cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.x95x69pj1
title: Boardman River 2019 eDNA metabarcoding water sample data

description: Understanding biodiversity in aquatic systems is critical to ecological
 research and conservation efforts, but accurately measuring species
 richness using traditional methods can be challenging. Environmental DNA
 (eDNA) metabarcoding, which uses high-throughput sequencing and universal
 primers to amplify DNA from multiple species present in an environmental
 sample, has shown great promise for augmenting results from traditional
 sampling to characterize fish communities in aquatic systems. Few studies,
 however, have compared exhaustive traditional sampling with eDNA
 metabarcoding of corresponding water samples at a small spatial scale. We
 intensively sampled Boardman Lake (1.4 km2) in Michigan, USA from May to
 June in 2019 using gill and fyke nets and paired each net set with lake
 water samples collected in triplicate. We analyzed water samples using
 eDNA metabarcoding with 12S and 16S fish-specific primers and compared
 estimates of fish diversity among methods. In total, we set 60 nets and
 analyzed 180 1 L lake water samples. We captured a total of 12 fish
 species in our traditional gear and detected 40 taxa in the eDNA water
 samples, which included all the species observed in nets. The 12S and 16S
 assays detected a comparable number of taxa, but taxonomic resolution
 varied between the two genes. In our traditional gear, there was a clear
 difference in the species selectivity between the two net types, and there
 were several species commonly detected in the eDNA samples that were not
 captured in nets. Finally, we detected spatial heterogeneity in fish
 community composition across relatively small scales in Boardman Lake with
 eDNA metabarcoding, but not with traditional sampling. Our results
 demonstrated that eDNA metabarcoding was substantially more efficient than
 traditional gear for estimating community composition, highlighting the
 utility of eDNA metabarcoding for assessing species diversity and
 informing management and conservation.
DOI: 10.5061/dryad.59zw3r26t
title: Investigating cooccurrence patterns and dynamics for many imperfectly detected species, using a log-linear modelling parameterisation

description: Patterns in, and the underlying dynamics of, species cooccurrence is of
 interest in many ecological applications. Unaccounted for, imperfect
 detection of the species can lead to misleading inferences about the
 nature and magnitude of any interaction. A range of different
 parameterisations have been published that could be used with the same
 fundamental modelling framework that accounts for imperfect detection,
 although each parameterisation has different advantages and disadvantages.
 We propose a parameterisation based on log-linear modelling that does not
 require a species hierarchy to be defined (in terms of dominance), and
 enables a numerically robust approach for estimating covariate effects.
 Conceptually the parameterisation is equivalent to using the presence of
 species in the current, or a previous, time period as predictor variables
 for the current occurrence of other species. This leads to natural,
 ’symmetric’, interpretations of parameter estimates. The parameterisation
 can be applied to many species, in either a maximum-likelihood or Bayesian
 estimation framework. We illustrate the method using camera trapping data
 collected on three mesocarnivore species in South Texas.
description: Coded detection histories for which species were detected within
 14 seasons, of five 4-week periods (five occasions) per season, and R
 script files for conducting the example analysis in the paper. All data is
 stored within an R format.
DOI: 10.5061/dryad.kkwh70s4b
title: Modeling pulsed evolution and time-independent variation improves the confidence level of ancestral and hidden state predictions

description: Ancestral state reconstruction is not only a fundamental tool for studying
 trait evolution, but also very useful for predicting the unknown trait
 values (hidden states) of extant species. A well-known problem in
 ancestral and hidden state predictions is that the uncertainty associated
 with predictions can be so large that predictions themselves are of little
 use. Therefore, for meaningful interpretation of predicted traits and
 hypothesis testing, it is prudent to accurately assess the uncertainty of
 the predictions. Commonly used constant-rate Brownian motion (BM) model
 fails to capture the complexity of tempo and mode of trait evolution in
 nature, making predictions under the BM model vulnerable to lack-of-fit
 errors from model misspecification. Using empirical data (mammalian body
 size and bacterial genome size), we show that the distribution of residual
 Z-scores under the BM model is neither homoscedastic nor normal as
 expected. Consequently, the 95% confidence intervals (CIs) of predicted
 traits are so unreliable that the actual coverage probability ranges from
 33% (strongly permissive) to 100% (strongly conservative). Alternative
 methods such as BayesTraits and StableTraits that allow variable rates in
 evolution improve the predictions but are computationally expensive. Here
 we develop RasperGade, a method of ancestral and hidden state prediction
 that uses the Levy process to explicitly model gradual evolution, pulsed
 evolution and time-independent variation. Using the same empirical data,
 we show that RasperGade outperforms both BayesTraits and StableTraits and
 is orders-of-magnitude faster. Our results suggest that, when predicting
 the ancestral and hidden states of continuous traits, the tempo and mode
 of evolution should always be assessed and the quality of confidence
 estimates should always be examined.
DOI: 10.5061/dryad.v6wwpzgvn
title: Genomic regions associated with adaptation to predation in Daphnia often include members of expanded gene families

description: Predation has been a major driver of the evolution of prey species, which
 consequently develop antipredator adaptations. However, little is known
 about the genetic basis underpinning the adaptation of prey to intensive
 predation. Here, we describe a high-quality chromosome-level genome
 assembly (approx. 145 Mb, scaffold N50 11.45 Mb) of Daphnia mitsukuri, a
 primary forage for many fish species. Transcriptional profiling of D.
 mitsukuri exposed to fish kairomone revealed that this cladoceran responds
 to predation risk through regulating activities of Wnt signalling, cuticle
 pattern formation, cell cycle regulation and anti-apoptosis pathways.
 Genes differentially expressed in response to predation risk are more
 likely to be members of expanded families. Our results suggest that
 expansions of multiple gene families associated with chemoreception and
 vision allow Daphnia to enhance detection of predation risk, and that
 expansions of those associated with detoxification and cuticle formation
 allow Daphnia to mount an efficient response to perceived predation risk.
 This study increases our understanding of the molecular basis of prey
 defences, being important evolutionary adaptations playing a stabilizing
 role in community dynamics.
DOI: 10.5061/dryad.6q573n5zg
title: Simulation Data from: The EOS/Resolution Conspiracy: Convergence in Proto-Planetary Collision Simulations

description: We investigate how the choice of equation of state (EOS) and resolution
 conspire to affect the outcomes of giant impact (GI) simulations. We focus
 on the simple case of equal mass collisions of two Earth-like 0.5ME
 proto-planets showing that the choice of EOS has a profound impact on the
 outcome of such collisions as well as on the numerical convergence with
 resolution. In simulations where the Tillotson EOS is used, impacts
 generate an excess amount of vapour due to the lack of a thermodynamically
 consistent treatment of phase transitions and mixtures. In oblique
 collisions this enhances the artificial angular momentum (AM) transport
 from the planet to the circum-planetary disc reducing the planet’s
 rotation period over time. Even at a resolution of  1.3x106
 particles the result is not converged. In head-on collisions the lack of a
 proper treatment of the solid/liquid-vapour phase transition allows the
 bound material to expand to very low densities which in turn results in
 very slow numerical convergence of the critical specific impact energy for
 catastrophic disruption QRD with increasing resolution as reported in
 prior work. The simulations where ANEOS is used for oblique impacts are
 already converged at a modest resolution of 105 particles, while head-on
 collisions converge when they evidence the post-shock formation of a dense
 iron-rich ring, which promotes gravitational re-accumulation of material.
 Once sufficient resolution is reached to resolve the liquid-vapour phase
 transition of iron in the ANEOS case, and this ring is resolved, the value
 of QRD has then converged.
description: The data consists of initial conditions and simulation outputs
 from the 3D hydrodynamic simulations presented in our paper.
description: Please read the Readme file for details.
DOI: 10.5061/dryad.t4b8gtj1s
title: No evidence for female kin association, indications for extragroup paternity, and sex‐biased dispersal patterns in wild western gorillas

description: Characterizing animal dispersal patterns and the rational behind
 individuals’ transfer choices is a long-standing question of interest in
 evolutionary biology. In wild western gorillas (Gorilla gorilla), a
 one-male polygynous species, previous genetic findings suggested that,
 when dispersing, females might favor groups with female kin to promote
 cooperation, resulting in higher-than-expected within-group female
 relatedness. The extent of male dispersal remains unclear with studies
 showing conflicting results. To investigate male and female dispersal
 patterns and extra-group paternity, we analyzed long-term field
 observations, including female spatial proximity data, together with
 genetic data (10 autosomal microsatellites) on individuals from a unique
 set of four habituated western gorilla groups, and four additional
 extra-group males (49 individuals in total). The majority of offspring (25
 of 27) were sired by the group male. For two offspring, evidence for
 extra-group paternity was found. Contrarily to previous findings, adult
 females were not significantly more related within groups than across
 groups. Consistently, adult female relatedness within groups did not
 correlate with their spatial proximity inferred from behavioral data.
 Adult females were similarly related to adult males from their group than
 from other groups. Using RST statistics, we found significant genetic
 structure and a pattern of isolation by distance, indicating limited
 dispersal in this species. Comparing relatedness among females and among
 males revealed that males disperse farer than females, as expected in a
 polygamous species. Our study on habituated western gorillas shed light on
 the dispersal dynamics and reproductive behavior of this polygynous
 species and challenge some of the previous results based on unhabituated
 groups.
description: See material and methods of the article.
description: Missing values are indicated by "0".
DOI: 10.7291/d1gd50
title: Standardizing protocols for determining the cause of mortality in wildlife studies

description: Mortality site investigations of telemetered wildlife are important for
 cause-specific survival analyses and understanding underlying causes of
 observed population dynamics. Yet eroding ecoliteracy and a lack of
 quality control in data collection can lead researchers to make incorrect
 conclusions, which may negatively impact management decisions for wildlife
 populations. We reviewed a random sample of 50 peer-reviewed studies
 published between 2000 and 2019 on survival and cause-specific mortality
 of ungulates monitored with telemetry devices. This concise review
 revealed extensive variation in reporting of field procedures, with many
 studies omitting critical information for cause of mortality inference.
 Field protocols used to investigate mortality sites and ascertain the
 cause of mortality are often minimally described and frequently fail to
 address how investigators dealt with uncertainty. We outline a
 step-by-step procedure for mortality site investigations of telemetered
 ungulates, including evidence that should be documented in the field.
 Specifically, we highlight data that can be useful to differentiate
 predation from scavenging and more conclusively identify the predator
 species that killed the ungulate. We also outline how uncertainty in
 identifying the cause of mortality could be acknowledged and reported. We
 demonstrate the importance of rigorous protocols and prompt site
 investigations using data from our 5-year study on survival and
 cause-specific mortality of telemetered mule deer (Odocoileus hemionus) in
 northern California. Over the course of our study, we visited mortality
 sites of neonates (n = 91) and adults (n = 23) to ascertain the cause of
 mortality. Rapid site visitations significantly improved the successful
 identification of the cause of mortality and confidence levels for
 neonates. We discuss the need for rigorous and standardized protocols that
 include measures of confidence for mortality site investigations. We
 invite reviewers and journal editors to encourage authors to provide
 supportive information associated with the identification of causes of
 mortality, including uncertainty.
description: Three datasets on neonate and adult mule deer
 (<em>Odocoileus hemionus</em>) mortality site investigations
 were generated through ecological fieldwork in northern California, USA
 (2015-2020). The datasets in Dryad are: Does.csv (for
 use with R); Fawns.csv (for use with R); Full_data.xlsx (which
 combines the 2 .csv files and includes additional information)
 Two R code files associated with the 2 .csv datasets above are
 available in Zenodo:  RScript_Does.R;
 RScript_Fawns.R The data were analyzed using RStudio
 v.1.1.447 and a variety of packages, including: broom, caret, ciTools,
 effects, lattice, modEvA, nnet, and tidyverse. The data are associated
 with the publication "Standardizing protocols for determining the
 cause of mortality in wildlife studies" in <em>Ecology and
 Evolution</em>.
description: The datasets can be opened using Microsoft Excel and R.
DOI: 10.5061/dryad.gqnk98sms
title: Data from: Selection on fish personality differs between a no-take marine reserve and fished areas

description: Marine reserves can protect fish populations by increasing abundance and
 body size, but less is known about the effect of protection on fish
 behaviour. We looked for individual consistency in movement behaviours of
 sea trout in the marine habitat using acoustic telemetry to investigate
 whether they represent personality traits and if so, do they affect
 survival in relation to protection offered by a marine reserve. Home range
 size had a repeatability of 0.21, suggesting that it represents a
 personality trait, while mean swimming depth, activity and diurnal
 vertical migration were not repeatable movement behaviours. The effect of
 home range size on survival differed depending on the proportion of time
 fish spent in the reserve, where individuals spending more time in the
 reserve experienced a decrease in survival with larger home ranges while
 individuals spending little time in the reserve experienced an increase in
 survival with larger home ranges. We suggest that the diversity of fish
 home range sizes could be preserved by establishing networks of marine
 reserves encompassing different habitat types, ensuring both a
 heterogeneity in environmental conditions and fishing pressure.
description: Movement data
 were collected in the Tvedestrand fjord (3.8 km<sup>2</sup>,
 max depth: 87 m) located in southern Norway between spring 2013 and fall
 2017. A telemetry array consisting of 50 Vemco VR2-W receivers (VEMCO
 Ltd., Halifax, Canada) was deployed in the fjord, with the receivers being
 attached to moorings and kept at three metres depth aided by sub-surface
 buoys. Sea trout were caught around the centre islands of the fjord in
 2013 (April: n = 3; May: n = 26; September: n = 24; November: n = 7), 2015
 (June: n = 3; October: n = 14; November: n = 5) and 2016 (April: n = 4;
 May: n = 7) using a beach seine, and also by electrofishing in the
 spawning river at November 11, 2016 (n = 23). We used Vemco V9P and V13P
 transmitters, which had a maximum battery life of 508-696 and 1292 days,
 respectively. Signals were emitted with a random delay of 180 ± 70
 seconds. Accuracy and resolution of depth measurements were ± 2.5 m and
 0.22 m, respectively, and max depth was 50 m or more for the different
 tags.
description: There
 are three types of data sets: Fish tagging
 data: Individual information on tag ID, tag type, tagging location,
 capture method, time of tagging, body length and weight.
   Tvedestrand receiver
 locations   
 Detection data per individual fish (xxxx_VUE_Export_edited):
 Detection data exported from VUE. Time stamps are in local time for
 Norway. Data after assumed death has been removed and single detections
 within one day has been removed. Depth data from malfunctioning depth
 sensors has been removed.
DOI: 10.5061/dryad.37pvmcvk6
title: Sea temperature effects on depth use and habitat selection in a marine fish community

description: 1. Understanding the responses of aquatic animals to temperature
 variability is essential to predict impacts of future climate change and
 to inform conservation and management. Most ectotherms such as fish are
 expected to adjust their behaviour to avoid extreme temperatures and
 minimize acute changes in body temperature. In coastal Skagerrak, Norway,
 sea surface temperature (SST) ranges seasonally from 0 to over 20 °C,
 representing a challenge to the fish community which includes both cold-,
 cool- and warm-water affinity species. 2. By acoustically tracking 111
 individuals of Atlantic cod (Gadus morhua), pollack (Pollachius
 pollachius) and ballan wrasse (Labrus bergylta) in 2015 - 2018, we
 examined how coexisting species within a fish community adjusted their
 behaviour (i.e. vertical distribution in the water column and habitat
 selection) to cope with the thermal variation. 3. Mixed-effect models
 showed that thermal preference was a main driver of behaviour and habitat
 use of the fish community in a southern Norwegian fjord. Cod used colder
 waters, compared with pollack and ballan wrasse. Increases in SST during
 summer were associated with the use of deeper, colder waters by cod,
 especially by larger individuals, and conversely with the occupancy of
 shallower areas by pollack and ballan wrasse. During winter, when SST
 dropped and the thermal stratification reversed, pollack and ballan wrasse
 moved to deeper, relatively warmer areas, while cod selected shallower,
 colder habitats. Though habitat selection was affected by temperature,
 species-specific habitat selection was observed even when temperature was
 similar throughout habitats. 4. This study shows how cohabiting fish
 species respond to thermal heterogeneity, suggesting that i) temperature
 regulates the access to the different depths and habitats and ii)
 behavioural plasticity may be an important factor for coping with
 temperature variability and potentially for adaptation to climate change.
DOI: 10.5061/dryad.ncjsxkstz
title: Plastome and RAD-seq of Polygonatum odoratum

description: Polygonatum odoratum (Mill.) Druce (Asparagaceae, Asparagales) is a widely
 cultivated medicinal herb in China. However, this useful herb is
 understudied despite being known as a medicinal resource with top grade
 medical and edible properties since long. In this study, P. odoratum and
 four cultivars were investigated. The variations in morphological
 characteristics and vegetative phases of each cultivars were observed. For
 genetic aspect, the plastid genome of P. odoratum varies in length from
 154,569 bp to 155,491 bp, containing a large single-copy region of
 83,486—84,459 bp, a small single-copy region of 18,292—18,471 bp, and two
 inverted repeats of 26,302—26,370 bp. A total of 131 genes were predicted,
 including 85 protein-coding, 38 tRNA, and eight rRNA genes. Genome
 comparisons revealed a slight variation in the sequence across the five
 accessions, but two highly variable regions (trnC-petN and rpl32-trnL)
 were detected when comparing the four different cultivars. For the RAD-seq
 markers, a total of 33.64 Gb of clean data, with an average value of 1.08
 Gb per sample, were analyzed for presence of single nucleotide
 polymorphisms (SNPs). Well-resolved phylogenies of the P. odoratum
 cultivars are constructed; the non-monophyletic relationship in the
 plastome-based phylogenetic trees, yet monophyletic form in the RAD-based
 linkage map suggested possibility of hybrid cultivar for P. odoratum
 “Dazhu” (GDDZ), which was further supported by morphological observations.
 Quality assessment based on the standards of the Chinese Pharmacopoeia on
 Polygonati Odorati Rhizoma (POR) on the four cultivars used in this study
 recorded that PORs from P. odoratum ‘Zhongzhu’ (GDZZ) met the minimum
 criteria for the acceptance as raw material for medicinal drug production.
 This study has provided insights on the morphological variations, genetic
 background, and medicinal qualities of P. odoratum cultivars that could be
 explored for future genetic improvement as well as breeding programs of P.
 odoratum for POR production.
DOI: 10.5061/dryad.pvmcvdnks
title: No evidence that grooming is exchanged for coalitionary support in the short- or long-term via direct or generalized reciprocity in unrelated rhesus macaques

description: Reciprocity is a prominent explanation for cooperation
 between non-kin. Studies seeking to demonstrate reciprocity often focus on
 direct reciprocity in the timescale of minutes to hours, whereas
 alternative mechanisms like generalised reciprocity and the possibility of
 reciprocation over longer timescales of months and years are less often
 explored. Using a playback experiment, we tested for evidence of direct
 and generalised reciprocity, across short and longer timescales. We
 examined the exchange of grooming for coalitionary support between female
 rhesus macaques in a population with a complete genetic pedigree. Females
 that received grooming were not more responsive to calls for coalitionary
 support from female groupmates compared to control females that received
 agonism or no interaction – even when the call belonged to a females’ most
 recent grooming partner. Similarly, females were not more responsive to
 calls for support from their most frequent grooming partner of the last
 two years, nor if they received large amounts of grooming from all other
 females in their group. We interpret these results as an absence of
 evidence for direct or generalised reciprocity on any timescale in the
 exchange of grooming for coalitionary support in rhesus macaques. If
 grooming is exchanged for support in this population, it is with an
 intensity below our ability to detect or over a longer timescale than we
 examined. We propose by-product explanations may be responsible and
 highlight the importance of investigating multiple mechanisms when testing
 apparently cooperative behaviours.
description: The dataset was collected using playback experiments with rhesus
 macaques (<em>Macaca mulatta</em>) on Cayo Santiago in 2017.
 The data was processed with generalized linear mixed models to produce a
 MS submitted for publication in Behavioral Ecology and
 Sociobiology.
description: The readme file contains an explanation of each of the variables
 in the dataset and its measurement units.