cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.ghx3ffbp6
title: One size does not fit all: Tuning eDNA protocols for high and low turbidity water sampling

description: Findings from eDNA metabarcoding are strongly influenced by experimental
 approach, yet the effect of pre‐PCR sample processing on taxon detection
 and estimates of biodiversity across different water types is still poorly
 resolved. To fill this data gap, we investigated the impact of sampling
 effort, extraction method, and filter pore size on DNA yield, PCR
 inhibition, and 16S rDNA metabarcoding results for fishes in water samples
 collected from inshore turbid‐ and offshore clear‐water environments. The
 turbid‐water samples had high concentrations of suspended organic and/or
 inorganic material and yielded ~3.2× more DNA and exhibited high levels of
 PCR inhibition compared with the low‐turbidity, clear‐water samples.
 Importantly, there were no striking differences in the results of our
 metabarcoding experiments based on extraction method or filter pore size.
 While a small number of unique species of relatively low read count were
 detected in all turbid‐water treatments, most species were consistently
 detected across samples. Results for the clear‐water samples were
 strikingly different, with low DNA yield, high levels of variation across
 replicates, and a high number of non‐overlapping species across
 treatments. These findings indicate a patchy distribution of eDNA in
 offshore environments, which means higher volumes of water (≥ 2 L
 per replicate) must be filtered in habitats where target DNA is likely to
 be sparse. In semi‐closed systems such as estuaries, higher concentrations
 of target DNA are expected, and we found that either a 1.0 or 3.0 µm
 filter pore size was sufficient to capture standing diversity, while
 decreasing the risk of clogging. For economical DNA extraction and
 inhibitor removal, we recommend a combination of Omega Bio‐tek E.Z.N.A
 Tissue DNA kit followed by a PCR inhibitor removal step using the Zymo
 Kit. Finally, we emphasize that pilot studies should be undertaken
 whenever sampling in a new environment to identify which protocol is most
 appropriate.
description: Water samples were filtered on different filter pore sizes and
 then DNA was extracted using DNA extraction kits. The DNA was then
 sequenced using Illumina MiSeq. Raw fastq files were processed
 bioinformatically to generate unique ASVs.
description: Each folder contains four
 following four files: ASV_counts
 ASVs blasted_ASVs lineage_with_header
 ASV_counts =
 number of ASV generated for each of the replicates along with read number.
 Each replicate has been uniquely named. ASVs = This file contains
 sequences for each of the ASVs in FASTA format. blasted_ASVs = NCBI blast results
 for each of the ASVs. Lineage_with_header = This file
 contains list of all the taxa obtained after NCBI blast with their
 taxonomic designations.
DOI: 10.5061/dryad.rfj6q57b0
title: Why don't all animals avoid inbreeding?

description: Individuals are expected to avoid mating with relatives as inbreeding can
 reduce offspring fitness, a phenomenon known as inbreeding depression.
 This has led to the widespread assumption that selection will favour
 individuals that avoid mating with relatives. However, the strength of
 inbreeding avoidance is variable across species and there are numerous
 cases where related mates are not avoided. Here we test if the
 frequency that related males and females encounter each other explains
 variation in inbreeding avoidance using phylogenetic
 meta-analysis of 41 different species from six classes across the animal
 kingdom. In species reported to mate randomly with respect to
 relatedness, individuals were either unlikely to encounter relatives, or
 inbreeding had negligible effects on offspring
 fitness. Mechanisms for avoiding inbreeding, including active
 mate choice, post-copulatory processes and sex biased dispersal, were only
 found in species with inbreeding depression. These results help explain
 why some species seem to care more about inbreeding than others:
 inbreeding avoidance through mate choice only evolves when there is both a
 risk of inbreeding depression and related sexual partners frequently
 encounter each other. 
description: <strong>Data: </strong>
 <strong>Table S1-S26:</strong>
 <b>Table S1: </b>Data table for our meta-analysis. A
 separate ReadMe file is provided. <b>Table
 S2-S13: </b>Output of main models from our meta-analysis.
 <b>Table S14-S23: </b>Output associated with all
 supplementary models from our meta-analysis.
 <b>Table S24-S26:</b> Details and output of
 literature searches (note this file also contains a key for Tables
 S25&26). <strong>ReadMe file
 </strong>- a readme file is provided for the main data table (Table
 S1). <strong>Inbreeding_analyses.RData
 - </strong>RData file with the data files and model objects. Also
 saved within this RData file is the session information about the loaded
 packages. <strong>Code: </strong>
 <strong>InbreedingSI.Rproj -</strong> R project for
 the meta-analysis. <strong>Data_analyses.R
 - </strong>code for the main and supplementary analysis in our
 meta-analysis. <b>Figures.R - </b>code for
 all figures and supplementary figures.
DOI: 10.5061/dryad.hmgqnk9h8
title: Mountain lions reduce movement, increase efficiency during the COVID-19 shutdown

description: Wildlife strongly alter behavior in response to human disturbance;
 however, fundamental questions remain regarding the influence of human
 infrastructure and activity on animal movement. The Covid-19 pandemic
 created a natural experiment providing an opportunity to evaluate wildlife
 movement during a period of greatly reduced human activity. Speculation in
 scientific reviews and the media suggested that wildlife might be
 increasing movement and colonizing urban landscapes during pandemic
 slowdowns. However, theory predicts that animals should move and use space
 as efficiently as possible, suggesting that movement might actually be
 reduced relative to decreased human activity. We quantified space use,
 movement, and resource-selection of 12 GPS-collared mountain lions (8
 females, 4 males) occupying parklands in greater Los Angeles during the
 Spring 2020 California stay-at-home order when human activity was far
 below normal. We also tested the hypothesis that reduced traffic on Los
 Angeles area roadways increased permeability of these barriers to animal
 movement. Contrary to expectations that wildlife roamed more widely during
 pandemic shutdowns, resident mountain lions used smaller areas and moved
 shorter distances relative to their historical behavior in greater Los
 Angeles. They also relaxed avoidance of anthropogenic landscape features
 such as trails and development, which likely facilitated increased
 traveling efficiency. However, there was no detectable change in
 road-crossing, despite reduced traffic volume. Our results support the
 theoretical prediction that animals maximize movement efficiency and
 suggest that carnivores incur energetic costs while avoiding humans. While
 mountain lions may restrict movement at the landscape-level relative to
 barriers, they appear to increase distances moved at finer scales when
 avoiding human activity - highlighting the scale-dependent nature of
 animal responses to human disturbance. Avoiding humans can reduce direct
 mortality of large carnivores and is often suggested to be an important
 mechanism promoting coexistence in shared landscapes. However, energetic
 costs incurred by increased movement and space-use while avoiding human
 activity may have important consequences for population viability,
 predator-prey interactions, community structure, and human-wildlife
 conflict. Management providing sufficient wild prey and education
 regarding best practices for protection of domestic animals are important
 for conserving large carnivores in human-dominated landscapes.
DOI: 10.5061/dryad.k3j9kd57j
title: Guppy MHC and microsatellite genotypes, gyrodactylid infection trials, and analysis code

description: Natural host populations differ in their susceptibility to infection by
 parasites, and these intra-population differences are still an
 incompletely understood component of host-parasite dynamics. In this
 study, we used controlled infection experiments with wild-caught guppies
 (Poecilia reticulata) and their ectoparasite Gyrodactylus turnbulli to
 investigate the roles of local adaptation and host genetic composition
 (immunogenetic and neutral) in explaining differences in susceptibility to
 infection. We found differences between our four study host populations
 that were consistent between two parasite source populations, with no
 indication of local adaptation by either host or parasite at two tested
 spatial scales. Greater host population genetic variability metrics
 broadly aligned with lower population mean infection intensity, with the
 best alignments associated with Major Histocompatibility Complex (MHC)
 ‘supertypes’. Controlling for intra-population differences and potential
 inbreeding variance, we found a significant negative relationship between
 individual-level functional MHC variability and infection: fish carrying
 more MHC supertypes experienced infections of lower severity, with limited
 evidence for supertype-specific effects. We conclude that population-level
 differences in host infection susceptibility likely reflect variation in
 parasite selective pressure and/or host evolutionary potential,
 underpinned by functional immunogenetic variation.
description: Data collection is described in the associated manuscript,
 accepted for publication 11/08/2021, which we intend to make Open Access.
 All processing is described in the dataset's readMe and in the
 extensive annotations to the uploaded R scripts.
description: The upload's readMe lists the R packages used in the work.
 Somebody working through the full pipeline as is will need the software
 CERVUS (details and citation in the readMe), though this is for a tool
 also available elsewhere.
DOI: 10.15468/dl.v8rbqy
title: Occurrence Download

description: A dataset containing 21 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Rhododendron klossii"
 ]
}

 The dataset includes 21 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002882-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.sqv9s4n4c
title: Code and resulting candidate gene datasets from Anopheles genome environment association testing

description: The concept of a fundamental ecological niche is central to questions of
 geographic distribution, population demography, species conservation, and
 evolutionary potential. But robust inference of genomic regions associated
 with evolutionary adaptation to particular environmental conditions
 remains difficult due to the myriad of potential confounding processes
 that can generate heterogeneous patterns of variation across the
 genome.  Here, we interrogate the potential role of genome
 environment association (GEA) testing as an initial step in building an
 understanding of the genetic basis of ecological niche. We leverage
 publicly available genomic data from the Anopheles gambiae 1000 Genomes
 (Ag1000g) Consortium to test the ability of multiple, unique analytical
 GEA methods to handle confounding genetic variation, control false
 positive rates, and discern associations with broadly relevant climate
 variables from randomly correlated allele frequency patterns throughout
 the genome. We find evidence supporting the ability of commonly
 implemented GEA methods to account for confounding patterns of spatial and
 genetic variation, and control false positive rates. But we subsequently
 fail to find evidence supporting the ability of GEA tests to reject
 signals of adaptation to randomly simulated environmental variables,
 indicating that discerning between true signals of genome environment
 adaptation and genome environment correlations resulting from alternative
 evolutionary processes remains challenging. Because signals of
 environmental adaptation are so diffuse and confounded throughout the
 genome, we argue that genomic adaptation to ecological niche is likely
 best understood under an omnigenic model wherein highly interconnected,
 genome-wide gene regulatory networks shape genomic adaptation to key
 environmental conditions.
description: This is a stable version of the github
 repository: https://github.com/DevonDeRaad/Anopheles
 Metadata: Herein, we have included all scripts
 necessary to completely understand and reproduce the genome environment
 association analyses performed in this manuscript. Raw
 data: The variant call format files for each chromosome
 arm containing all SNPs from 765 wild caught individuals from the phase 1
 Ag1000g sampling effort are publicly available for download by following
 this link: https://www.malariagen.net/data/ag1000g-phase1-ar3.1 The variant call format files for each chromosome arm containing all SNPs from 1,142 wild caught individuals from the phase 2 Ag1000g sampling effort are publicly available for download by following this link: http://www.malariagen.net/data/ag1000g-phase2-ar1
description: Repository is organized hierarchically, with an informative
 readme.md file
DOI: 10.5061/dryad.6m905qg0c
title: Data from: Trade-offs between reproduction and behavioural resistance against ectoparasite infection

description: In these experiments we tested if 1) mated female flies (Drosophila
 nigrospiracula) are more vulnerable to ectoparasite mite
 (Macrocheles subbadius) infection then unmated conspecifics. 2)
 If a rest period to recover from male harassment following mating improved
 resistance to mites and 3) if reduced endurance following mating may
 explain differential resistance abilities between mated and unmated female
 flies.
description: Data was originally collected from lab observations of
 <em>Drosophila nigrospiracula</em> exposed to the mite
 <em>Macrocheles subbadius. </em>Exposure experiments were
 conducted in micro-areans (cropped pippette tips) with 5 mites: 1 Fly.
 Geotaxis assays were conducted in indivdual vials. All methods are
 described in "Trade-offs between reproduction and behavioural
 resistance against ectoparasite infection" in Physiology &
 Behavior, by Collin J Horn and Lien T Luong (2021). Original data (lab
 observations) are reported here prior to analysis (stastical analysis
 performed in Horn and Luong 2021).
description: Consult "Trade-offs between reproduction and behavioural
 resistance against ectoparasite infection" in Physiology &
 Behavior, by Collin J Horn and Lien T Luong (2021) for statistical
 analysis. Summary Meta Data (experiment and variable descriptions) is
 included as an additional file
DOI: 10.25338/b8v64t
title: Phylogenomic variation at the population-species interface and assessment of gigantism in a model wolf spider genus (Lycosidae, Schizocosa)

description: Animal body size has important evolutionary implications. The wolf spider
 genus Schizocosa has developed as a model for studies on courtship, with
 visual and vibratory signals receiving attention; however, body size has
 never been carefully evaluated. Although species of Schizocosa can be
 distinguished from their close relatives by differences in genitalic
 structures, male ornamentation, and behavior, some species are
 morphologically similar, making diagnosis, and identification difficult.
 Evaluation of species boundaries using genetic data across Schizocosa is
 limited. The similar species S. maxima and S. mccooki are separated
 predominantly on the basis of size differences, with S. maxima being
 larger. We evaluate the evolution of size in these two Schizocosa species
 distributed in western North America, where gigantism of S. maxima is
 hypothesized to occur, particularly in California. We sampled sub-genomic
 data (RADseq) and inferred the phylogeny of S. mccooki, S. maxima, and
 relatives. We apply a variational autoencoder machine learning approach to
 visualize population structuring within widespread S. mccooki and evaluate
 size within the context of a comparative phylogenetic framework to test
 the hypotheses related to genetic clustering of populations and gigantism.
 Our data show S. mccooki populations are not genealogically exclusive with
 respect to S. maxima. Likewise, S. maxima individuals are not recovered as
 a lineage and do not form an isolated genetic cluster, suggesting that the
 observed differences in size cannot be used to accurately delimit species.
 The cause of gigantism in S. maxima remains unexplained, but provides a
 framework for future studies of size variation and speciation. ESA
 Editorial Office: 3 Park Place, Suite 307, Annapolis, MD 21401-3722, USA.
 Editorial Office Phone: 1-301-731-4535.
DOI: 10.25338/b8qd1h
title: Hypothalamic remodeling of thyroid hormone signaling during hibernation in the arctic ground squirrel

description: These data were collected from arctic ground
 squirrels (Urocitellus parryii) between Summer 2016 and Spring
 2019 on a collaborative NSF-funded project examining the
 neuroendocrine regulation of the transition between hibernation and
 reproduction. The three experiments consist of (1) a repeated
 cross-sectional study conducted in both males and females hibernating in
 constant darkness and constant temperature (2) an
 extreme mid-winter warming study conducted in males only and (3)
 an end of hibernation warming study conducted in both males and females
 under biologically relevant hibernaculum temperatures.  These
 datasets quantify changes in retrograde thyroid hormone signaling between
 the pars tuberalis and hypothalamus; ultrastructural changes in
 pars tuberalis thyrotrophs, anterior pituitary gonadotrophs, and tanycytic
 endfeet at the median eminence; hypothalamic changes in the expression of
 nestin and Vimentin, and changes in reproductive parameters
 across the hypothalamic-pituitary-gonadal axis. 
description: Missing data are denoted with "NA". Data are organized
 by experiment number (1, 2, 3) and by type (csv, image).
DOI: 10.5061/dryad.cnp5hqc51
title: Why signal if you are not attractive? Courtship synchrony in a fiddler crab

description: Synchronised male courtship signals are puzzling because males generally
 compete with each other for females. Male Austruca mjoebergi fiddler crabs
 wave in synchrony to attract females, but, all else being equal, females
 have a strong preference for ‘leader’ males that can produce waves before
 other males (‘followers’). So why do followers participate in synchrony?
 Here, we experimentally investigate three explanations for why followers
 might wave in synchrony: 1) followers obtain a small proportion of
 matings, 2) followers are more likely than a leader to attract females if
 they are positioned closer to her than is the leader, and 3) synchrony
 functions as a long-distance visual signal that attracts females so there
 is a net benefit to synchrony for all males. Using robotic male crabs, we
 found that females show a strong preference for leading males, but
 followers obtain a ‘better-than-nothing’ proportion of mates. We also
 showed that closer proximity of a follower to the female did not affect
 her preference for leaders, although being a leader increased a male’s
 success when he was further from the female than were rival males.
 Finally, females were more likely to approach a distant group if there was
 a leader present, suggesting that followers do benefit from participating
 in synchrony.
description: Data was collected in the field using wild-caught
 female <em>Austruca mjoebergi </em>fiddler crabs and robotic
 crabs mimicking male <em>A. mjoebergi </em>crabs.
 For experiments 1-2, we conducted female mate choice trials and
 recorded female preferences for individual robotic male crabs based on
 their wave timing role (i.e. leader or follower). For
 experiment 3, we recorded whether females approached a group of males
 based on 1) her distance from the group and 2) the wave rhythm of the
 group of males (synchrony, asynchrony or leader-follower).
 Provided dataset is the raw data collected from the field. For
 more detailed experimental methods, please see the Methods section of the
 research article.  
description: Meta-data: Column name / Variable
 description Trial_No / if a female did not respond, we
 tested female preferences up to three times before excluding
 her. Female_Size / in mm; carapace width 
 Female_Preference / which robocrab the female chose (number of
 robocrab) Pref_Robocrab_Role / what was the wave timing
 of the female's preferred robocrab? Leader, Follower or Far Follower
 (Experiment 2 only) Success / binary success of each
 trial where 1 = female chose leader/far follower and 0 = female chose
 follower Time / in seconds; time to choice
 Female_status / whether a female was actively mate-searching or
 whether she was burrowless (we did not observe her
 mate-searching)
DOI: 10.5061/dryad.2v6wwpznp
title: Data and original code for: A generalized approach to characterise optical properties of natural objects

description: To understand the diversity of ways in which natural materials interact
 with light, it is important to consider how their reflectance changes with
 the angle of illumination or viewing and to consider wavelengths beyond
 the visible. We chose a set of existing measurements and
 parameters that are generalisable to any wavelength range and spectral
 shape and we highlight which subsets of measures are relevant to different
 biological questions. As a case study, we applied these measures to 30
 species of Christmas beetles. Here we provide the raw spectral data of
 angle integrated and angle-dependent reflection by the beetle elytra. We
 also provide the original code used for our analysis and figures.
description: We provide angle-integrated and angle-resolved spectral data
 (Reflectance % per Wavelength nm) obtained with two spectrophotometers,
 the USB 2000+ (400-1000 nm) and NIRQuest (1000-2100 nm). 
 The angle-integrated spectra (hemispherical reflectance) were
 taken with an integrating sphere with an inbuilt tungsten-halogen light
 source (400-2100 nm; ISP-REF; Ocean Optics Inc., Dunedin, FL, USA.) and 4
 mm diameter sampling port. The integrating sphere was connected to the two
 spectrometers via a bifurcated optic fibre. The angle-resolved spectral
 data was obtained by coupling the two spectrometers obtained with a
 goniometer measure the light reflectance in different combinations of
 angles of incident light and collector. The reflectance
 per wavelength is reported as a % compared to a diffuse 99% reflectance
 spectralon standard (Labsphere, North Sutton, NH, USA). Measurements were
 recorded using the software OceanView 1.6.7. and analyzed with R
 programing language particularly the R package PAVO (Maia et al. 2019). In
 our manuscript we explain the process and rationale to calculate spectral
 parameters to describe different spectral shapes. In addition, we provide
 an RMarkDown file with the code to calculate these parameters for both
 visible and near infrared light.