarity, its long-term variability, and the relative
 importance of several influencing variables and processes. This
 investigation focused on factors relevant to the apparent divergence in
 clarity between summer and winter periods, on how in-lake physical and
 ecological drivers influenced both seasonal and historic clarity trends.
 The trend analyses confirm that clarity declines during the
 winter period (Dec-Mar) have plateaued (i.e. there is no longer a
 statistically significant trend up or down) over the last 20
 years. The reasons for this are complex and not caused by a single factor
 but are the net result of multiple physical and biological processes.
 In-lake physical and ecological drivers also influenced seasonal and
 historic trends, with winter mixing having a significant impact on
 seasonal trends.  Winter clarity improves during the winter
 months because deep winter mixing dilutes light attenuating particles and
 brings up clearer water from depth to the near surface.  Months
 following deep mixing are influenced by the increase in nitrate that is
 brought to the surface and contributes to algal productivity during the
 spring and summer periods.  Increases in lake temperatures due to
 climate change have resulted in the lake becoming
 stratified earlier and stratification lasting
 longer.  The increase in temperatures at the near surface of the
 lake, combined with changing stream temperatures, affects
 the relative buoyancy of the lake and the
 insertion depths of incoming stream flows. This analysis
 also provides insight on how the abundance of a small diatom, Cyclotella,
 influences fall and summer clarity.  Counts of Cyclotella greater
 than 100 cells/mL have direct negative impact on clarity, whereas counts
 below this threshold do not show much impact.