cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.cs1k4
title: Data from: Identification and independence morphometrics of Cenozoic New Zealand Spissatella and Eucrassatella (Bivalvia, Crassatellidae)

description: Fossil bivalve shells are well-suited for landmark/semilandmark
 morphometric analysis because they preserve both traces of the internal
 anatomy and the whole shell outline. Utilizing landmarks and
 semilandmarks, we have characterized internal and external shape variation
 in a monophyletic clade of Cenozoic New Zealand and Australian
 crassatellid bivalves, to test the contiguity in morphospace of
 species-level taxa and to quantitatively examine the "Concept of
 Independent Entities" of Yonge (1953). Thirteen species from two
 genera (Spissatella Finlay 1926 and Eucrassatella Iredale 1924) are
 investigated. Spissatella n. sp. C is confirmed as forming a contiguous
 group separate to S. trailli and S. clifdenensis. Shell outline and
 internal anatomy are found to covary in shape, refuting the "Concept
 of Independent Entities" in the study group.
description: Collection and
 methodological details - Morphometrics of Cenozoic New Zealand Spissatella
 and Eucrassatella (Bivalvia, Crassatellidae)Details of collections
 used for morphometrics, comparisons of morphometric methods, and testing
 of left/right valve inequality.SOM -
 morphometrics.pdf
DOI: 10.5061/dryad.13vk0
title: Data from: Lowland biotic attrition revisited: body size and variation among climate change ‘winners’ and ‘losers’

description: The responses of lowland tropical communities to climate change will
 critically influence global biodiversity but remain poorly understood. If
 species in these systems are unable to tolerate warming, the
 communities—currently the most diverse on Earth—may become depauperate
 (‘biotic attrition’). In response to temperature changes, animals can
 adjust their distribution in space or their activity in time, but these
 two components of the niche are seldom considered together. We assessed
 the spatio-temporal niches of rainforest mammal species in Borneo across
 gradients in elevation and temperature. Most species are not predicted to
 experience changes in spatio-temporal niche availability, even under
 pessimistic warming scenarios. Responses to temperature are not
 predictable by phylogeny but do appear to be trait-based, being much more
 variable in smaller-bodied taxa. General circulation models and weather
 station data suggest unprecedentedly high midday temperatures later in the
 century; predicted responses to this warming among small-bodied species
 range from 9% losses to 6% gains in spatio-temporal niche availability,
 while larger species have close to 0% predicted change. Body mass may
 therefore be a key ecological trait influencing the identity of climate
 change winners and losers. Mammal species composition will probably change
 in some areas as temperatures rise, but full-scale biotic attrition this
 century appears unlikely.
description: DetectionsDetections by location, time, and body massDryad.csv
DOI: 10.5061/dryad.09j1d65
title: Data from: Inbreeding, inbreeding depression and infidelity in a cooperatively-breeding bird

description: Inbreeding depression plays a major role in shaping mating systems: in
 particular, inbreeding avoidance is often proposed as a mechanism
 explaining extra-pair reproduction in socially-monogamous species. This
 suggestion relies on assumptions which are rarely comprehensively tested:
 that inbreeding depression is present, that higher kinship between social
 partners increases infidelity, and that infidelity reduces the frequency
 of inbreeding. Here, we test these assumptions using 26 years of data for
 a cooperatively-breeding, socially-monogamous bird with high female
 infidelity, the superb fairy-wren (Malurus cyaneus). Although inbred
 individuals were rare (~6% of offspring), we found evidence of inbreeding
 depression in nestling mass (but not in fledgling survival). Mother-son
 social pairings resulted in 100% infidelity, but kinship between a social
 pair did not otherwise predict female infidelity. Nevertheless, extra-pair
 offspring were less likely to be inbred than within-pair offspring.
 Finally, the social environment (the number of helpers in a group) did not
 affect offspring inbreeding coefficients or inbreeding depression levels.
 In conclusion, despite some agreement with the assumptions that are
 necessary for inbreeding avoidance to drive infidelity, the apparent
 scarcity of inbreeding events and the observed levels of inbreeding
 depression seem insufficient to explain the ubiquitous infidelity in this
 system, beyond the mother-son mating avoidance.
description: individual-level data
 for superb fairy-wrensThe data have been
 collected in the wild between 1988 and 2013. They were then prepared in R.
 For column headings see the README file.individualLeveL.csvbrood-level data for superb fairy-wrensThe data have been collected in the wild between 1988 and 2013. They were then prepared in R. For column headings see the README file.broodLevel.csv
DOI: 10.5061/dryad.c50sf
title: Data from: Fear and lethality in snowshoe hares: the deadly effects of non-consumptive predation risk

description: Predators play a critical, top-down role in shaping ecosystems, driving
 prey population and community dynamics. Traditionally, studies of
 predator-prey interactions have focused on direct effects of predators,
 namely the killing of prey. More recently, the non-consumptive effects of
 predation risk are being appreciated; e.g., the Ecology of Fear. Prey
 responses to predation risk can be morphological, behavioural, and
 physiological, and are assumed to come at a cost to prey fitness. However,
 few studies have examined the relationship between predation risk and
 survival in wild animals. We tested the hypothesis that predation risk
 itself could reduce survival in wild-caught snowshoe hares. We exposed
 female snowshoe hares to a simulated predator (a trained dog) during
 gestation only, and measured adult survival and, in surviving females,
 their ability to successfully wean offspring. We show for the first time
 in a wild mammal that the risk of predation can itself be lethal.
 Predation risk reduced adult female survival by 30%, and had
 trans-generational effects, reducing offspring survival to weaning by over
 85% - even though the period of risk ended at birth. As a consequence of
 these effects the predator-exposed group experienced a decrease in number,
 while the control group substantially increased. Challenges remain in
 determining the importance of risk-induced mortality in natural field
 settings; however, our findings show that non-lethal predator encounters
 can influence survival of both adults and offspring. Future work is needed
 to test these effects in free-living animals.
description: MACLEOD et al. Data on
 snowshoe hare survival after predator exposureData from a maternal
 predator-exposure experiment testing effects of exposure on adult
 survival, and offspring survival to weaning. Metadata is provided in a
 separate sheet.MACLEOD_et_al_HARE_DATA.xls
DOI: 10.5061/dryad.g8c0r3s
title: Data from: Investigating clinical handover and healthcare communication for outpatients with chronic disease in India: a mixed-methods study

description: Objectives: Research concentrating on continuity of care for chronic,
 non-communicable disease (NCD) patients in resource-constrained settings
 is currently limited and focusses on inpatients. Outpatient care requires
 attention as this is where NCD patients often seek treatment and optimal
 handover of information is essential. We investigated handover, healthcare
 communication and barriers to continuity of care for chronic NCD
 outpatients in India. We also explored potential interventions for
 improving storage and exchange of healthcare information. Methods: A
 mixed-methods design was used across five healthcare facilities in Kerala
 and Himachal Pradesh states. Questionnaires from 513 outpatients with
 cardiovascular disease, chronic respiratory disease, or diabetes covered
 the form and comprehensiveness of information exchange between healthcare
 professionals (HCPs) and between HCPs and patients. Semi-structured
 interviews with outpatients and HCPs explored handover, healthcare
 communication and intervention ideas. Barriers to continuity of care were
 identified through triangulation of all data sources. Results: Almost half
 (46%) of patients self-referred to hospital outpatient clinics (OPCs).
 Patient-held healthcare information was often poorly recorded on
 unstructured sheets of paper; 24% of OPC documents contained the
 following: diagnosis, medication, long-term care and follow-up
 information. Just 55% of patients recalled receiving verbal follow-up and
 medication instructions during OPC appointments. Qualitative themes
 included patient preference for hospital visits, system factors,
 inconsistent doctor-patient communication and attitudes towards medical
 documents. Barriers were hospital time constraints, inconsistent referral
 practices and absences of OPC medical record-keeping, structured
 patient-held medical documents and clinical handover training. Patients
 and HCPs were in favour of the introduction of patient-held booklets for
 storing and transporting medical documents. Conclusions: Deficiencies in
 communicative practices are compromising the continuity of chronic NCD
 outpatient care. Targeted systems-based interventions are urgently
 required to improve information provision and exchange. Our findings
 indicate that well-designed patient-held booklets are likely to be an
 acceptable, affordable and effective part of the solution.
description: 2015 India Handover
 Outpatient DataMixed-methods data from
 research investigating continuity of care for chronic, non-communicable
 disease patients visiting government healthcare facilities in Himachal
 Pradesh and Kerala states, India. The data file contains quantitative
 survey data from outpatients with an associated READ ME document and
 qualitative interview transcripts from outpatients and
 doctors.2015_HANDOVER_OUTPATIENT_DATA_FILES.zip
DOI: 10.5061/dryad.3ps1513
title: Data from: Multiple mechanisms confer stability to isolated populations of a rare endemic plant

description: The persistence of small populations remains a puzzle for ecology and
 conservation. Especially interesting is how naturally small, isolated
 populations are able to persist in the face of multiple environmental
 forces that create fluctuating conditions and should, theory predicts,
 lead to high probabilities of extirpation. We used a combination of long
 term census data and a five-year demographic study of a naturally rare,
 endemic plant, Yermo xanthocephalus, to evaluate the importance of several
 possible mechanisms for small population persistence: negative density
 dependence, vital rate buffering, demographic compensation, asynchrony in
 dynamics among sub-populations, and source-sink dynamics. These
 non-exclusive explanations for population persistence all have been shown
 to operate in some systems, but have rarely if ever been simultaneously
 examined for the same population or species. We hypothesized that
 asynchrony in dynamics and demographic compensation would be more powerful
 than the other three mechanisms. We found partial support for our
 hypothesis: density dependence, asynchrony among population segments, and
 source-sink patterns appear to be the most important mechanisms
 maintaining population viability in this species. Importantly, these
 processes all appear to operate strongly at very fine spatial scales for
 Yermo, allowing the only two, extremely small, populations to persist. We
 also found considerable differences in the results of our census and
 demographic analyses. In general, we estimated substantially greater
 chances of survival from the census data than from the shorter-term
 demographic studies. In part, this difference is due to drier than average
 climate conditions during the years of the demographic work. These results
 emphasize that while demographic information is necessary to understand
 various components of population dynamics, longer term studies, even if
 much less detailed, can be more powerful in uncovering some mechanisms
 that may be critical in stabilizing population numbers, especially in
 variable environments.
description: Dibner_etal_metadataNOAA_weather_1907_2015 Riverton WYYermo_Census_Data_CompiledYermoDemoData
DOI: 10.5061/dryad.t8vg3
title: Data from: Saguaro (Carnegiea gigantea) mortality and population regeneration in the cactus forest of Saguaro National Park: seventy-five years and counting

description: Annual census data spanning seventy-five years document mortality and
 regeneration in a population of saguaro cactus (Carnegiea gigantea) in the
 Cactus Forest of the Rincon Mountain District of Saguaro National Park
 near Tucson, AZ. On 6 four-hectare plots, each saguaro was censused and a
 methodical search for new saguaros was conducted annually each year from
 1942 through 2016, with the exception of 1955. Regeneration has been
 episodic with 828 plants established from 1959 through 1993 compared with
 34 plants established between 1942 and 1958 and only three plants
 established after 1993. The years preceding 1959 and following 1993,
 include some of the driest decades in centuries in southern Arizona. While
 woodcutting and cattle grazing are believed to be among the causes of
 decades of failed regeneration prior to 1958, neither of these factors
 contributed to the failed regeneration following 1993. The height
 structure of the population from 1942 to 2016 shifted dramatically from a
 population dominated by large saguaros (&gt; 5.4 m tall) in the first
 three decades of the study to a population dominated by small saguaros
 (&lt; 1.8 m tall) in the most recent two decades. Mortality is shown
 to be strongly age dependent. In the year following the 2011 catastrophic
 freeze, 21 of 59 plants older than 80 years died compared with zero deaths
 in 270 plants between the ages of 29 and 80 years. Saguaros under 40 years
 old, growing under small shrubs or in the open, have a lower probability
 of survival than better protected saguaros. Long-term population
 monitoring is essential to understanding the complex impacts of human and
 environmental factors on the population dynamics of long-lived species.
description: SaguaroCensusData
 csvData included are for
 all plants in 6 4-hectare plots from 1942 to 2016. Identifiers for plot
 and plant are associated with height, nurse plant cover, height, branches,
 year of establishment and year of death.SaguaroYearHeightGrowth
 csvAnnual height data for
 saguaros discovered after plot establishment.HeightClasses1942Survivorship csvAnnual survival by height class for Figure 7
DOI: 10.5061/dryad.k47p7
title: Data from: Molecular determinants of agonist selectivity in glutamate-gated chloride channels which likely explain the agonist selectivity of the vertebrate glycine and GABAA-ρ receptors

description: Orthologous Cys-loop glutamate-gated chloride channels (GluClR’s) have
 been cloned and described electrophysiologically and pharmacologically in
 arthropods and nematodes (both members of the invertebrate ecdysozoan
 superphylum). Recently, GluClR’s from Aplysia californica (a mollusc from
 the lophotrochozoan superphylum) have been cloned and similarly studied.
 In spite of sharing a common function, the ecdysozoan and lophotrochozoan
 receptors have been shown by phylogenetic analyses to have evolved
 independently. The recent crystallization of the GluClR from C. elegans
 revealed the binding pocket of the nematode receptor. An alignment of the
 protein sequences of the nematode and molluscan GluClRs showed that the
 Aplysia receptor does not contain all of the residues defining the binding
 mode of the ecdysozoan receptor. That the two receptors have slightly
 different binding modes is not surprising since earlier
 electrophysiological and pharmacological experiments had suggested that
 they were differentially responsive to certain agonists. Knowledge of the
 structure of the C. elegans GluClR has permitted us to generate a homology
 model of the binding pocket of the Aplysia receptor. We have analyzed the
 differences between the two binding modes and evaluated the relative
 significance of their non-common residues. We have compared the GluClRs
 electrophysiologically and pharmacologically and we have used
 site-directed mutagenesis on both receptor types to test predictions made
 from the model. Finally, we propose an explanation derived from the model
 for why the nematode receptors are gated only by glutamate, whereas the
 molluscan receptors can also be activated by β-alanine, GABA and taurine.
 Like the Aplysia receptor, the vertebrate glycine and GABAA-ρ receptors
 also respond to these other agonists. An alignment of the sequences of the
 molluscan and vertebrate receptors shows that the reasons we have given
 for the ability of the other agonists to activate the Aplysia receptor
 also explain the agonist profile seen in the glycine and GABAA-ρ
 receptors.
description: Glutamate docked in the
 homology model of GluClAc2 (Aplysia californica)Coordinates of the
 homology model of GluClAc2, the glutamate-gated chloride channel receptor
 of Aplysia californica with docked glutamate.GluClAc2_Aplysia_Glutamate.pdb
DOI: 10.5061/dryad.ph40n
title: Data from: Mate finding, Allee effects, and selection for sex-biased dispersal

description: Although dispersal requires context-dependent decision-making in three
 distinct stages (emigration, transit, immigration), these decisions are
 commonly ignored in simple models of dispersal. For sexually reproducing
 organisms, mate availability is an important factor in dispersal
 decisions. Difficulty finding mates can lead to an Allee effect where
 population growth decreases at low densities. Surprisingly, theoretical
 studies on mate finding and on sex-biased dispersal produce opposing
 predictions: in the former one sex is predicted to move less if the other
 sex evolves to search more, whereas in the latter mate-finding
 difficulties can select for less sex bias in dispersal when mate finding
 occurs after dispersal. Here we develop a pair of models to examine the
 joint evolution of dispersal and settlement behaviour. Our first model
 resolves the apparent contradiction from the mate-search and dispersal
 literatures. Our second model demonstrates that the relationship between
 mating system and sex-biased dispersal is more complex than a simple
 contrast between resource-defence monogamy and female-defence polygyny.
 Our results highlight that a key factor is the timing of mating relative
 to dispersal (before, during, or after). We also show that although
 movement has the potential to alleviate a mate-finding Allee effect, in
 some cases it can actually exacerbate the effect.
description: readme: instructions for
 using code and simulation data heremodel simulation data
 and Matlab code for generating paper figuresfiles_plotcode.zipMatlab code for running model simulationsfiles_runcode.zip
DOI: 10.5061/dryad.bk334
title: Data from: Actuarial senescence in a long-lived orchid challenges our current understanding of ageing

description: The dominant evolutionary theory of actuarial senescence—an increase in
 death rate with advancing age—is based on the concept of a germ cell line
 that is separated from the somatic cells early in life. However, such a
 separation is not clear in all organisms. This has been suggested to
 explain the paucity of evidence for actuarial senescence in plants. We
 used a 32 year study of Dactylorhiza lapponica that replaces its organs
 each growing season, to test whether individuals of this tuberous orchid
 senesce. We performed a Bayesian survival trajectory analysis accounting
 for reproductive investment, for individuals under two types of land use,
 in two climatic regions. The mortality trajectory was best approximated by
 a Weibull model, showing clear actuarial senescence. Rates of senescence
 in this model declined with advancing age, but were slightly higher in
 mown plots and in the more benign climatic region. At older ages,
 senescence was evident only when accounting for a positive effect of
 reproductive investment on mortality. Our results demonstrate actuarial
 senescence as well as a survival–reproduction trade-off in plants, and
 indicate that environmental context may influence senescence rates. This
 knowledge is crucial for understanding the evolution of demographic
 senescence and for models of plant population dynamics.
description: Dahlgren et al 2016 proc
 b dataA tab-delimited .txt
 file containing a table of the data used in Actuarial senescence in a
 long-lived orchid challenges our current understanding of ageing. The
 variables are Individual ID, Population, Treatment, Year, Survival and
 Reproductive effort.
DOI: 10.26008/1912/bco-dmo.986518.1
title: Sequence accession numbers for 16S rRNA genes characterizing microbiome changes in Agaricia tenuifolia and Siderastrea siderea coral species after being exposed to hypoxia and after a short period of recovery in 2022 experiments

description: This dataset includes accession numbers and related information for 16S rRNA genes characterizing microbiome changes in Agaricia tenuifolia and Siderastrea siderea coral species after being exposed to hypoxia and after a short period of recovery. Corals for the experiment were collected by SCUBA divers in summer 2022. Sequence data are available in The National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) under BioProject accession PRJNA1197146.
DOI: 10.5061/dryad.vr280
title: Data from: Migratory divides and their consequences for dispersal, population size and parasite-host interactions

description: Populations of migratory birds differ in their direction of migration with
 neighboring populations often migrating in divergent directions separated
 by migratory divides. A total of 26% of 103 passerine bird species in
 Europe had migratory divides that were located disproportionately often
 along a longitudinal gradient in Central Europe, consistent with the
 assumption of a Quaternary glacial origin of such divides in the Iberian
 and Balkan peninsulas followed by re-colonization. Given that studies have
 shown significant genetic differentiation and reduced gene flow across
 migratory divides we hypothesized that an absence of migratory divides
 would result in elevated rates of gene flow and hence a reduced level of
 local adaptation. In a comparative study, species with migratory divides
 had larger population sizes and population densities and longer dispersal
 distances than species without migratory divides. Species with migratory
 divides tended to be habitat generalists. Bird species with migratory
 divides had higher richness of blood parasites and higher growth rates of
 Staphylococcus on their eggs during the incubation period. There was
 weaker cell-mediated immunity in adults and stronger cell lysis in species
 with migratory divides. These findings may suggest that migratory divides
 constitute barriers to dispersal with consequences for ecology and
 evolution of distributions, population sizes, habitats, and parasite-host
 interactions. They also suggest that migratory divides may play a role in
 local adaptation in host-parasite interactions.
description: ESMFull data
 set