Publications by authors named "Javier Cabello"

24 Publications

  • Page 1 of 1

A multiple-trait analysis of ecohydrological acclimatisation in a dryland phreatophytic shrub.

Oecologia 2021 Aug 31;196(4):1179-1193. Epub 2021 Jul 31.

Department of Biology and Geology, University of Almería, Carretera de Sacramento s.n, La Cañada de San Urbano, 04120, Almería, Spain.

Water is the main limiting factor for groundwater-dependent ecosystems (GDEs) in drylands. Predicted climate change (precipitation reductions and temperature increases) and anthropogenic activities such as groundwater drawdown jeopardise the functioning of these ecosystems, presenting new challenges for their management. We developed a trait-based analysis to examine the spatiotemporal variability in the ecophysiology of Ziziphus lotus, a long-lived phreatophyte that dominates one of the few terrestrial GDEs of semiarid regions in Europe. We assessed morpho-functional traits and stem water potential along a naturally occurring gradient of depth-to-groundwater (DTGW, 2-25 m) in a coastal aquifer, and throughout the species-growing season. Increasing DTGW and salinity negatively affected photosynthetic and transpiration rates, increasing plant water stress (lower predawn and midday water potential), and positively affected Huber value (sapwood cross-sectional area per leaf area), reducing leaf area and likely, plant hydraulic demand. However, the species showed greater salt-tolerance at shallow depths. Despite groundwater characteristics, higher atmospheric evaporative demand in the study area, which occurred in summer, fostered higher transpiration rates and water stress, and promoted carbon assimilation and water loss more intensively at shallow water tables. This multiple-trait analysis allowed us to identify plant ecophysiological thresholds related to the increase in salinity, but mostly in DTGW (13 m), and in the evaporative demand during the growing season. These findings highlight the existence of tipping points in the functioning of a long-lived phreatophyte in drylands and can contribute to the sustainable management of GDEs in southern Europe, paving the way for further studies on phreatophytic species.
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http://dx.doi.org/10.1007/s00442-021-04993-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8367881PMC
August 2021

Widespread Infection with Hemotropic Mycoplasmas in Free-Ranging Dogs and Wild Foxes Across Six Bioclimatic Regions of Chile.

Microorganisms 2021 Apr 24;9(5). Epub 2021 Apr 24.

Facultad de Ciencias de la Vida, Universidad Andres Bello, República 440, Santiago 8320000, Chile.

Blood samples of 626 rural dogs, 140 Andean foxes (), and 83 South American grey foxes () from six bioregions of Chile spanning 3000 km were screened for DNA by conventional PCR and sequencing. Risk factors of infection were inferred using Generalized Linear Mixed Models and genetic structure by network analyses. Overall, / (/) and Mycoplasma haematoparvum (Mhp) observed prevalence was 23.8% and 12.8% in dogs, 20.1% and 7.2% in Andean foxes, and 26.5% and 8.4% in grey foxes, respectively. Both hemoplasmas were confirmed in all the bioregions, with higher prevalence in those where ticks from the species group were absent. M. haematominutum and a sp. previously found in South American carnivores were detected in one fox each. Although the most prevalent and Mhp sequence types were shared between dogs and foxes, network analysis revealed genetic structure of between hosts in some regions. Male sex was associated with a higher risk of and Mhp infection in dogs, and adult age with Mhp infection, suggesting that direct transmission is relevant. No risk factor was identified in foxes. Our study provides novel information about canine hemoplasmas with relevance in distribution, transmission routes, and cross-species transmission.
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http://dx.doi.org/10.3390/microorganisms9050919DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8145368PMC
April 2021

Cross-species transmission of retroviruses among domestic and wild felids in human-occupied landscapes in Chile.

Evol Appl 2021 Apr 27;14(4):1070-1082. Epub 2021 Jan 27.

Instituto de Ecología y Biodiversidad (IEB) Santiago Chile.

Human transformation of natural habitats facilitates pathogen transmission between domestic and wild species. The guigna (), a small felid found in Chile, has experienced habitat loss and an increased probability of contact with domestic cats. Here, we describe the interspecific transmission of feline leukemia virus (FeLV) and feline immunodeficiency virus (FIV) between domestic cats and guignas and assess its correlation with human landscape perturbation. Blood and tissue samples from 102 free-ranging guignas and 262 domestic cats were collected and analyzed by PCR and sequencing. Guigna and domestic cat FeLV and FIV prevalence were very similar. Phylogenetic analysis showed guigna FeLV and FIV sequences are positioned within worldwide domestic cat virus clades with high nucleotide similarity. Guigna FeLV infection was significantly associated with fragmented landscapes with resident domestic cats. There was little evidence of clinical signs of disease in guignas. Our results contribute to the understanding of the implications of landscape perturbation and emerging diseases.
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http://dx.doi.org/10.1111/eva.13181DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8061269PMC
April 2021

Squandering water in drylands: the water-use strategy of the phreatophyte Ziziphus lotus in a groundwater-dependent ecosystem.

Am J Bot 2021 02 14;108(2):236-248. Epub 2021 Feb 14.

Department of Biology and Geology, Universidad de Almería, Carretera de Sacramento s.n, La Cañada de San Urbano, Almería, 04120, Spain.

Premise: Water is the most limiting factor in dryland ecosystems, and plants are adapted to cope with this constraint. Particularly vulnerable are phreatophytic plants from groundwater-dependent ecosystems (GDEs) in regions that have to face water regime alterations due to the impacts of climate and land-use changes.

Methods: We investigated two aspects related to the water-use strategy of a keystone species that dominates one of the few terrestrial GDEs in European drylands (Ziziphus lotus): where it obtains water and how it regulates its use. We (1) evaluated plants' water sources and use patterns using a multiple-isotope approach (δ H, δ O, and Δ C); (2) assessed the regulation of plant water potential by characterizing the species on an isohydric-anisohydric continuum; and (3) evaluated plants' response to increasing water stress along a depth-to-groundwater (DTGW) gradient by measuring foliar gas exchange and nutrient concentrations.

Results: Ziziphus lotus behaves as a facultative or partial phreatophyte with extreme anisohydric stomatal regulation. However, as DTGW increased, Z. lotus (1) reduced the use of groundwater, (2) reduced total water uptake, and (3) limited transpiration water loss while increasing water-use efficiency. We also found a physiological threshold at 14 m depth to groundwater, which could indicate maximum rooting length beyond which optimal plant function could not be sustained.

Conclusions: Species such as Z. lotus survive by squandering water in drylands because of a substantial groundwater uptake. However, the identification of DTGW thresholds indicates that drawdowns in groundwater level would jeopardize the functioning of the GDE.
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http://dx.doi.org/10.1002/ajb2.1606DOI Listing
February 2021

Mask R-CNN and OBIA Fusion Improves the Segmentation of Scattered Vegetation in Very High-Resolution Optical Sensors.

Sensors (Basel) 2021 Jan 5;21(1). Epub 2021 Jan 5.

Andalusian Center for Assessment and monitoring of global change (CAESCG), University of Almeria, 04120 Almeria, Spain.

Vegetation generally appears scattered in drylands. Its structure, composition and spatial patterns are key controls of biotic interactions, water, and nutrient cycles. Applying segmentation methods to very high-resolution images for monitoring changes in vegetation cover can provide relevant information for dryland conservation ecology. For this reason, improving segmentation methods and understanding the effect of spatial resolution on segmentation results is key to improve dryland vegetation monitoring. We explored and analyzed the accuracy of Object-Based Image Analysis (OBIA) and Mask Region-based Convolutional Neural Networks (Mask R-CNN) and the fusion of both methods in the segmentation of scattered vegetation in a dryland ecosystem. As a case study, we mapped , the dominant shrub of a habitat of conservation priority in one of the driest areas of Europe. Our results show for the first time that the fusion of the results from OBIA and Mask R-CNN increases the accuracy of the segmentation of scattered shrubs up to 25% compared to both methods separately. Hence, by fusing OBIA and Mask R-CNNs on very high-resolution images, the improved segmentation accuracy of vegetation mapping would lead to more precise and sensitive monitoring of changes in biodiversity and ecosystem services in drylands.
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http://dx.doi.org/10.3390/s21010320DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7796453PMC
January 2021

Identification of Novel Feline Paramyxoviruses in Guignas () from Chile.

Viruses 2020 12 6;12(12). Epub 2020 Dec 6.

Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, Avenida Fuchslocher 1305, Osorno 5290000, Chile.

The family of paramyxoviruses has received growing attention as several new species have been identified recently, notably two different clusters in domestic cats, designated as feline morbillivirus (FeMV) and feline paramyxovirus (FPaV). Their phylogenetic origin and whether wild felids also harbor these viruses are currently unknown. Kidney samples from 35 guignas (), a wild felid from Chile, were investigated for paramyxoviruses using consensus-RT-PCR. In addition, thirteen serum samples of guignas were screened for the presence of FeMV-specific antibodies by an immunofluorescence assay (IFA). Viral RNA was detected in 31% of the kidney samples. Phylogenetic analyses revealed two well-supported clusters, related to isolates from domestic cats, rodents and bats. No significant histopathology changes were recorded in infected guignas. Serology identified two samples which were positive for FeMV-specific antibodies. Our study highlights the diversity of paramyxovirus infections in felids with special emphasis on guignas from Chile.
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http://dx.doi.org/10.3390/v12121397DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7762136PMC
December 2020

Epidemiology and molecular characterization of Carnivore protoparvovirus-1 infection in the wild felid Leopardus guigna in Chile.

Transbound Emerg Dis 2020 Nov 25. Epub 2020 Nov 25.

Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, Osorno, Chile.

Landscape anthropization has been identified as one of the main drivers of pathogen emergence worldwide, facilitating pathogen spillover between domestic species and wildlife. The present study investigated Carnivore protoparvovirus-1 infection using molecular methods in 98 free-ranging wild guignas (Leopardus guigna) and 262 co-occurring owned, free-roaming rural domestic cats. We also assessed landscape anthropization variables as potential drivers of infection. Protoparvovirus DNA was detected in guignas across their entire distribution range, with observed prevalence of 13.3% (real-time PCR) and 9% (conventional PCR) in guignas, and 6.1% (conventional PCR) in cats. Prevalence in guigna did not vary depending on age, sex, study area or landscape variables. Prevalence was higher in juvenile cats (16.7%) than in adults (4.4%). Molecular characterization of the virus by amplification and sequencing of almost the entire vp2 gene (1,746 bp) from one guigna and five domestic cats was achieved, showing genetic similarities to canine parvovirus 2c (CPV-2c) (one guigna and one cat), feline panleukopenia virus (FPV) (one cat), CPV-2 (no subtype identified) (two cats), CPV-2a (one cat). The CVP-2c-like sequence found in a guigna clustered together with domestic cat and dog CPV-2c sequences from South America, suggesting possible spillover from a domestic to a wild species as the origin of infection in guigna. No clinical signs of disease were found in PCR-positive animals except for a CPV-2c-infected guigna, which had haemorrhagic diarrhoea and died a few days after arrival at a wildlife rescue centre. Our findings reveal widespread presence of Carnivore protoparvovirus-1 across the guigna distribution in Chile and suggest that virus transmission potentially occurs from domestic to wild carnivores, causing severe disease and death in susceptible wild guignas.
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http://dx.doi.org/10.1111/tbed.13937DOI Listing
November 2020

A forest-specialist carnivore in the middle of the desert?Comments on https://onlinelibrary.wiley.com/doi/full/10.1002/ece3.5230.

Ecol Evol 2020 Apr 25;10(8):3825-3830. Epub 2020 Mar 25.

Departamento de Ecología y Gestión Ambiental Centro Universitario Regional Este (CURE-Maldonado) Universidad de la República Maldonado Uruguay.

We present comments on an article recently published in Ecology and Evolution ("High-resolution melting of the cytochrome B gene in fecal DNA: A powerful approach for fox species identification of the genus in Chile") by Anabalon that reported the presence of Darwin's fox (), a temperate forest specialist, in the hyperarid Atacama Desert of northern Chile. We argue that this putative record lacks ecological support in light of ongoing research on this endangered species, and contains numerous methodological flaws and omissions related to the molecular identification of the species. Based on these issues, we suggest the scientific community and conservation decision-makers disregard the alleged presence of the Darwin's fox in the Atacama Desert.
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http://dx.doi.org/10.1002/ece3.6132DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7160171PMC
April 2020

Hemoplasmas Are Endemic and Cause Asymptomatic Infection in the Endangered Darwin's Fox (Lycalopex fulvipes).

Appl Environ Microbiol 2020 06 2;86(12). Epub 2020 Jun 2.

Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile.

is prevalent in the endangered Darwin's fox () in its main stronghold, Chiloé Island (Chile). The origin of the infection, its dynamics, its presence in other fox populations and the potential consequences for fox health remain unexplored. For 8 years, hemoplasmal DNA was screened and characterized in blood from 82 foxes in Chiloé and two other fox populations and in 250 free-ranging dogs from Chiloé. The prevalence of in foxes was constant during the study years, and coinfection with " Mycoplasma haematoparvum" was confirmed in 30% of the foxes. Both hemoplasma species were detected in the two mainland fox populations and in Chiloé dogs. was significantly more prevalent and more genetically diverse in foxes than in dogs. Two of the seven haplotypes identified were shared between these species. Network analyses did not show genetic structure by species (foxes versus dogs), geographic (island versus mainland populations), or temporal (years of study) factors. The probability of infection with increased with fox age but was not associated with sex, season, or degree of anthropization of individual fox habitats. Some foxes recaptured years apart were infected with the same haplotype in both events, and no hematological alterations were associated with hemoplasma infection, suggesting tolerance to the infection. Altogether, our results indicate that is enzootic in the Darwin's fox and that intraspecific transmission is predominant. Nevertheless, such a prevalent pathogen in a threatened species represents a concern that must be considered in conservation actions. is enzootic in Darwin's foxes. There is a higher genetic diversity and prevalence in foxes than in sympatric dogs, although haplotypes are shared between the two carnivore species. There is an apparent tolerance of Darwin's foxes to .
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http://dx.doi.org/10.1128/AEM.00779-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7267207PMC
June 2020

An interdisciplinary assessment of private conservation areas in the Western United States.

Ambio 2021 Jan 21;50(1):150-162. Epub 2020 Feb 21.

Social-Ecological Research Lab, Department of Biological Sciences, Idaho State University, 921 South 8th Avenue, Pocatello, ID, 83209, USA.

Conservation easements are the fastest growing private conservation strategy in the United States. However, mechanisms to assess private land conservation as well as their support by the general public are not well understood. This study uses the ecosystem services framework for assessing existing private lands in Idaho and identifies areas for future conservation easements. Using conservation targets of the land trust as a guide for selecting ecosystem services, we (a) mapped the spatial delivery of conservation targets across public and private lands, (b) explored public awareness in terms of social importance and vulnerability, and (c) mapped future priority areas by characterizing conservation bundles. We found that public lands provided the highest levels of conservation targets, and we found no difference in conservation target provision between private areas and conservation easements. The spatial characterization of conservation target bundles identified potential future priority areas for conservation easements, which can guide planning of land trust conservation efforts.
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http://dx.doi.org/10.1007/s13280-020-01323-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7708591PMC
January 2021

An Eight-Year Survey for Canine Distemper Virus Indicates Lack of Exposure in the Endangered Darwin's Fox ().

J Wildl Dis 2020 04 13;56(2):482-485. Epub 2019 Dec 13.

Facultad de Ciencias de la Vida, Universidad Andres Bello, República 252, Santiago, Chile.

No evidence of exposure to canine distemper virus (CDV) was detected in 70 samples corresponding to 58 wild-trapped Darwin's foxes () in Chile. Given its current endangered status and it being immunologically naïve, in the event of a CDV spillover from dogs to foxes, high population mortality is expected.
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http://dx.doi.org/10.7589/2019-08-195DOI Listing
April 2020

Antibiotic resistance genes as landscape anthropization indicators: Using a wild felid as sentinel in Chile.

Sci Total Environ 2020 Feb 1;703:134900. Epub 2019 Nov 1.

Instituto de Ecología y Biodiversidad (IEB), Santiago, Chile; Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, Osorno, Chile. Electronic address:

Antimicrobial resistance is a global emerging public health issue whose presence and impact in wildlife are widely unknown. Antimicrobial resistance genes (ARGs) are considered environmental contaminants, suitable to evaluate the degree of anthropic impact on wildlife and the environment. We used a wild felid, the guigna (Leopardus guigna), as a sentinel for the presence of ARGs in anthropized and pristine areas across their entire distribution range in Chile. We evaluated fecal samples from 51 wild guignas, collected between 2009 and 2018. Real-time PCR essays were employed to detect and quantify 22 selected ARGs in their fecal microbiome. All animals (100%) were positive for at least one ARG. The most prevalent ARG families were those that confer resistance to tetracycline (88.2%) and beta-lactamase (68.9%), with tet(Q) (60.8%), tet(W) (60.8%), and bla (66.7%) as the most prevalent ARGs. Multi-resistance profiles were observed in 43% of the guignas. Statistically significant differences were found between anthropized and pristine areas for tet(Q) (p = 0.014), tet(W) (p = 0.0037), tetracycline family (p = 0.027), multi-resistance profile prevalence (p = 0.043) and tet(W) quantification (p = 0.004). Two animals from anthropized landscapes were positive for mecA, a gene associated with Staphylococcus aureus and other staphylococci resistant to methicillin, while three animals from anthropized areas were positive for bla, that encodes class A extended-spectrum beta-lactamase. Both genes have been identified in bacteria causing relevant nosocomial infections worldwide. This is the first study on ARGs in wild felids from Chile and the first detection of mecA in South American wild felids. We observed an association between the degree of landscape anthropization and ARG prevalence, confirming that ARGs are important indicators of wildlife exposure to human activity/presence, with a widespread distribution.
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http://dx.doi.org/10.1016/j.scitotenv.2019.134900DOI Listing
February 2020

Six Collective Challenges for Sustainability of Almería Greenhouse Horticulture.

Int J Environ Res Public Health 2019 10 24;16(21). Epub 2019 Oct 24.

Department of Engineering, CIAMBITAL Research Centre, University of Almería, Carretera de Sacramento s/n, La Cañada, 04120 Almería, Spain.

Globally, current food consumption and trade are placing unprecedented demand on agricultural systems and increasing pressure on natural resources, requiring tradeoffs between food security and environmental impacts especially given the tension between market-driven agriculture and agro-ecological goals. In order to illustrate the wicked social, economic and environmental challenges and processes to find transformative solutions, we focus on the largest concentration of greenhouses in the world located in the semi-arid coastal plain of South-east Spain. Almería family farming, predominantly cooperative, greenhouse intensive production, commenced after the 1960s and has resulted in very significant social and economic benefits for the region, while also having important negative environmental and biodiversity impacts, as well as creating new social challenges. The system currently finds itself in a crisis of diminishing economic benefits and increasing environmental and social dilemmas. Here, we present the outcomes of multi-actor, transdisciplinary research to review and provide collective insights for solutions-oriented research on the sustainability of Almeria's agricultural sector. The multi-actor, transdisciplinary process implemented collectively, and supported by scientific literature, identified six fundamental challenges to transitioning to an agricultural model that aims to ameliorate risks and avoid a systemic collapse, whilst balancing a concern for profitability with sustainability: (1) Governance based on a culture of shared responsibility for sustainability, (2) Sustainable and efficient use of water, (3) Biodiversity conservation, (4) Implementing a circular economy plan, (5) Technology and knowledge transfer, and (6) Image and identity. We conclude that the multi-actor transdisciplinary approach successfully facilitated the creation of a culture of shared responsibility among public, private, academic, and civil society actors. Notwithstanding plural values, challenges and solutions identified by consensus point to a nascent acknowledgement of the strategic necessity to locate agricultural economic activity within social and environmental spheres.This paper demonstrates the need to establish transdisciplinary multi-actor work-schemes to continue collaboration and research for the transition to an agro-ecological model as a means to remain competitive and to create value.
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http://dx.doi.org/10.3390/ijerph16214097DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6862680PMC
October 2019

Molecular and serological survey of carnivore pathogens in free-roaming domestic cats of rural communities in southern Chile.

J Vet Med Sci 2019 Dec 15;81(12):1740-1748. Epub 2019 Oct 15.

Institute of Ecology and Biodiversity (IEB), Las Palmeras 3425, Ñuñoa, Santiago, Chile.

Owned, free-roaming domestic cats are abundant in the Chilean countryside, having high probability of contact with wildlife and potentially participating as reservoirs of zoonotic pathogens. In the present study, 131 cats from two remote study areas (Valdivia and Chiloe Island) in southern Chile were analyzed for infection/exposure to eight pathogens. Serum samples from 112 cats were tested for antigens against feline leukemia virus (FeLV antigen-ELISA) and antibodies against feline immunodeficiency virus (FIV-ELISA) and canine distemper virus (CDV-serum neutralization), yielded occurrence of 8.9, 1.7 and 0.8% respectively. The presence of DNA of five vector-borne pathogens, piroplasmids, Ehrlichia spp., Anaplasma spp., Rickettsia spp. and Bartonella spp. was investigated in thirty cats. Overall observed occurrence was 6.6% (2/30) for both Anaplasma platys, and B. henselae, and 3.3% (1/30) for both Bartonella sp. and Theileria equi. Observed occurrence for all vector-borne pathogens in Valdivia area was significantly higher than in Chiloe Island (5/15 vs 0/15; P=0.04). Our results represent the first description of exposure to CDV and DNA detection of T. equi and A. platys in domestic cats in Chile. The results highlight the importance of performing pathogen screening in owned, free-roaming rural cats to evaluate their potential role as reservoirs of infection and vectors for disease transmission to wildlife.
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http://dx.doi.org/10.1292/jvms.19-0208DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6943315PMC
December 2019

What is socio-ecological research delivering? A literature survey across 25 international LTSER platforms.

Sci Total Environ 2018 May 13;622-623:1225-1240. Epub 2017 Dec 13.

Research Institute for Nature and Forest (INBO), Kliniekstraat 25, 1070 Brussels, Belgium.

With an overarching goal of addressing global and regional sustainability challenges, Long Term Socio-Ecological Research Platforms (LTSER) aim to conduct place-based research, to collect and synthesize both environmental and socio-economic data, and to involve a broader stakeholder pool to set the research agenda. To date there have been few studies examining the output from LTSER platforms. In this study we enquire if the socio-ecological research from 25 self-selected LTSER platforms of the International Long-Term Ecological Research (ILTER) network has produced research products which fulfil the aims and ambitions of the paradigm shift from ecological to socio-ecological research envisaged at the turn of the century. In total we assessed 4983 publically available publications, of which 1112 were deemed relevant to the socio-ecological objectives of the platform. A series of 22 questions were scored for each publication, assessing relevance of responses in terms of the disciplinary focus of research, consideration of human health and well-being, degree of stakeholder engagement, and other relevant variables. The results reflected the diverse origins of the individual platforms and revealed a wide range in foci, temporal periods and quantity of output from participating platforms, supporting the premise that there is a growing trend in socio-ecological research at long-term monitoring platforms. Our review highlights the challenges of realizing the top-down goal to harmonize international network activities and objectives and the need for bottom-up, self-definition for research platforms. This provides support for increasing the consistency of LTSER research while preserving the diversity of regional experiences.
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http://dx.doi.org/10.1016/j.scitotenv.2017.11.324DOI Listing
May 2018

Ecological niche modeling re-examined: A case study with the Darwin's fox.

Ecol Evol 2018 May 16;8(10):4757-4770. Epub 2018 Apr 16.

Biodiversity Institute University of Kansas Lawrence KS USA.

Many previous studies have attempted to assess ecological niche modeling performance using receiver operating characteristic (ROC) approaches, even though diverse problems with this metric have been pointed out in the literature. We explored different evaluation metrics based on independent testing data using the Darwin's Fox () as a detailed case in point. Six ecological niche models (ENMs; generalized linear models, boosted regression trees, Maxent, GARP, multivariable kernel density estimation, and NicheA) were explored and tested using six evaluation metrics (partial ROC, Akaike information criterion, omission rate, cumulative binomial probability), including two novel metrics to quantify model extrapolation versus interpolation (E-space index I) and extent of extrapolation versus Jaccard similarity (E-space index II). Different ENMs showed diverse and mixed performance, depending on the evaluation metric used. Because ENMs performed differently according to the evaluation metric employed, model selection should be based on the data available, assumptions necessary, and the particular research question. The typical ROC AUC evaluation approach should be discontinued when only presence data are available, and evaluations in environmental dimensions should be adopted as part of the toolkit of ENM researchers. Our results suggest that selecting Maxent ENM based solely on previous reports of its performance is a questionable practice. Instead, model comparisons, including diverse algorithms and parameterizations, should be the for every study using ecological niche modeling. ENM evaluations should be developed using metrics that assess desired model characteristics instead of single measurement of fit between model and data. The metrics proposed herein that assess model performance in environmental space (i.e., E-space indices I and II) may complement current methods for ENM evaluation.
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http://dx.doi.org/10.1002/ece3.4014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5980497PMC
May 2018

Remote-sensing based approach to forecast habitat quality under climate change scenarios.

PLoS One 2017 3;12(3):e0172107. Epub 2017 Mar 3.

Andalusian Center for the Assessment and Monitoring of Global Change (CAESCG), University of Almería, Almería, Spain.

As climate change is expected to have a significant impact on species distributions, there is an urgent challenge to provide reliable information to guide conservation biodiversity policies. In addressing this challenge, we propose a remote sensing-based approach to forecast the future habitat quality for European badger, a species not abundant and at risk of local extinction in the arid environments of southeastern Spain, by incorporating environmental variables related with the ecosystem functioning and correlated with climate and land use. Using ensemble prediction methods, we designed global spatial distribution models for the distribution range of badger using presence-only data and climate variables. Then, we constructed regional models for an arid region in the southeast Spain using EVI (Enhanced Vegetation Index) derived variables and weighting the pseudo-absences with the global model projections applied to this region. Finally, we forecast the badger potential spatial distribution in the time period 2071-2099 based on IPCC scenarios incorporating the uncertainty derived from the predicted values of EVI-derived variables. By including remotely sensed descriptors of the temporal dynamics and spatial patterns of ecosystem functioning into spatial distribution models, results suggest that future forecast is less favorable for European badgers than not including them. In addition, change in spatial pattern of habitat suitability may become higher than when forecasts are based just on climate variables. Since the validity of future forecast only based on climate variables is currently questioned, conservation policies supported by such information could have a biased vision and overestimate or underestimate the potential changes in species distribution derived from climate change. The incorporation of ecosystem functional attributes derived from remote sensing in the modeling of future forecast may contribute to the improvement of the detection of ecological responses under climate change scenarios.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0172107PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5336225PMC
August 2017

Survey of infectious agents in the endangered Darwin's fox (Lycalopex fulvipes): high prevalence and diversity of hemotrophic mycoplasmas.

Vet Microbiol 2013 Dec 9;167(3-4):448-54. Epub 2013 Oct 9.

Instituto de Investigación en Recursos Cinegéticos, IREC (UCLM, CSIC, JCCM), Ronda de Toledo s/n, 13005 Ciudad Real, Spain; Centro de Conservación de la Biodiversidad, Chiloe-Silvestre, Las Américas 1060, Ancud, Chiloé, Chile.

Very little is known about the diseases affecting the Darwin's fox (Lycalopex fulvipes), which is considered to be one of the most endangered carnivores worldwide. Blood samples of 30 foxes captured on Chiloé Island (Chile) were tested with a battery of PCR assays targeting the following pathogens: Ehrlichia/Anaplasma sp., Rickettsia sp., Bartonella sp., Coxiella burnetti, Borrelia sp., Mycoplasma sp., Babesia sp., Hepatozoon canis, Hepatozoon felis, Leishmania donovani complex, and Filariae. Analysis of the 16S rRNA gene revealed the presence of Mycoplasma spp. in 17 samples (56.7%, 95% Confidence Intervals= 38.2-73.7). Of these, 15 infections were caused by a Mycoplasma belonging to the M. haemofelis/haemocanis (Mhf/Mhc) group, whereas two were caused by a Mycoplasma showing between 89% and 94% identity with different Candidatus Mycoplasma turicensis from felids and rodents hemoplasmas. The analysis of the sequence of the RNA subunit of the RNase P gene of 10 of the foxes positive for Mhf/Mhc showed that eight were infected with M. haemocanis (Mhc), one with a Mycoplasma showing 94% identity with Mhc, and one by M. haemofelis (Mhf). One of the foxes positive for Mhc was infected with a Ricketssia closely related to R. felis. All foxes were negative for the other studied pathogens. Our results are of interest because of the unexpectedly high prevalence of Mycoplasma spp. detected, the variability of species identified, the presence of a potentially new species of hemoplasma, and the first time a hemoplasma considered to be a feline pathogen (Mhf) has been identified in a canid. Though external symptoms were not observed in any of the infected foxes, further clinical and epidemiological studies are necessary to determine the importance of hemoplasma infection in this unique species.
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http://dx.doi.org/10.1016/j.vetmic.2013.09.034DOI Listing
December 2013

Borrelia chilensis, a new member of the Borrelia burgdorferi sensu lato complex that extends the range of this genospecies in the Southern Hemisphere.

Environ Microbiol 2014 Apr 27;16(4):1069-80. Epub 2013 Nov 27.

Department of Microbiology and Immunology, New York Medical College, Valhalla, New York, USA.

Borrelia burgdorferi sensu lato (s.l.), transmitted by Ixodes spp. ticks, is the causative agent of Lyme disease. Although Ixodes spp. ticks are distributed in both Northern and Southern Hemispheres, evidence for the presence of B. burgdorferi s.l. in South America apart from Uruguay is lacking. We now report the presence of culturable spirochetes with flat-wave morphology and borrelial DNA in endemic Ixodes stilesi ticks collected in Chile from environmental vegetation and long-tailed rice rats (Oligoryzomys longicaudatus). Cultured spirochetes and borrelial DNA in ticks were characterized by multilocus sequence typing and by sequencing five other loci (16S and 23S ribosomal genes, 5S-23S intergenic spacer, flaB, ospC). Phylogenetic analysis placed this spirochete as a new genospecies within the Lyme borreliosis group. Its plasmid profile determined by polymerase chain reaction and pulsed-field gel electrophoresis differed from that of B. burgdorferi B31A3. We propose naming this new South American member of the Lyme borreliosis group B. chilensis VA1 in honor of its country of origin.
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http://dx.doi.org/10.1111/1462-2920.12310DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3997230PMC
April 2014

Molecular identification of a novel gammaherpesvirus in the endangered Darwin's fox (Lycalopex fulvipes).

J Gen Virol 2013 Dec 17;94(Pt 12):2745-2749. Epub 2013 Sep 17.

Servei d'Ecopatologia de Fauna Salvatge (SEFaS) (Wildlife Diseases Research Group), Departament de Medicina i Cirurgia Animals, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.

We report the detection and characterization of a novel gammaherpesvirus in the critically endangered Darwin's fox (Lycalopex fulvipes; syn. Pseudalopex fulvipes) on Chiloé Island, Chile. Out of 28 analysed blood samples stored in alcohol, four were positive for this herpesvirus using a previously described pan-herpesvirus PCR assay targeting the herpesvirus DNA polymerase. Positive samples were subsequently characterized by means of a PCR targeting a 500 bp fragment of the glycoprotein B of the gammaherpesviruses. This novel herpesvirus was most closely related to other gammaherpesviruses from terrestrial carnivores, and is tentatively named Darwin's fox gammaherpesvirus. No apparent lesions were observed in the surveyed foxes. This is the first report of a gammaherpesvirus infecting a canid worldwide, and also of one infecting a carnivore from South America.
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http://dx.doi.org/10.1099/vir.0.057851-0DOI Listing
December 2013

Evaluating the consistency of the 1982-1999 NDVI trends in the Iberian Peninsula across four time-series derived from the AVHRR sensor: LTDR, GIMMS, FASIR, and PAL-II.

Sensors (Basel) 2010 8;10(2):1291-314. Epub 2010 Feb 8.

Departamento de Biología Vegetal y Ecología, Centro Andaluz para la Evaluación y Seguimiento del Cambio Global-CAESCG, Universidad de Almería, Ctra. Sacramento s/n. Almería, 04120, Spain.

Successive efforts have processed the Advanced Very High Resolution Radiometer (AVHRR) sensor archive to produce Normalized Difference Vegetation Index (NDVI) datasets (i.e., PAL, FASIR, GIMMS, and LTDR) under different corrections and processing schemes. Since NDVI datasets are used to evaluate carbon gains, differences among them may affect nations' carbon budgets in meeting international targets (such as the Kyoto Protocol). This study addresses the consistency across AVHRR NDVI datasets in the Iberian Peninsula (Spain and Portugal) by evaluating whether their 1982-1999 NDVI trends show similar spatial patterns. Significant trends were calculated with the seasonal Mann-Kendall trend test and their spatial consistency with partial Mantel tests. Over 23% of the Peninsula (N, E, and central mountain ranges) showed positive and significant NDVI trends across the four datasets and an additional 18% across three datasets. In 20% of Iberia (SW quadrant), the four datasets exhibited an absence of significant trends and an additional 22% across three datasets. Significant NDVI decreases were scarce (croplands in the Guadalquivir and Segura basins, La Mancha plains, and Valencia). Spatial consistency of significant trends across at least three datasets was observed in 83% of the Peninsula, but it decreased to 47% when comparing across the four datasets. FASIR, PAL, and LTDR were the most spatially similar datasets, while GIMMS was the most different. The different performance of each AVHRR dataset to detect significant NDVI trends (e.g., LTDR detected greater significant trends (both positive and negative) and in 32% more pixels than GIMMS) has great implications to evaluate carbon budgets. The lack of spatial consistency across NDVI datasets derived from the same AVHRR sensor archive, makes it advisable to evaluate carbon gains trends using several satellite datasets and, whether possible, independent/additional data sources to contrast.
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http://dx.doi.org/10.3390/s100201291DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3244014PMC
June 2012

Use of descriptors of ecosystem functioning for monitoring a national park network: a remote sensing approach.

Environ Manage 2009 Jan 15;43(1):38-48. Epub 2008 Jul 15.

Department of Environmental Sciences, University of Virginia, Clark Hall, 291, McCormick Road, Charlottesville, VA 22904, USA.

Baseline assessments and monitoring of protected areas are essential for making management decisions, evaluating the effectiveness of management practices, and tracking the effects of global changes. For these purposes, the analysis of functional attributes of ecosystems (i.e., different aspects of the exchange of matter and energy) has advantages over the traditional use of structural attributes, like a quicker response to disturbances and the fact that they are easily monitored through remote sensing. In this study, we described the spatiotemporal patterns of different aspects of the ecosystem functioning of the Spanish national parks and their response to environmental changes between 1982 and 2006. To do so, we used the NOAA/AVHRR-GIMMS dataset of the Normalized Difference Vegetation Index (NDVI), a linear estimator of the fraction of photosynthetic active radiation intercepted by vegetation, which is the main control of carbon gains. Nearly all parks have significantly changed during the last 25 years: The radiation interception has increased, the contrast between the growing and nongrowing seasons has diminished, and the dates of maximum and minimum interception have advanced. Some parks concentrated more changes than others and the degree of change varied depending on their different environmental conditions, management, and conservation histories. Our approach identified reference conditions and temporal changes for different aspects of ecosystem functioning, which can be used for management purposes of protected areas in response to global changes.
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http://dx.doi.org/10.1007/s00267-008-9154-yDOI Listing
January 2009

House staff attitudes about influenza vaccination after participation in a clinical trial to improve vaccination of hospital patients.

Infect Control Hosp Epidemiol 2008 Feb;29(2):174-6

Department of Medicine, Cook County Hospital, Chicago, Illinois, USA.

We surveyed house staff who had participated in a trial that compared influenza vaccination strategies for inpatients. House staff who were exposed to computer-generated vaccination orders were more likely to report that they recommended vaccination to their inpatients and outpatients, compared with house staff who were not exposed to a vaccination intervention. Also, house staff did not recognize pregnant women as a high-priority population for influenza vaccination.
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http://dx.doi.org/10.1086/526445DOI Listing
February 2008
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