cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.mb79n
title: Data from: Quantifying the relative effects of environmental and direct transmission of norovirus

description: Background: Norovirus is a common cause of outbreaks of acute
 gastroenteritis in health- and child-care settings, with serial outbreaks
 also frequently observed aboard cruise ships. The relative contributions
 of environmental and direct person-to-person transmission of norovirus has
 hitherto not been quantified. Objective: We employ a novel mathematical
 model of norovirus transmission, and fit the model to daily incidence data
 from a major norovirus outbreak on a cruise ship, and examine the relative
 efficacy of potential control strategies aimed at reducing environmental
 and/or direct transmission. Results: The reproduction number for
 environmental and direct transmission combined is Rtot = 7.2 [6.1,9.5],
 and of environmental transmission alone is Renviron = 1.6 [0.9,2.6].
 Direct transmission is overwhelmingly due to passenger-to-passenger
 contacts, but crew can act as a reservoir of infection from
 cruise-to-cruise. Implications: This is the first quantification of the
 relative roles of environmental and direct transmission of norovirus.
 While environmental transmission has the potential to maintain a sustained
 series of outbreaks aboard a cruise ship in the absence of strict
 sanitation practices, direct transmission dominates. We find that
 intensive promotion of good hand washing practices may prevent outbreaks.
 Isolation of ill passengers and cleaning are beneficial, but appear to be
 less efficacious at outbreak control.
description: isakbaeva_2005_cruise_norovirus_outbreak_dataNorovirus outbreak data, taken from Isakbaeva, Elmira T., et al. "Norovirus transmission on cruise ship." Emerging infectious diseases 11.1 (2005): 154.
DOI: 10.5061/dryad.2752g
title: Data from: The fate of W chromosomes in hybrids between wild silkmoths, Samia cynthia ssp.: no role in sex determination and reproduction

description: Moths and butterflies (Lepidoptera) have sex chromosome systems with
 female heterogamety (WZ/ZZ or derived variants). The maternally inherited
 W chromosome is known to determine female sex in the silkworm, Bombyx
 mori. However, little is known about the role of W chromosome in other
 lepidopteran species. Here we describe two forms of the W chromosome, W
 and neo-W, that are transmitted to both sexes in offspring of hybrids from
 reciprocal crosses between subspecies of wild silkmoths, Samia cynthia. We
 performed crosses between S. c. pryeri (2n=28, WZ/ZZ) and S. c. walkeri
 (2n=26, neo-Wneo-Z/neo-Zneo-Z) and examined fitness and sex chromosome
 constitution in their hybrids. The F1 hybrids of both reciprocal crosses
 had reduced fertility. Fluorescence in situ hybridization revealed not
 only the expected sex chromosome constitutions in the backcross and F2
 hybrids of both sexes but also females without the W (or neo-W) chromosome
 and males carrying the W (or neo-W) chromosome. Furthermore, crosses
 between the F2 hybrids revealed no association between the presence or
 absence of W (or neo-W) chromosome and variations in the hatchability of
 their eggs. Our results clearly suggest that the W (or neo-W) chromosome
 of S. cynthia ssp. plays no role in sex determination and reproduction,
 and thus does not contribute to the formation of reproductive barriers
 between different subspecies.
description: Hatchability of eggs in
 crosses between Samia cynthia ssp.These are original
 dataset to Figure 2 and Supplementary Table S1. Hatchability of eggs in
 the control (C), parental (P) and F1 crosses, and backcrosses (B1) between
 Samia cynthia walkeri (SCW) and Samia cynthia pryeri
 (SCP).original dataset to Figure 2
 and supplementary Table S1.csv
DOI: 10.5061/dryad.68nj4
title: Data from: Higher rate of tissue regeneration in polyploid asexual vs. diploid sexual freshwater snails

description: Characterizing phenotypic differences between sexual and asexual organisms
 is a critical step towards understanding why sexual reproduction is so
 common. Because asexuals are often polyploid, understanding how ploidy
 influences phenotype is directly relevant to the study of sex and will
 provide key insights into the evolution of ploidy-level variation. The
 well-established association between genome size and cell cycle duration,
 evidence for a link between genome size and tissue regeneration rate and
 the growing body of research showing that ploidy influences growth rate
 and gene expression led us to hypothesize that healing and tissue
 regeneration might be affected by ploidy-level variation. We evaluated
 this hypothesis by measuring the rate of regeneration of antenna tissue of
 Potamopyrgus antipodarum, a New Zealand snail characterized by frequent
 coexistence between diploid sexuals and polyploid asexuals. Antennae of
 triploid and presumptive tetraploid asexuals regenerated more rapidly than
 the antennae of diploid sexuals, but regeneration rate did not differ
 between triploids and tetraploids. These results suggest either that
 ploidy elevation has nonlinear positive effects on tissue regeneration
 and/or that factors associated directly with reproductive mode affect
 regeneration rate more than ploidy level. The results of this study also
 indicate that the lower ploidy of sexual P. antipodarum is unlikely to
 confer advantages associated with more rapid regeneration.
description: Krois et al. antenna and
 length dataThese data represent the
 shell length and antenna regrowth data collected in a laboratory
 experiment, originally entered into an Excel file, and then analyzed in
 IBM SPSS. Shell length and antenna regrowth values are in
 millimeters.Krois et
 al.csv
DOI: 10.5061/dryad.374q4
title: Data from: Fishing-induced changes in adult length are mediated by skipped-spawning

description: Elucidating fishing effects on fish population dynamics is a critical step
 toward sustainable fisheries management. Despite previous studies that
 have suggested age or size truncation in exploited fish populations, other
 aspects of fishing effects on population demography, e.g., via altering
 life histories and density, have received less attention. Here, we
 investigated the fishing effects altering adult demography via shifting
 reproductive trade-offs in the iconic, overexploited, Pacific bluefin tuna
 Thunnus orientalis. We found that, contrary to our expectation, mean
 lengths of catch increased over time in longline fisheries. On the other
 hand, mean catch lengths for purse seine fisheries did not show such
 increasing trends. We hypothesized that the size-dependent energetic cost
 of the spawning migration and elevated fishing mortality on the spawning
 grounds potentially drive size-dependent skipped spawning for adult tuna,
 mediating the observed changes in the catch lengths. Using eco-genetic
 individual-based modeling, we demonstrated that fishing-induced evolution
 of skipped spawning and size truncation interacted to shape the observed
 temporal changes in mean catch lengths for tuna. Skipped spawning of the
 small adults led to increased mean catch lengths for the longline
 fisheries, while truncation of small adults by the purse seines could
 offset such a pattern. Our results highlight the eco-evolutionary dynamics
 of fishing effects on population demography and caution against using
 demographic traits as a basis for fisheries management of the Pacific
 bluefin tuna as well as other migratory species.
description: BFspawner_mean_length_dataThis file contains the time series of mean catch length data of adult Pacific bluefin tuna based on three fisheries: Taiwanese longline (TWL), Japanese coastal longline (JCL), and Japanese purse seine (JPS). The unit of length is cm. FYEAR: fishing year. Description of the sampling methods is available in the Material and Methods of the paper and supplemental material Table S1.
DOI: 10.5061/dryad.sr398
title: Data from: Fission–fusion processes weaken dominance networks of female Asian elephants in a productive habitat

description: Dominance hierarchies are expected to form in response to socioecological
 pressures and competitive regimes. We assess dominance relationships among
 free-ranging female Asian elephants (Elephas maximus) and compare them
 with those of African savannah elephants (Loxodonta africana), which are
 known to exhibit age-based dominance hierarchies. Both species are
 generalist herbivores, however, the Asian population occupies a more
 productive and climatically stable environment relative to that of the
 African savannah population. We expected this would lower competition
 relative to the African taxon, relaxing the need for hierarchy. We tested
 whether 1) observed dominance interactions among individuals were
 transitive, 2) outcomes were structured either by age or by social unit
 according to 4 independent ranking methods, and 3) hierarchy steepness
 among classes was significant using David’s score. Elephas maximus
 displayed less than a third the number of dominance interactions as
 observed in L. africana, with statistically insignificant transitivity
 among individuals. There was weak but significant order as well as
 steepness among age-classes but no clear order among social units.
 Loxodonta africana showed significant transitivity among individuals, with
 significant order and steepness among age-classes and social units.
 Elephas maximus had a greater proportion of age-reversed dominance
 outcomes than L. africana. When dominance hierarchies are weak and
 nonlinear, signals of dominance may have other functions, such as
 maintaining social exclusivity. We propose that resource dynamics
 reinforce differences via influence on fission–fusion processes, which we
 term “ecological release.” We discuss implications of these findings for
 conservation and management when animals are spatially constrained.
description: Asian elephant dominance
 edgelistThis is a two-column
 edge list with outcomes of dominance interactions for female Asian
 elephants, Elephas maximus. Column headers indicate dominant and
 subordinate.asian.el.csvIndividual attributesThis includes the social unit and age class assignment of each individual, where 1 is the oldest and 6 is the youngest. Please see paper for bins. Social unit numeric designations are arbitrary and do not indicate rank. All individuals are female.attributes.asian.csv
DOI: 10.5061/dryad.b022b
title: Data from: Developing state and transition models of floodplain vegetation dynamics as a tool for conservation decision-making: a case study of the Macquarie Marshes Ramsar wetland

description: 1. Floodplain vegetation states (communities) exhibit spatiotemporal
 dynamics in vegetation structure and composition, which reflect unique
 hydrological and connectivity patterns. Shifts in inundation regimes can
 drive succession and establish new stable states, determined by the
 magnitude and duration of the hydrological perturbation. 2. We aimed to
 develop a modelling approach that is able to capture ecosystem dynamics,
 identify and quantify the main drivers of change, and provide a tool for
 conservation decision-making. We developed state and transition models for
 floodplain vegetation states based on surveys in 1991 and 2008 in the
 Macquarie Marshes (Australia), a Ramsar wetland of international
 importance. We used a Bayesian logistic regression approach to model state
 and transitions between vegetation states and investigated how flood
 frequency, distance to stream and fire frequency were associated with
 vegetation dynamics during this period. 3. During 1991–2008, significant
 transitions have occurred towards drier states. Semi-permanent wetland
 vegetation had the lowest persistence probability (ppsis = 0·456) and a
 significant threshold response of transitioning to terrestrial vegetation
 (ptran = 0·505). Transition to drier states was driven by lower inundation
 probabilities followed by increased fire probability, and distance to
 nearest stream. 4. Using developed models, we predicted persistence
 probabilities of vegetation states under an unregulated (i.e. no dams or
 diversions) and regulated water availability system. Under a regulated
 system, semi-permanent wetland vegetation had an average persistence of
 ppsis = 0. 67 and 0·08 in the northern and southern sections of the nature
 reserve, respectively. Under an unregulated system, the predicted
 persistence of semi-permanent wetland vegetation was considerably higher:
 ppsis = 0·87 and 0·38, respectively. 5. Synthesis and applications.
 Developing quantitative models of state transitions significantly improved
 our understanding of ecosystem dynamics, identifying sensitive indicators
 for monitoring and thus supporting conservation decision-making. This
 helps managers understand potential trajectories of change in ecosystems
 in response to management options. For example, increasing environmental
 flows in the Macquarie Marshes is predicted to shift the community towards
 more of a wetland than the terrestrial state, resulting from river
 regulation. State and transition models identified how key ecological
 assets respond to drivers of change, particularly where these can be
 managed. This is critical for ensuring that all ecosystem components are
 managed and that these do not shift into undesirable states.
description: Open bug code for state
 and transitions modelsSTM_openbugs.txt
DOI: 10.5061/dryad.60n75dd
title: Data from: Diversity increases with elevation: empidine dance flies (Diptera, Empididae) challenge a predominant pattern

description: Tropical mountain forests are important reservoirs of biodiversity. They
 are usually species rich and often support endemic species making them
 prime targets for conservation effort. The aim of this study is to
 investigate elevational patterns of species diversity and phenology in
 order to provide a meaningful understanding of insects’ spatio-temporal
 distributions along a tropical gradient of elevation. Our study focuses on
 the Empidinae communities (Diptera, Empididae) from Doi Inthanon (north
 Thailand, gradient 400–2556 m.a.s.l), sampled during two entire years
 (2006–2007, 2014). This group of insects is more diverse in temperate
 localities than in the tropics and we found that (1) increase in altitude
 and latitude has a similar effect, so that the diversity of our model
 increases with elevation, (2) the phenology is strongly influenced by
 seasonality with a peak of diversity occurring during the transition
 between the dry and rainy seasons, (3) there is no phenological shift in
 the diversity peak with elevations, (4) the species composition changes
 along the altitudinal gradient and through the year (high beta diversity).
 The increase of diversity with increasing elevation and the peak of
 diversity occuring at the transitional period both strongly coincide with
 abiotic factors, the decreasing temperature and the arrival of the
 monsoon, respectively.
description: Number of
 individualsNumber of individuals
 collected for each altitude and month for all EmpidinaeNumber of
 speciesNumber of species
 collected for each altitude and month for all Empidinae. The numbers given
 in the columns and rows "Total" correspond to the total numbers
 of different species collected
DOI: 10.5061/dryad.g1hk2
title: Data from: Noise affects resource assessment in an invertebrate

description: Anthropogenic noise is a global pollutant, affecting animals across taxa.
 However, how noise pollution affects resource acquisition is unknown.
 Hermit crabs (Pagurus bernhardus) engage in detailed assessment and
 decision-making when selecting a critical resource, their shell; this is
 crucial as individuals in poor shells suffer lower reproductive success
 and higher mortality. We experimentally exposed hermit crabs to
 anthropogenic noise during shell selection. When exposed to noise, crabs
 approached the shell faster, spent less time investigating it, and entered
 it faster. Our results demonstrate that changes in the acoustic
 environment affect the behaviour of hermit crabs by modifying the
 selection process of a vital resource. This is all the more remarkable
 given that the known cues used in shell selection involve chemical, visual
 and tactile sensory channels. Thus, our study provides rare evidence for a
 cross-modal impact of noise pollution.
description: Walsh et al
 data
DOI: 10.5061/dryad.4g0m4
title: Data from: Fear of the human “super predator” far exceeds the fear of large carnivores in a model mesocarnivore

description: The fear (perceived predation risk) large carnivores inspire in
 mesocarnivores can affect ecosystem structure and function, and loss of
 the “landscape of fear” large carnivores create adds to concerns regarding
 the worldwide loss of large carnivores. Fear of humans has been proposed
 to act as a substitute, but new research identifies humans as a “super
 predator” globally far more lethal to mesocarnivores, and thus presumably
 far more frightening. Although much of the world now consists of
 human-dominated landscapes, there remains relatively little research
 regarding how behavioral responses to humans affect trophic networks, to
 the extent that no study has yet experimentally tested the relative
 fearfulness mesocarnivores demonstrate in reaction to humans versus
 nonhuman predators. Badgers (Meles meles) in Britain are a model
 mesocarnivore insofar as they no longer need fear native large carnivores
 (bears, Ursus arctos; wolves, Canis lupus) and now perhaps fear humans
 more. We tested the fearfulness badgers demonstrated to audio playbacks of
 extant (dog) and extinct (bear and wolf) large carnivores, and humans, by
 assaying the suppression of foraging behavior. Hearing humans affected
 latency to feed, vigilance, foraging time, number of feeding visits, and
 number of badgers feeding. Hearing dogs and bears had far lesser effects
 on latency to feed, and hearing wolves had no effects. Our results
 indicate fear of humans evidently cannot substitute for the fear large
 carnivores inspire in mesocarnivores because humans are perceived as far
 more frightening, which we discuss in light of the recovery of large
 carnivores in human-dominated landscapes.
description: Data_from_Clinchy_et_al_2016_Behavioral_Ecology
DOI: 10.5061/dryad.1h7p0
title: Data from: Oxygen supply limits the heat tolerance of lizard embryos

description: The mechanisms that set the thermal limits to life remain uncertain.
 Classically, researchers thought that heating kills by disrupting the
 structures of proteins or membranes, but an alternative hypothesis focuses
 on the demand for oxygen relative to its supply. We evaluated this
 alternative hypothesis by comparing the lethal temperature for lizard
 embryos developing at oxygen concentrations of 10–30%. Embryos exposed to
 normoxia and hyperoxia survived to higher temperatures than those exposed
 to hypoxia, suggesting that oxygen limitation sets the thermal maximum. As
 all animals pass through an embryonic stage where respiratory and
 cardiovascular systems must develop, oxygen limitation may limit the
 thermal niches of terrestrial animals as well as aquatic ones.
description: Data_SmithEtAl_2015_BiologyLettersFile contains data on oxygen treatments and the maximum temperatures where heart beats were observed in Sceloporus tristichus eggs. Data on egg masses are also provided.
DOI: 10.5061/dryad.4kr93
title: Data from: Sex determination in the wild: a field application of loop-mediated isothermal amplification successfully determines sex across three raptor species

description: PCR-based methods are the most common technique for sex determination of
 birds. Although these methods are fast, easy and accurate, they still
 require special facilities that preclude their application outdoors.
 Consequently, there is a time lag between sampling and obtaining results
 that impedes researchers to take decisions in situ and in real time
 considering individuals’ sex. We present an outdoor technique for sex
 determination of birds based on the amplification of the duplicated
 sex-chromosome-specific gene Chromo-Helicase-DNA binding protein using a
 loop-mediated isothermal amplification (LAMP). We tested our method on
 Griffon Vulture (Gyps fulvus), Egyptian Vulture (Neophron percnopterus)
 and Black Kite (Milvus migrans) (family Accipitridae). We introduce the
 first fieldwork procedure for sex determination of animals in the wild,
 successfully applied to raptor species of three different subfamilies
 using the same specific LAMP primers. This molecular technique can be
 deployed directly in sampling areas because it only needs a voltage
 inverter to adapt a thermo-block to a car lighter and results can be
 obtained by the unaided eye based on colour change within the reaction
 tubes. Primers and reagents are prepared in advance to facilitate their
 storage at room temperature. We provide detailed guidelines how to
 implement this procedure, which is simpler (no electrophoresis required),
 cheaper and faster (results in c. 90 min) than PCR-based laboratory
 methods. Our successful cross-species application across three different
 raptor subfamilies posits our set of markers as a promising tool for
 molecular sexing of other raptor families and our field protocol
 extensible to all bird species.
description: Alignment of partial
 sequences of the CHD gene located in the Z-chromosome of Gyps fulvus,
 Milvus migrans and Neophron percnopterusDNA sequences of the
 CHD-Z fragments of Gyps fulvus, Milvus migrans and Neophron percnopterus
 used for design of LAMP primers suitable for sex determination. These
 sequences were obtained after Sanger sequencing of the CHD-Z fragments
 obtained by PCR using 2550F and 2718R primers (Fridolfsson & Ellegren
 1999)Centeno-Cuadros_CHD-Z_Accipitridae.fasta
DOI: 10.5061/dryad.bm4672c
title: Data from: Effect of temperature on oviposition behavior and egg load of blow flies (Diptera: Calliphoridae)

description: Making optimal oviposition decisions is especially important for female
 carrion colonizing insects whose larvae often depend on ephemeral
 resources. Oviposition can be influenced by a variety of factors,
 including temperature. The aim of this study was to investigate the
 effects of temperature on the oviposition behavior and egg load of two
 blow fly species native to southern Ontario: Phormia regina Meigen and
 Lucilia sericata Meigen (Diptera: Calliphoridae). Using fetal pig
 carcasses as an oviposition substrate, we assessed the length of time
 until the first oviposition event, preferred oviposition sites, and the
 total number of eggs oviposited. For each of the two species, five
 different temperature treatments ranging from 15° to 35°C were used.
 Temperature influenced time to the first oviposition event, as well as the
 number of eggs deposited by L. sericata and P. regina. As temperature
 increased, oviposition occurred faster with more eggs deposited for these
 two species. Female P. regina, in particular, demonstrated a higher egg
 load with increasing temperature. Differences in optimal temperatures for
 reproduction, including egg load and oviposition, may be a mechanism
 driving seasonal temporal resource partitioning leading to species
 co-existence utilizing ephemeral resources.
description: Oviposition
 DataThis data set contains
 the raw data for the length of time (hours) until the first oviposition
 event occurred at each temperature, the number of eggs laid at each
 temperature and the oviposition sites selected at each temperature for
 each species studied.ovidata.csv