cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.547d7wm4j
title: Data from: Abundance, survival, and annual rate of change in Cuvier's beaked whales (Ziphius cavirostris) on a Navy sonar range

description: Bayesian mark-recapture estimates of survival, abundance, and trend are
 reported for Cuvier’s beaked whales (Ziphius cavirostris) using a Navy
 training range off southern California. The deep-diving beaked whale
 family is exceptionally vulnerable to mid-frequency active sonar (MFAS),
 which has been implicated in mass strandings and altered foraging
 behavior. Extremely low sighting probabilities impede studies of
 population-level impacts of MFAS on beaked whales. The San Nicolas Basin
 hosts a Navy training range subject to frequent MFAS use and attracts high
 densities of Z. cavirostris. An eleven-year (2007–2018)
 photo-identification program leveraged automated acoustic detection and
 location capabilities on the range’s 1,800-km2 hydrophone array to enhance
 capture probability. Estimated population parameters for Z. cavirostris
 using the range included mean (90% credibility intervals) apparent annual
 survival of 0.950 (0.899–0.986), the annual number of individuals as 121
 (71–219), and the annual rate of change of -0.8% (-5.6 – 4.1%).
 Simulations show the probability of detecting abundance changes is
 currently low, but can be greatly improved through continued monitoring
 and increased effort. Complementary data collection on habitat use and
 demographic rates in San Nicolas and surrounding basins is also essential
 to relating the direct effects of MFAS use to changes in vital rates and
 broader population outcomes.
description: Data_key.docx defines data fields for 
 XLSX file TXT files 
 <br>KML file contains geocoordinates of the study area and
 is used in R scripts<br>for data selection and
 plotting.<br><br>R and BUG files are used for processing,
 analysis, and plotting.
DOI: 10.5061/dryad.ns1rn8pp5
title: The interplay between habitat use, morphology and locomotion in subterranean crustaceans of the genus Niphargus

description: Locomotion is an important, fitness-related functional trait. Environment
 selects for type of locomotion and shapes the morphology of
 locomotion-related traits such as body size and appendages. In
 subterranean aquatic arthropods, these traits are subjected to multiple,
 at times opposing selection pressures. Darkness selects for enhanced
 mechano- and chemosensory systems and hence elongation of appendages.
 Conversely, water currents have been shown to favor short appendages.
 However, no study has addressed the variation in locomotion of
 invertebrates inhabiting cave streams and cave lakes, or questioned the
 relationship between species’ morphology and locomotion. To fill this
 knowledge gap, we studied the interplay between habitat use, morphology
 and locomotion in amphipods of the subterranean genus Niphargus. Previous
 studies showed that lake and stream species differ in morphology. Namely,
 lake species are large, stout and long-legged, whereas stream species are
 small, slender and short-legged. We here compared locomotion mode and
 speed between three lake and five stream species. In addition, we tested
 whether morphology predicts locomotion. We found that the stream species
 lie on their body sides and move using slow crawling or tail-flipping. The
 species inhabiting lakes move comparably faster, and use a variety of
 locomotion modes. Noteworthy, one of the lake species almost exclusively
 moves in an upright or semi-upright position that resembles walking. Body
 size and relative length of appendages predict locomotion mode and speed
 in all species. We propose that integrating locomotion in the studies of
 subterranean species might improve our understanding of their
 morphological evolution.
DOI: 10.5061/dryad.t4b8gthz4
title: Dietary Vitamin D in female rock lizards induces condition-transfer effects in their offspring

description: One way that maternal effects may benefit the offspring is by informing
 them about the characteristics of the environment. Through gestation,
 environmentally induced maternal effects might promote in the offspring
 specific behavioral responses like dispersal or residence, according to
 their new habitat characteristics. Females of the Carpetan rock lizard
 (Iberolacerta cyreni) seem to choose their home ranges using the smell of
 provitamin D3 in scent marks produced by males. Here, we supplemented
 gravid females of I. cyreni with dietary provitamin D3 or vitamin D3 to
 examine whether these food resources, also associated with the scent of
 males, affect the motivation to disperse and the locomotor performance of
 their offspring. Our results suggest that the supplementary availability
 of the resource (vitamin D3) to mothers may provoke condition-transfer
 maternal effects that motivate the residence or the dispersal of the
 offspring in their postnatal habitat. Thus, hatchlings of supplemented
 females had a lower dispersal trend in spite that they had a greater
 climbing ability than hatchlings from non-supplemented females. This
 suggests that the levels of provitamin D3 and vitamin D3 inside the body
 of the mother could act as an informative compound of the habitat quality
 for the offspring.
DOI: 10.5061/dryad.x3ffbg7fc
title: Eco‐evolutionary dynamics driven by fishing: from single species models to dynamic evolution within complex food webs

description: Evidence of contemporary evolution across ecological time scales
 stimulated research on the eco-evolutionary dynamics of natural
 populations. Aquatic systems provide a good setting to study
 eco-evolutionary dynamics owing to a wealth of long-term monitoring data
 and the detected trends in fish life-history traits across intensively
 harvested marine and freshwater systems. In the present study, we focus on
 modelling approaches to simulate eco-evolutionary dynamics of fishes and
 their ecosystems. Firstly, we review the development of modelling from
 single-species to multispecies approaches. Secondly, we advance the
 current state-of-the-art methodology by implementing evolution of
 life-history traits of a top predator into the context of complex food web
 dynamics as described by the allometric trophic network (ATN) framework.
 The functioning of our newly developed eco-evolutionary ATNE framework is
 illustrated using a well-studied lake food web. Our simulations show how
 both natural selection arising from feeding interactions and
 size-selective fishing cause evolutionary changes in the top predator and
 how those feed back to its prey species and further cascade down to lower
 trophic levels. Finally, we discuss future directions, particularly the
 need to integrate genomic discoveries into eco-evolutionary projections.
description: Perch trait evolution. These videos demonstrate how the
 life-history traits evolve dynamically from year-to-year.
DOI: 10.5061/dryad.9w0vt4bbf
title: Drivers and dynamics of a massive adaptive radiation in cichlid fishes

description: Adaptive radiation is the likely source of much of the ecological and
 morphological diversity of life. How adaptive radiations proceed and what
 determines their extent remains elusive in most cases. Here we report the
 in-depth examination of the spectacular adaptive radiation of cichlid
 fishes in African Lake Tanganyika. Based on whole-genome phylogenetic
 analyses, multivariate morphological measurements of three ecologically
 relevant trait complexes (body shape, upper oral jaw morphology, and lower
 pharyngeal jaw shape), scoring of pigmentation patterns, and
 approximations of the ecology of virtually all ~240 cichlid species
 endemic to Lake Tanganyika, we show that the radiation occurred within the
 confines of the lake and that morphological diversification proceeded in
 consecutive trait-specific pulses of morphospace expansion. We provide
 empirical support for two theoretical predictions on how adaptive
 radiations proceed, the ‘early-burst’ scenario (for body shape) and the
 stages model (for all traits investigated). Through the analysis of two
 genomes per species and by taking advantage of the uneven distribution of
 species in subclades of the radiation, we further show that species
 richness scales positively with per individual heterozygosity, but is not
 correlated with transposable element content, number of gene duplications,
 or genome-wide levels of selection in coding sequences.
DOI: 10.6084/m9.figshare.31164328
title: Regional Business Continuity under Climate Disasters in South Korea (2010–2019)

description: This dataset contains a regional panel of 248 South Korean districts (2010–2019) with indicators of business continuity, Area BCP, climate exposure, and regional resilience, designed for panel and causal analysis of climate-related business disruptions.
DOI: 10.6084/m9.figshare.31164328.v1
title: Regional Business Continuity under Climate Disasters in South Korea (2010–2019)

description: This dataset contains a regional panel of 248 South Korean districts (2010–2019) with indicators of business continuity, Area BCP, climate exposure, and regional resilience, designed for panel and causal analysis of climate-related business disruptions.
DOI: 10.5061/dryad.70rxwdbt9
title: Dataset of mountain pine beetle outbreak dynamics and direct control in Cypress Hills, SK

description: The data presented in this article are related to the research article
 entitled “Mountain pine beetle outbreak duration and pine mortality depend
 on direct control effort” [1]. This article provides presence of mountain
 pine beetle infested trees detected by the Saskatchewan Forest Service on
 a grid covering the spatial extent of the Saskatchewan portion of the
 Cypress Hills interprovincial park between 2006 and 2018. For each grid
 cell, associated ecological and environmental covariates, such as
 topography, weather and vegetation, are also provided. These data cover
 the spatio-temporal extent of an almost entire mountain pine beetle
 outbreak and contribute to the understanding of mountain pine beetle
 outbreak dynamics.  
description: This dataset provides the presence and number of mountain pine
 beelte infested trees on the grid covering the spatio-temporal extent of
 an almost complete outbreak in Cypress Hills interprovincial park,
 Saskatchewan, Canada from 2006 to 2018. Data collection
 and processing are described in Kunegel-Lion <em>et al.</em>,
 2020, <em>Data in Brief</em> (https://doi.org/10.1016/j.dib.2020.105293)
DOI: 10.5061/dryad.pk0p2ngjg
title: Data from: Endosymbiont diversity in natural populations of Tetranychus mites is rapidly lost under laboratory conditions

description: Although the diversity of bacterial endosymbionts in arthropods is well
 documented, whether and how such diversity is maintained remains an open
 question. We investigated the temporal changes occurring in the prevalence
 and composition of endosymbionts after transferring natural
 populations of Tetranychus spider-mites from the field
 to the laboratory. These populations, belonging to three
 different Tetranychus species (T. urticae, T.
 ludeni and T. evansi) carried variable infection
 frequencies of Wolbachia, Cardinium,
 and Rickettsia. We report a rapid change of the infection status
 of these populations after only 6 months of laboratory rearing, with an
 apparent loss of Rickettsia and Cardinium,
 while Wolbachia apparently either reached fixation or
 was lost. We show that Wolbachia had variable
 effects on host longevity and fecundity, and induced variable levels of
 cytoplasmic incompatibility (CI) in each fully infected population,
 despite no sequence divergence in the markers used and full CI rescue
 between all populations. This suggests that such effects are largely
 dependent upon the host genotype. Subsequently, we used these data to
 parameterize a theoretical model for the invasion of CI-inducing symbionts
 in haplodiploids, which shows that symbiont effects are sufficient to
 explain their dynamics in the laboratory. This further suggests
 that symbiont diversity and prevalence in the field are likely maintained
 by environmental heterogeneity, which is reduced in the laboratory.
 Overall, this study highlights the lability of endosymbiont infections
 and draws attention to the limitations of laboratory studies to
 understand host-symbiont interactions in natural populations.
description: Four different datasets are provided as Tab delimited Text files. All information necessary for re-use of these datasets are provided in the file “Zélé et al. Heredity_ReadMe.txt”.
DOI: 10.5061/dryad.b5mkkwh8t
title: The bivalve shell biomineralization toolbox: bulging, not barren

description: Bivalve molluscs synthesize remarkably complex shells from calcium
 carbonate and an organic matrix of proteins secreted from the dorsal edge
 of the mantle. Molecular analyses of shell matrix proteins (SMPs) have
 suggested high rates of gene turnover despite the conserved nature of the
 shell itself. Here, we used proteomic and transcriptomic data to identify
 the SMPs and other biomineralization proteins from seven bivalve species
 that diverged 3-513 Mya. Contrary to previous studies that identified only
 a few shared biomineralization transcripts across the Bivalvia, we found
 83 that were ubiquitous, all validated by proteomic analysis. 46 of these
 candidates are homologous to annotated genes with functions central to
 shell deposition, including interacting with polysaccharides, forming
 extracellular matrix, inhibiting proteases, and binding calcium. These
 shell-associated proteins mark a 20-fold increase in the size of the
 bivalve biomineralization toolbox. Our results suggest that bivalve
 biomineralization is underpinned by a conserved suite of many genes and
 call into question the need to invoke high levels of novel gene
 recruitment to explain the evolution of SMP diversity.
DOI: 10.5061/dryad.r2280gb98
title: Nonaggressive behavior: A strategy employed by an obligate nest invader to avoid conflict with its host species

description: In addition to its builders, termite nests are known to house a variety of
 secondary opportunistic termite species so‐called inquilines, but little
 is known about the mechanisms governing the maintenance of these
 symbioses. In a single nest, host and inquiline colonies are likely to
 engage in conflict due to nestmate discrimination, and an intriguing
 question is how both species cope with each other in the long term.
 Evasive behaviour has been suggested as one of the mechanisms reducing the
 frequency of host‐inquiline encounters, yet, the confinement imposed by
 the nests' physical boundaries suggests that cohabiting species would
 eventually come across each other. Under these circumstances, it is
 plausible that inquilines would be required to behave accordingly to
 secure their housing. Here, we show that once inevitably exposed to hosts
 individuals, inquilines exhibit nonthreatening behaviours, displaying
 hence a less threatening profile and preventing conflict escalation with
 their hosts. By exploring the behavioural dynamics of the encounter
 between both cohabitants, we find empirical evidence for a lack of
 aggressiveness by inquilines towards their hosts. Such a nonaggressive
 behaviour, somewhat uncommon among termites, is characterised by evasive
 manoeuvres that include reversing direction, bypassing and a defensive
 mechanism using defecation to repel the host. The behavioural adaptations
 we describe may play an important role in the stability of cohabitations
 between host and inquiline termite species: by preventing conflict
 escalation, inquilines may improve considerably their chances of
 establishing a stable cohabitation with their hosts.
description: The present data was collected in laboratorial conditions using a
 focal animal sampling. Observations were taken from video-sample of
 controlled experimental arenas.
description: The dataset includes (i) all data required in tables (ii) an R
 script with analysis to reproduce the results and (iii) additional video
 files as supportive information.
DOI: 10.5061/dryad.5dv41ns34
title: Listening and watching: do camera traps or acoustic sensors more efficiently detect wild chimpanzees in an open habitat?

description: 1. With one million animal species at risk of extinction, there is an
 urgent need to regularly monitor threatened species. However, in practice
 this is challenging, especially with wide-ranging, elusive and cryptic
 species or those that occur at low density. 2. Here we compare two
 non-invasive methods, passive acoustic monitoring (n=12) and camera
 trapping (n=53), to detect chimpanzees (Pan troglodytes) in a
 savanna-woodland mosaic habitat at the Issa Valley, Tanzania. With
 occupancy modelling we evaluate the efficacy of each method, using the
 estimated number of sampling days needed to establish chimpanzee absence
 with 95% probability, as our measure of efficacy. 3. Passive acoustic
 monitoring was more efficient than camera trapping in detecting wild
 chimpanzees. Detectability varied over seasons, likely due to social and
 ecological factors that influence party size and vocalization rate. The
 acoustic method can infer chimpanzee absence with less than ten days of
 recordings in the field during the late dry season, the period of highest
 detectability, which was five times faster than the visual method. 4.
 Synthesis and applications: Despite some technical limitations, we
 demonstrate that passive acoustic monitoring is a powerful tool for
 species monitoring. Its applicability in evaluating presence/absence,
 especially but not exclusively for loud call species, such as cetaceans,
 elephants, gibbons or chimpanzees provides a more efficient way of
 monitoring populations and inform conservation plans to mediate
 species-loss.
description: This dataset was collected with a passive acoustic monitoring and
 camera trap systems. We manually processed audio files and videos to
 confirm chimpanzee detections and create matrices of presence/absence for
 occupancy modelling. These matrices presented in the archive are the raw
 matrices: for the passive acoustic monitoring, the values correspond to
 detection/non detection per 30min files and for the camera traps, the
 values corresponds to detection/non detection per day of deployment.
 Further steps, as detailed in the manuscript (i.e. divide the sampling
 period into sampling occasions of 8 days) have been conducted to create
 the occupancy model.
description: Detection histories were compiled into matrices containing two
 different values: (0) non detection and (1) detection. When no survey was
 conducted during a sampling occasion (e.g. due to camera or audio recorder
 malfunctioning or not deployed), a value of NA was assigned. The value (1)
 corresponds to at least one detection during a sampling
 occasion.
DOI: 10.5061/dryad.q573n5tff
title: CoP vs. CoM stabilization strategies: the tightrope balancing case

description: This study proposes a generalization of the ankle and hip postural
 strategies to be applied to the large class of skills that share the same
 basic challenge of defeating the destabilizing effect of gravity on the
 basis of the same neuromotor control organization, adapted and specialized
 to variable number of degrees of freedom, different body parts, different
 muscles, and different sensory feedback channels. In all the cases we can
 identify two crucial elements (the CoP - Center of Pressure and the CoM -
 Center of Mass) and the central point of the paper is that most balancing
 skills can be framed in the CoP-CoM interplay and can be modeled as a
 combination/alternation of two basic stabilization strategies: the
 standard well investigated COPS (or CoP strategy, the default option),
 where the CoM is the controlled variable and the CoP is the control
 variable, and the less investigated COMS (or CoM strategy), where CoP and
 CoM must exchange their role because the range of motion of the CoP is
 strongly constrained by environmental conditions. The paper focuses on the
 tightrope balancing skill where sway control in the sagittal plane is
 modeled in terms of the COPS while the more challenging sway in the
 coronal plane is modeled in terms of the COMS, with the support of a
 suitable balance pole. Both stabilization strategies are implemented as
 state-space intermittent, delayed feedback controllers, independent of
 each other. Extensive simulations support the degree of plausibility,
 generality, and robustness of the proposed approach.
description: This is a Matlab Simulation
 Script, named tightrope.m, that was used for generating the figures and
 for computing the numerical results discusses in the paper.
description: The user needs Matlab
 R2017a or later version. He/she must import the script in the current
 folder. The it is sufficient to type the name of the script in the command
 window and the results will appear in the workspace. Please note that each
 simulation run produces slightly different results because the control
 variables are affected by white noise that is refreshed for each
 run.
DOI: 10.5061/dryad.12jm63xtg
title: Recent immigrants alter the quantitative genetic architecture of paternity in song sparrows

description: Quantifying additive genetic variances and cross-sex covariances in
 reproductive traits, and identifying processes that shape and maintain
 such (co)variances, is central to understanding the evolutionary dynamics
 of reproductive systems. Gene flow resulting from among-population
 dispersal could substantially alter additive genetic variances and
 covariances in key traits in recipient populations, thereby altering forms
 of sexual conflict, indirect selection and evolutionary responses.
 However, the degree to which genes imported by immigrants do in fact
 affect quantitative genetic architectures of key reproductive traits and
 outcomes is rarely explicitly quantified. We applied structured
 quantitative genetic analyses to multi-year pedigree, pairing and
 paternity data from free-living song sparrows (Melospiza melodia) to
 quantify the differences in mean breeding values for major sex-specific
 reproductive traits, specifically female extra-pair reproduction and male
 paternity loss, between recent immigrants and the previously existing
 population. We thereby quantify effects of natural immigration on the
 means, variances and cross-sex covariance in total additive genetic values
 for extra-pair paternity arising within the complex socially monogamous
 but genetically polygynandrous reproductive system. Recent immigrants had
 lower mean breeding values for male paternity loss, and somewhat lower
 values for female extra-pair reproduction, than the local recipient
 population, and would therefore increase the emerging degree of
 reproductive fidelity of social pairings. Furthermore, immigration
 increased the variances in total additive genetic values for these traits,
 but decreased the magnitudes of the negative cross-sex genetic covariation
 and correlation below those evident in the existing population.
 Immigration thereby increased the total additive genetic variance but
 could decrease the magnitude of indirect selection acting on sex-specific
 contributions to paternity outcomes. These results demonstrate that
 dispersal and resulting immigration and gene flow can substantially affect
 quantitative genetic architectures of complex local reproductive systems,
 implying that comprehensive theoretical and empirical efforts to
 understand mating system dynamics will need to incorporate spatial
 population processes.
description: The data come from the long-term study of song sparrows on
 Mandarte island, BC, Canada.
description: Please see notes included in the data files.