cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.dr7sqvb0j
title: ModEst - Precise estimation of genome size from NGS data

description: Accurate estimates of genome sizes are important parameters for both
 theoretical and practical biodiversity genomics. We present here a fast,
 easy-to-implement and precise method to estimate genome size from the
 number of bases sequenced and the mean sequencing depth. To estimate the
 latter, we take advantage of the fact that a precise estimation of the
 Poisson distribution parameter lambda is possible from truncated data,
 restricted to the part of the sequencing depth distribution representing
 the true underlying distribution. With simulations we could show that
 reasonable genome size estimates can be gained even from low-coverage
 (10X), highly discontinuous genome drafts. Comparison of estimates from a
 wide range of taxa and sequencing strategies with flow-cytometry estimates
 of the same individuals showed a very good fit and suggested that both
 methods yield comparable, interchangeable results.
description: To illustrate the influence of factors like sequencing depth,
 genome size, repeat content and -distribution on the different genome size
 estimation methods, we simulated five different genomes according to real
 examples. The latest genome assemblies and annotations of Saccharomyces
 cerevisae, Caenorhabditis elegans, Arabidopsis thaliana, Drosophila
 melanogaster and Scophthalmus maximus were used to obtain distributions of
 size and distance between annotated repeat regions. Simulated genomes of
 the size of the five genome assemblies mentioned above were then created
 using a custom Python-tool, available at
 https://github.com/Croxa/Simulate-Genome. Regions annotated as repeat
 regions (rr) were filled with random repeat units up to 10 bp length, high
 complexity regions with random nucleotides. For sake of ease, we simulated
 the genomes on a single chromosome. A mean GC content of 0.5 was applied
 to both categories.
DOI: 10.5061/dryad.kwh70rz4z
title: Avian disease surveillance on the island of San Cristóbal, Galápagos

description: Endemic island species face unprecedented threats, with many populations
 in decline or at risk of extinction. One important threat is the
 introduction of novel and potentially devastating diseases, made more
 pressing due to accelerating global connectivity, urban development, and
 climatic changes. In the Galápagos archipelago two important wildlife
 diseases: avian pox (Avipoxvirus spp.) and avian malaria
 (Plasmodium spp. and related Haemosporidia) challenge endemic
 species. San Cristóbal island has seen a paucity of disease surveillance
 in avian populations, despite the island's connectedness to the
 continent and the wider archipelago. To survey prevalence and better
 understand the dynamics of these two diseases on San Cristóbal, we
 captured 1205 birds of 11 species on the island between 2016 and
 2020. Study sites included urban and rural lowland localities as well as
 rural highland sites in 2019. Of 995 blood samples screened for avian
 haemosporidia, none tested positive for infection. In contrast, evidence
 of past and active pox infection was observed in 97 birds and identified
 as strains Gal1 and Gal2. Active pox prevalence differed significantly
 with contemporary climatic conditions, being highest during El Niño events
 (~11% in 2016 and in 2019 versus &lt;1% in the La Niña year of 2018).
 Pox prevalence was also higher at urban sites than rural (11% to 4%, in
 2019) and prevalence varied between host species, ranging from 12% in
 medium ground finches (Geospiza fortis) to 4% in Yellow Warblers
 (Setophaga petechial aureola). In the most common infected species (Small
 Ground Finch: Geospiza fuliginosa), birds recovered from pox had
 significantly longer wings, which may suggest a selective cost to
 infection. These results illustrate the threat future climate changes and
 urbanization may present in influencing disease dynamics in the Galápagos,
 while also highlighting unknowns regarding species-specific
 susceptibilities to avian pox and the transmission dynamics facilitating
 outbreaks within these iconic species.
description: This dataset pertains to birds caught by mist-netting. Infection
 status for Avipoxviruses was obtained using the methods detailed in the
 associated manuscript.
DOI: 10.5061/dryad.stqjq2c4f
title: Thermal-metabolic phenotypes of the lizard Podarcis muralis differ across elevation, but converge in high elevation hypoxia

description: In response to a warming climate, many montane species are shifting
 upslope to track the emergence of preferred temperatures. Characterizing
 patterns of variation in metabolic, physiological and thermal traits along
 an elevational gradient, and the plastic potential of these traits, is
 necessary to understand current and future responses to abiotic
 constraints at high elevations, including limited oxygen availability. We
 performed a transplant experiment with the upslope-colonizing common wall
 lizard (Podarcis muralis) in which we measured nine aspects of thermal
 physiology and aerobic capacity in lizards from replicate low- (400 m
 above sea level, ASL) and high-elevation (1700 m ASL) populations. We
 first measured traits at their elevation of origin and then transplanted
 half of each group to extreme high elevation (2900 m ASL; above the
 current elevational range limit of this species), where oxygen
 availability is reduced by ∼25% relative to sea level. After 3 weeks of
 acclimation, we again measured these traits in both the transplanted and
 control groups. The multivariate thermal–metabolic phenotypes of lizards
 originating from different elevations differed clearly when measured at
 the elevation of origin. For example, high-elevation lizards are more heat
 tolerant than their low-elevation counterparts (counter-gradient
 variation). Yet, these phenotypes converged after exposure to reduced
 oxygen availability at extreme high elevation, suggesting limited plastic
 responses under this novel constraint. Our results suggest that
 high-elevation populations are well suited to their oxygen environments,
 but that plasticity in the thermal–metabolic phenotype does not pre-adapt
 these populations to colonize more hypoxic environments at higher
 elevations.
DOI: 10.5061/dryad.dncjsxm17
title: Large and exaggerated sexually selected weapons comprise high proportions of metabolically inexpensive exoskeleton

description: The cost-minimization hypothesis proposes that positive allometry in
 sexually selected traits can be explained if the proportional energetic
 maintenance costs of weapons decrease as traits increase in size.
 Energetic maintenance costs are the costs of maintaining homeostasis. They
 are slow, persistent energy sinks that are distinct from ephemeral costs
 of growth. Because some tissues expend more energy on maintenance than
 others, energetic maintenance costs can be inferred from proportional
 tissue composition. For example, soft tissues require more energy for
 maintenance than exoskeleton, so an arthropod claw that is 50% soft tissue
 and 50% exoskeleton would have higher energetic maintenance costs than one
 that is 30% soft tissue and 70% exoskeleton. I tested the
 cost-minimization hypothesis using proportional tissue composition as a
 proxy for energetic maintenance costs in snapping shrimp ( Alpheus
 heterochaelis and Alpheus estuariensis ) and fiddler crabs ( Uca pugilator
 ). As predicted, larger weapons comprised proportionally less soft tissue
 mass and more exoskeleton mass than smaller weapons. Furthermore, I
 extended cost-minimization to explain trait exaggeration: individuals
 might exaggerate traits by investing more mass in exoskeleton. As
 predicted, exoskeleton mass proportional to weapon mass increased as
 exaggeration increased. These results support and extend the
 cost-minimization hypothesis to explain positive allometry and weapon
 exaggeration.
DOI: 10.5061/dryad.ksn02v75g
title: Data from: High methane emissions from an anoxic fjord driven by mixing and oxygenation

description: Tracking sources, sinks and long-term trends of methane emissions is
 imperative under climate change. Marine methane fluxes remain elusive and
 uncertain even though the ocean plays a major role in global budgets.
 High-latitude fjord ecosystems are widespread, store large amounts of
 sediment carbon, and undergo cycles of water column mixing, making them
 potential but still overlooked sources of methane to the atmosphere. Here,
 state-of-the-art benthic lander robots and multi annual observations
 revealed that anoxic fjords emit substantially more methane during mixing
 events than under water stratification. Fjords only cover 0.1% of global
 sea surface area, but may contribute as much methane as that released by
 the open ocean, which covers 84% of the global sea surface.
description: Data were collected using different methods. Salinity,
 temperature and oxygen (O2) were observed online with Seabird SBE911plus
 CTD and SBE43 oxygen sensors. Hydrogen sulfide (H2S) was analyzed
 according to Grasshoff et al. (2009). Methane (CH4) concentrations in the
 headspace were determined by GC analyses. Fluxes of dissolved inorganic
 carbon (DIC) in this dataset were extrapolated from Viktorsson et al.
 (2013). For more information regarding analyses and analytical equipment
 refer to the associated article and supporting information.
 References: Grasshoff K, Kremling K, Ehrhardt
 M (2009). Methods of seawater analysis. John Wiley &
 Sons. Viktorsson L, Kononets M, Roos P, Hall PO.
 Recycling and burial of phosphorus in sediments of an anoxic fjord—The By
 Fjord, western Sweden. J Mar Res 71: 351-374.(2013).
DOI: 10.5061/dryad.7d7wm37wp
title: Floral preferences of mountain bumble bees are constrained by functional traits but flexible through elevation and season

description: Patterns of resource use by animals can clarify how ecological communities
 have assembled in the past, how they currently function, and how they are
 likely to respond to future perturbations. Bumble bees (Hymentoptera:
 Bombus spp.) and their floral hosts provide a diverse yet tractable system
 in which to explore resource selection in the context of plant-pollinator
 networks. Under conditions of resource limitation, the ability of bumble
 bees species to coexist should depend on dietary niche overlap. In this
 study, we report patterns and dynamics of floral morphotype preferences in
 a mountain bumble bee community based on ~13,000 observations of bumble
 bee floral visits recorded along a 1400 m elevation gradient. We found
 that bumble bees are highly selective generalists, rarely visiting floral
 morphotypes at the rates predicted by their relative abundances.
 Preferences also differed markedly across bumble bee species, and these
 differences were well-explained by variation in bumble bee tongue length,
 generating patterns of preference similarity that should be expected to
 predict competition under conditions of resource limitation. Within
 species, though, morphotype preferences varied by elevation and season,
 possibly representing adaptive flexibility in response to the high
 elevational and seasonal turnover of mountain floral communities. Patterns
 of resource partitioning among bumble bee communities may determine which
 species can coexist under the altered distributions of bumble bees and
 their floral hosts caused by climate and land use change.
DOI: 10.5061/dryad.0zpc866zk
title: When expansion stalls: an extension to the concept of range pinning in ecology

description: Identifying the factors modulating range expansion is essential to
 accurately predict changes in the spatial distribution of populations. By
 preventing population growth after dispersal, Allee effects can lead to
 front stops in discrete space, called ’pinning’ if permanent. However,
 other mechanisms, such as positive density-dependent dispersal, have also
 been shown to affect the rate of range expansion and generate
 discrete-space front stops, albeit temporarily. In this study, we
 investigated the stability of the front stops generated by such mechanisms
 in relation to the carrying capacity of the environment. To this end, we
 performed artificial range expansions in discrete space using stochastic
 simulations and microcosm experiments. Simulation results confirmed that
 density-dependent dispersal alone can generate sustained front stops,
 albeit for a limited range of carrying capacities. We also highlighted the
 synergy between Allee effects and density-dependent dispersal on pinning
 emergence. Experimental results, obtained using a model species known to
 exhibit density-dependent dispersal, but without Allee effects, confirmed
 the model results. Furthermore, our study raises the issue of carefully
 considering the conditions for pinning stability, in a stochastic context
 and depending on the time-scale considered.
description: For "results_experiment.csv": this dataset corresponds
 to the experiment described in the article. All the information concerning
 the collection or processing of the data is present in the
 article. For "model.zip": the files
 correspond to the code used to run the simulations presented in the
 article. They have been specifically and entirely written for this
 article. The functioning of the underlying model is fully described in the
 article.
description: For "results_experiment.csv": The complete dataset is
 available, columns from P1 to P7 correspond to the population sizes in
 patches 1 to 7. The numbering used in the dataset is the same as the one
 presented in the article. For "model.zip" :
 the .R files placed in the "script" folder call functions from
 the file "simulation.r" in the "src" folder. They
 should be therefore used together. Each file in the "script"
 folder can be run independently. Simulate 100
 generations by running the following from the "model.zip"
 folder: Rscript script/simul_100_gen.r &lt;r&gt;
 &lt;rho&gt; &lt;tau&gt; &lt;alpha&gt;. The values
 between "&lt;&gt;" should be indicated, and are
 explained in the article. Simulate 10k generations by
 running the following from the "model.zip" folder: Rscript
 script/simul_10k_gen.r &lt;r&gt; &lt;rho&gt;
 &lt;tau&gt; &lt;alpha&gt;. The values between
 "&lt;&gt;" should be indicated, and are explained in the
 article.
DOI: 10.5061/dryad.8pk0p2npb
title: Echolocation clicks and anthropogenic detections with neural network labels in Hawaiian Island HARP data from Kona, Kaua`i, and Pearl and Hermes Reef

description: This dataset consists of echolocation clicks and detections of
 anthropogenic signals at three sites in the Hawaiian Islands Archipelago.
 These sites are Hawaii/Hawaii_K, Kauai/KA, and Pearl and Hermes
 Reef/PHR. Echolocation clicks were grouped into 5 minute bins, for which
 summary data is provided. Files are in .mat format that can be read using
 any desired coding language using a netcdf reading script. Files are
 separated by site, deployment, and neural network class (i.e.
 sitedeployment_cbins_class or site_deployment_cbins_class). Manual labels
 are provided.
description: A ReadMe file is included in the data as 'README.txt'
 and provides information about the data itself and the provided manual
 labels.
DOI: 10.6071/m3p39q
title: Mapping attitudes on wildlife trafficking: Implications for management and governance

description: Illegal wildlife trade or wildlife trafficking is a problem that affects
 societies and ecosystems alike. However, it remains unclear which
 management strategies are suitable for addressing this issue, particularly
 when one considers the diversity of actors, interests, and nuances of the
 problem. We argue that better management strategies require multiple – and
 at times, even opposite – actors to coalesce around the fundamentals of
 the problem. An initial step towards formulating management strategies is
 to identify how the multiple actors involved understand the problem and
 its possible solutions (i.e. their subjectivities). Although previous
 studies have addressed actors’ subjectivities regarding wildlife
 trafficking, they have rarely evaluated how subjectivities vary between
 different actors. Against this backdrop, this study uses mixed methods to
 evaluate convergences in the subjectivities of multiple actors (e.g.
 poachers, authorities, police forces and academics, among others) in
 Colombia. Contrary to previously-held theories, this work has revealed
 that trafficking-related subjectivities are not necessarily shaped by
 contextual factors (e.g. social relations); instead, subjectivities are
 explained by actors’ experiences and preferred governance forms. We
 conclude this work by reflecting on the implications of our findings for
 the management and governance of complex problems that occur at the
 intersection of social and ecological systems.
description: Each row corresponds to the question assessed. Columns correspond
 to individual actors. Authors names identify the region and the
 organization affiliation.
DOI: 10.5061/dryad.wpzgmsbnz
title: Modeling to determine when to re-open HIV services during COVID-19 pandemic

description: The Risks and Benefits of Providing HIV Services during the COVID-19
 Pandemic Introduction The COVID-19 pandemic has caused widespread
 disruptions including to health services. In the early response to the
 pandemic many countries restricted population movements and some health
 services were suspended or limited. In late 2020 and early 2021 some
 countries re-imposed restrictions. Health authorities need to balance the
 potential harms of additional SARS-CoV-2 transmission due to contacts
 associated with health services against the benefits of those services,
 including fewer new HIV infections and deaths. This paper examines these
 trade-offs for select HIV services.  Methods We used four HIV
 simulation models (Goals, HIV Synthesis, Optima HIV and EMOD) to estimate
 the benefits of continuing HIV services in terms of fewer new HIV
 infections and deaths. We used three COVID-19 transmission models
 (Covasim, Cooper/Smith and a simple contact model) to estimate the
 additional deaths due to SARS-CoV-2 transmission among health workers and
 clients. We examined four HIV services: voluntary medical male
 circumcision, HIV diagnostic testing, viral load testing and programs to
 prevent mother-to-child transmission. We compared COVID-19 deaths in 2020
 and 2021 with HIV deaths occurring now and over the next 50 years
 discounted to present value. The models were applied to countries with a
 range of HIV and COVID-19 epidemics. Results Maintaining these HIV
 services could lead to additional COVID-19 deaths of 0.002 to 0.15 per
 10,000 clients. HIV-related deaths averted are estimated to be much
 larger, 19 - 146 discounted deaths per 10,000 clients. Discussion While
 there is some additional short-term risk of SARS-CoV-2 transmission
 associated with providing HIV services, the risk of additional COVID-19
 deaths is at least 100 times less than the HIV deaths averted by those
 services. Ministries of Health need to take into account many factors in
 deciding when and how to offer essential health services during the
 COVID-19 pandemic. This work shows that the benefits of continuing key HIV
 services are far larger than the risks of additional SARS-CoV-2
 transmission.
description: The Excel file includes a model for estimating the impact of
 COVID and HIV on deaths as well as results from other complex
 mathermatical models applied to the same countries.
 Select the country of interest in the 'Country data'
 tab. See the results under each HIV intervention tab.
DOI: 10.5061/dryad.ksn02v75h
title: Rapid range expansion of a marine ectotherm reveals the demographic and ecological consequences of short-term variability in seawater temperature and dissolved oxygen

description: The distributions of marine ectotherms are governed by physiological
 sensitivities to long-term trends in seawater temperature and dissolved
 oxygen. Short-term variability in these parameters has the potential to
 facilitate rapid range expansions, and the resulting ecological and
 socioeconomic consequences may portend those of future marine communities.
 Here, we combine physiological experiments with ecological and demographic
 surveys to assess the causes and consequences of sudden but temporary
 poleward range expansions of a marine ectotherm with considerable life
 history plasticity (California market squid, Doryteuthis opalescens). We
 show that sequential factors related to resource accessibility in the core
 range may drive these expansions—the buildup of large populations due to
 competitive release, and climate-associated temperature increase and
 oxygen loss that constrain aerobic activity. We also reveal that poleward
 range expansion alters the body size—and therefore trophic role—of
 invading populations, with potential negative implications for
 socioeconomically valuable resident species. To help forecast rapid range
 expansions of marine ectotherms, we advocate that research efforts focus
 on factors impacting resource accessibility in core ranges. Determining
 how environmental conditions in receiving ecosystems affect body size, and
 how body size is related to trophic role, will help refine estimates of
 the impacts of future marine communities.
description: This excel file includes: envt_data_goa—seawater temperature
 trends in GOA determined from measurements reported by referenced data
 sources; abundance_data_goa—processed catch data of squid
 (presence/absence) in GOA from referenced data sources;
 pcrit_rmr_temp—critical oxygen partial pressures and routine metabolic
 rates for California market squid; pcrit_rmr_squid_metadata—metadata for
 squid specimens used in pcrit_rmr_temp; aerobic_scope—metabolic rates used
 for aerobic scope determination in California market squid, including
 those from referenced data sources; envt_data_ccs—seawater temperature and
 dissolved oxygen trends in CCS determined from measurements reported by
 referenced data sources; abundance_data_ccs—processed catch data of squid,
 anchovy, and sardine (counts) in CCS from referenced data sources;
 age_size_maturity_goa_ccs—age and size at maturity of California market
 squid in the GOA and CCS in 2016 and 2017; size_maturity_ccs_time—size at
 maturity of California market squid over the study period in the CCS;
 isotopes—carbon and nitrogen stable isotope data for GOA species,
 including those from referenced data sources;
 energy_density_proximal_comp—energy density, lipid content, and protein
 content data for GOA species, including those from referenced data
 sources.
DOI: 10.15468/dl.5bv2mp
title: Occurrence Download

description: A dataset containing 47750 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Asia",
 "Geometry POLYGON((106.75727 -6.09479,106.75857 -6.24066,106.90921 -6.23957,106.90618 -6.09283,106.75727 -6.09479))"
 ]
}

 The dataset includes 47750 records from 138 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003004-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.