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Article ; Online: Mapping global variation in dengue transmission intensity.

Cattarino, Lorenzo / Rodriguez-Barraquer, Isabel / Imai, Natsuko / Cummings, Derek A T / Ferguson, Neil M

2020 Volume 12, Issue 528

Abstract: Intervention planning for dengue requires reliable estimates of dengue transmission intensity. However, current maps of dengue risk provide estimates of disease burden or the boundaries of endemicity rather than transmission intensity. We therefore ... ...

Abstract	Intervention planning for dengue requires reliable estimates of dengue transmission intensity. However, current maps of dengue risk provide estimates of disease burden or the boundaries of endemicity rather than transmission intensity. We therefore developed a global high-resolution map of dengue transmission intensity by fitting environmentally driven geospatial models to geolocated force of infection estimates derived from cross-sectional serological surveys and routine case surveillance data. We assessed the impact of interventions on dengue transmission and disease using
MeSH term(s)	Basic Reproduction Number ; Cost of Illness ; Dengue/epidemiology ; Dengue/immunology ; Dengue/transmission ; Dengue/virology ; Dengue Vaccines/immunology ; Geography ; Humans ; Internationality ; Risk Factors
Chemical Substances	Dengue Vaccines
Language	English
Publishing date	2020-01-28
Publishing country	United States
Document type	Journal Article
ZDB-ID	2518854-9
ISSN	1946-6242 ; 1946-6234
ISSN (online)	1946-6242
ISSN	1946-6234
DOI	10.1126/scitranslmed.aax4144
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Article ; Online: Spatial scale and movement behaviour traits control the impacts of habitat fragmentation on individual fitness.

Cattarino, Lorenzo / McAlpine, Clive A / Rhodes, Jonathan R

The Journal of animal ecology

2016 Volume 85, Issue 1, Page(s) 168–177

Abstract: Habitat fragmentation, that is the breaking apart of habitat, can occur at multiple spatial scales at the same time, as a result of different land uses. Individuals of most species spend different amounts of times moving in different modes, during which ... ...

Abstract	Habitat fragmentation, that is the breaking apart of habitat, can occur at multiple spatial scales at the same time, as a result of different land uses. Individuals of most species spend different amounts of times moving in different modes, during which they cover different distances and experience different fitness impacts. The scale at which fragmentation occurs interacts with the distance that individuals move in a particular mode to affect an individual's ability to find habitat. However, there is little knowledge of the fitness consequences of different scales of fragmentation for individuals with different traits of movement behaviour. This is critical to understand the mechanisms of persistence of different species in fragmented landscapes. The aim of this study was to quantify the impacts of habitat fragmentation at different scales on the fitness components (reproduction and survival) of individuals with different traits of movement behaviour. We developed a demographic model of individuals that adopt short and tortuous movements within foraging areas (foraging mode) and long and straight movements between foraging areas (searching mode). We considered individuals that adopt different movement modes with varying frequencies, inherently move different searching distances and experience different risks of mortality during searching. We then applied the model within a spatially explicit simulation framework where we varied simultaneously the degree of fragmentation within (fine scale) and between foraging areas (coarse scale). Fine-scale fragmentation had a greater impact on reproduction and survival than coarse-scale fragmentation, for those individuals with a low searching propensity. The impact of fine-scale fragmentation on reproduction and survival interacted with the impact of coarse-scale fragmentation on reproduction and survival, to affect the fitness of individuals with a high searching propensity, large inherent searching distances and high searching mortality rates. Habitat selection strongly mitigated the impact of the scale at which fragmentation occurred on individual fitness. Our findings suggest that the land use to target with conservation actions to reduce fragmentation, such as financial schemes that promote re-vegetation or retention of standing vegetation, depends on the scale at which fragmentation occurs and the movement behaviour traits of the species of conservation concern.
MeSH term(s)	Animal Distribution ; Animals ; Appetitive Behavior ; Conservation of Natural Resources ; Ecosystem ; Feeding Behavior ; Homing Behavior ; Longevity ; Models, Biological ; Movement ; Reproduction
Language	English
Publishing date	2016-01
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	3024-7
ISSN	1365-2656 ; 0021-8790
ISSN (online)	1365-2656
ISSN	0021-8790
DOI	10.1111/1365-2656.12427
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Article: Information uncertainty influences conservation outcomes when prioritizing multi‐action management efforts

Cattarino, Lorenzo / Josie Carwardine / Mark J. Kennard / Simon Linke / Vanessa M. Adams / Virgilio Hermoso

Journal of applied ecology. 2018 Sept., v. 55, no. 5

2018

Abstract: In managing various threats to biodiversity, it is important to prioritize multiple management actions and the levels of effort to apply. However, a spatial conservation prioritization framework that integrates these key aspects, and can be generalized, ... ...

Abstract	In managing various threats to biodiversity, it is important to prioritize multiple management actions and the levels of effort to apply. However, a spatial conservation prioritization framework that integrates these key aspects, and can be generalized, is still missing. Moreover, assessing the robustness of prioritization frameworks to uncertainty in species responses to management is critical to avoid misallocation of limited resources. Yet, the impact of information uncertainty on prioritization of management effort remains unknown. We present an approach for prioritizing alternative levels of conservation management effort to multiple actions, based on the ecological responses of species to management. We estimated species responses through a structured email‐based expert elicitation process, where we also captured the uncertainty in individual experts' assessments. We identified priority locations and associated level of management of effort of four actions to abate threats to freshwater‐dependent fauna, using a northern Australia case study, and quantified sensitivity of the proposed solution to uncertainty in the answers of each individual expert. Achievement of conservation targets for freshwater‐dependent fauna in the Daly River catchment would require 9.4 million AU$ per year, for a total of approximately 189 million AU$ investment over 20 years. We suggest that this could be best achieved through a mix of aerial shooting of buffalos and pigs, riparian fencing and chemical spraying of weeds, applied at varying levels of management effort in key areas of the catchment. Uncertainty in experts' estimation of species responses to threats causes 60% of the species to achieve 80% of their conservation targets, which was consistent across target levels. Synthesis and applications. Our prioritization approach facilitates the planning of conservation management at fine spatial scales and is applicable to terrestrial, freshwater and marine realms. Plan implementation may require policy instruments ranging from landowner stewardship agreements, market‐based mechanisms and low‐intensity land use management schemes, to regulation of commercial activities within portions of marine protected areas. However, assessing plan sensitivity to uncertainty in species response to management and finding ways of dealing with it in the prioritization rather than ignoring it, as often done, remains vital for effective achievement of conservation objectives.
Keywords	biodiversity ; buffaloes ; case studies ; expert opinion ; experts ; fauna ; freshwater ; land use planning ; marine protected areas ; prioritization ; rivers ; spraying ; swine ; uncertainty ; watersheds ; weeds ; Australia
Language	English
Dates of publication	2018-09
Size	p. 2171-2180.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	410405-5
ISSN	1365-2664 ; 0021-8901
ISSN (online)	1365-2664
ISSN	0021-8901
DOI	10.1111/1365-2664.13147
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Article ; Online: Using next generation matrices to estimate the proportion of infections that are not detected in an outbreak.

Unwin, H Juliette T / Cori, Anne / Imai, Natsuko / Gaythorpe, Katy A M / Bhatia, Sangeeta / Cattarino, Lorenzo / Donnelly, Christl A / Ferguson, Neil M / Baguelin, Marc

Epidemics

2022 Volume 41, Page(s) 100637

Abstract: Contact tracing, where exposed individuals are followed up to break ongoing transmission chains, is a key pillar of outbreak response for infectious disease outbreaks. Unfortunately, these systems are not fully effective, and infections can still go ... ...

Abstract	Contact tracing, where exposed individuals are followed up to break ongoing transmission chains, is a key pillar of outbreak response for infectious disease outbreaks. Unfortunately, these systems are not fully effective, and infections can still go undetected as people may not remember all their contacts or contacts may not be traced successfully. A large proportion of undetected infections suggests poor contact tracing and surveillance systems, which could be a potential area of improvement for a disease response. In this paper, we present a method for estimating the proportion of infections that are not detected during an outbreak. Our method uses next generation matrices that are parameterized by linked contact tracing data and case line-lists. We validate the method using simulated data from an individual-based model and then investigate two case studies: the proportion of undetected infections in the SARS-CoV-2 outbreak in New Zealand during 2020 and the Ebola epidemic in Guinea during 2014. We estimate that only 5.26% of SARS-CoV-2 infections were not detected in New Zealand during 2020 (95% credible interval: 0.243 - 16.0%) if 80% of contacts were under active surveillance but depending on assumptions about the ratio of contacts not under active surveillance versus contacts under active surveillance 39.0% or 37.7% of Ebola infections were not detected in Guinea (95% credible intervals: 1.69 - 87.0% or 1.70 - 80.9%).
MeSH term(s)	Humans ; SARS-CoV-2 ; COVID-19/epidemiology ; Disease Outbreaks ; Contact Tracing/methods ; Hemorrhagic Fever, Ebola/diagnosis ; Hemorrhagic Fever, Ebola/epidemiology
Language	English
Publishing date	2022-10-06
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2467993-8
ISSN	1878-0067 ; 1755-4365
ISSN (online)	1878-0067
ISSN	1755-4365
DOI	10.1016/j.epidem.2022.100637
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Article: Correlations and variance among species traits explain contrasting impacts of fragmentation and habitat loss on functional diversity

Suárez-Castro, Andrés Felipe / Mayfield, Margaret M / Mitchell, Matthew G. E / Cattarino, Lorenzo / Maron, Martine / Rhodes, Jonathan R

Landscape ecology. 2020 Oct., v. 35, no. 10

2020

Abstract: CONTEXT: Understanding how landscape fragmentation affects functional diversity, defined as the distribution of functional traits in an assemblage, is critical for managing landscapes for biodiversity and ecosystem functions. Despite some scattered ... ...

Abstract	CONTEXT: Understanding how landscape fragmentation affects functional diversity, defined as the distribution of functional traits in an assemblage, is critical for managing landscapes for biodiversity and ecosystem functions. Despite some scattered evidence, we lack a clear understanding of how patterns of fragmentation drive changes in functional diversity, and its relationship with species richness as habitat is lost from a landscape. OBJECTIVES: To develop testable predictions about how landscape fragmentation, relative to the effects of habitat loss, impacts functional diversity and its relationship with species richness. METHODS: We used a spatially explicit metacommunity model that evaluates communities that vary in the distribution of response traits (traits involved in species responses to environmental change) and the correlation between response and effect traits (traits associated with species’ effects on ecosystem functioning). RESULTS: Compared to effects of habitat loss, relative effects of fragmentation on functional diversity increased as the variance in the distribution of response traits was high and the correlation among traits was high. Functional richness decreased faster than species richness in highly fragmented landscapes as habitat was lost. However, functional diversity remained unchanged or even increased in fragmented landscapes when either response and effect traits were not correlated (or weakly correlated), or when the proportion of generalist species with high dispersal capacities was high. CONCLUSIONS: Compared to effects of habitat loss, the relative effects of fragmentation on functional diversity and species richness are more dependent on the type of community evaluated. A careful evaluation of the variance in the distribution of response traits within a community, as well as the correlation among response and effect traits, can help to determine when it is important to manage landscape fragmentation to protect functional diversity.
Keywords	ecosystems ; functional diversity ; habitat destruction ; habitat fragmentation ; habitats ; landscape ecology ; landscapes ; models ; species richness ; variance
Language	English
Dates of publication	2020-10
Size	p. 2239-2253.
Publishing place	Springer Netherlands
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	1027798-5
ISSN	1572-9761 ; 0921-2973
ISSN (online)	1572-9761
ISSN	0921-2973
DOI	10.1007/s10980-020-01098-2
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Article ; Online: Temperature and population density influence SARS-CoV-2 transmission in the absence of nonpharmaceutical interventions.

Smith, Thomas P / Flaxman, Seth / Gallinat, Amanda S / Kinosian, Sylvia P / Stemkovski, Michael / Unwin, H Juliette T / Watson, Oliver J / Whittaker, Charles / Cattarino, Lorenzo / Dorigatti, Ilaria / Tristem, Michael / Pearse, William D

Proceedings of the National Academy of Sciences of the United States of America

2021 Volume 118, Issue 25

Abstract: As COVID-19 continues to spread across the world, it is increasingly important to understand the factors that influence its transmission. Seasonal variation driven by responses to changing environment has been shown to affect the transmission intensity ... ...

Abstract	As COVID-19 continues to spread across the world, it is increasingly important to understand the factors that influence its transmission. Seasonal variation driven by responses to changing environment has been shown to affect the transmission intensity of several coronaviruses. However, the impact of the environment on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remains largely unknown, and thus seasonal variation remains a source of uncertainty in forecasts of SARS-CoV-2 transmission. Here we address this issue by assessing the association of temperature, humidity, ultraviolet radiation, and population density with estimates of transmission rate (
MeSH term(s)	Basic Reproduction Number ; COVID-19/epidemiology ; COVID-19/prevention & control ; COVID-19/transmission ; Cold Temperature ; Communicable Disease Control/legislation & jurisprudence ; Forecasting ; Humans ; Movement ; Population Density ; SARS-CoV-2 ; Seasons ; United States/epidemiology
Language	English
Publishing date	2021-06-11
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2019284118
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Article ; Research data: (with research data) Catchment zoning for freshwater conservation: refining plans to enhance action on the ground

Hermoso, Virgilio / Cattarino, Lorenzo / Kennard, Mark J / Watts, Mathew / Linke, Simon / Mac Nally, Ralph

Journal of applied ecology. 2015 Aug., v. 52, no. 4

2015

Abstract: Recent advances in freshwater conservation planning allow addressing some of the specific needs of these systems. These include spatial connectivity or propagation of threats along stream networks, essential to ensure the maintenance of ecosystem ... ...

Abstract	Recent advances in freshwater conservation planning allow addressing some of the specific needs of these systems. These include spatial connectivity or propagation of threats along stream networks, essential to ensure the maintenance of ecosystem processes and the biodiversity they sustain. However, these peculiarities make conservation recommendations difficult to implement as they often require considering large areas that cannot be managed under conventional conservation schemes (e.g. strict protection). To facilitate the implementation of conservation in freshwater systems, a multizoning approach with different management zones subject to different management regimes was proposed. So far, this approach has only been used in post hoc exercises where zones were allocated using expert criteria. This might undermine the cost‐effectiveness of conservation recommendations, because both the allocation and extent of these zones have never been optimized using the principles of systematic planning. Here, we demonstrate how to create a catchment multizone plan by using a commonly applied tool in marine and terrestrial realms. We first test the capability of Marxan with Zones to address problems in rivers by using a simulated example and then apply the findings to a real case in the Daly River catchment, northern Australia. We also demonstrate how to address common conservation planning issues, such as accounting for threats or species‐specific connectivity needs in this multizone framework, and evaluate their effects on the spatial distribution and extent of different zones. We found that by prioritizing the allocation of zones subject to different management regimes, we could minimize the total area in need of strict conservation by a twofold factor. This reduction can be further reduced (threefold) when considering species’ connectivity needs. The integration of threats helped reduce the average threats of areas selected by a twofold factor. Synthesis and applications. Catchment zoning can help refine conservation recommendations and enhance cost‐effectiveness by prescribing different management regimes informed by ecological needs or distribution of threats. Reliable information on these factors is a key to ensure soundness of planning. Freely available software can be used to implement the approach we demonstrate here.
Keywords	biodiversity ; computer software ; cost effectiveness ; ecosystems ; freshwater ; planning ; rivers ; streams ; watersheds ; zoning ; Australia
Language	English
Dates of publication	2015-08
Size	p. 940-949.
Publishing place	Blackwell Scientific Publications
Document type	Article ; Research data
ZDB-ID	410405-5
ISSN	1365-2664 ; 0021-8901 ; 0021-8901
ISSN (online)	1365-2664
ISSN	0021-8901
DOI	10.1111/1365-2664.12454
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Article ; Online: Multi-action planning for threat management: a novel approach for the spatial prioritization of conservation actions.

Cattarino, Lorenzo / Hermoso, Virgilio / Carwardine, Josie / Kennard, Mark J / Linke, Simon

PloS one

2015 Volume 10, Issue 5, Page(s) e0128027

Abstract: Planning for the remediation of multiple threats is crucial to ensure the long term persistence of biodiversity. Limited conservation budgets require prioritizing which management actions to implement and where. Systematic conservation planning ... ...

Abstract	Planning for the remediation of multiple threats is crucial to ensure the long term persistence of biodiversity. Limited conservation budgets require prioritizing which management actions to implement and where. Systematic conservation planning traditionally assumes that all the threats in priority sites are abated (fixed prioritization approach). However, abating only the threats affecting the species of conservation concerns may be more cost-effective. This requires prioritizing individual actions independently within the same site (independent prioritization approach), which has received limited attention so far. We developed an action prioritization algorithm that prioritizes multiple alternative actions within the same site. We used simulated annealing to find the combination of actions that remediate threats to species at the minimum cost. Our algorithm also accounts for the importance of selecting actions in sites connected through the river network (i.e., connectivity). We applied our algorithm to prioritize actions to address threats to freshwater fish species in the Mitchell River catchment, northern Australia. We compared how the efficiency of the independent and fixed prioritization approach varied as the importance of connectivity increased. Our independent prioritization approach delivered more efficient solutions than the fixed prioritization approach, particularly when the importance of achieving connectivity was high. By spatially prioritizing the specific actions necessary to remediate the threats affecting the target species, our approach can aid cost-effective habitat restoration and land-use planning. It is also particularly suited to solving resource allocation problems, where consideration of spatial design is important, such as prioritizing conservation efforts for highly mobile species, species facing climate change-driven range shifts, or minimizing the risk of threats spreading across different realms.
MeSH term(s)	Algorithms ; Animal Distribution/physiology ; Animals ; Australia ; Climate Change ; Conservation of Natural Resources/economics ; Conservation of Natural Resources/methods ; Cost-Benefit Analysis ; Decision Making ; Endangered Species ; Fishes/physiology ; Rivers
Language	English
Publishing date	2015-05-28
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0128027
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Article: Accounting for continuous species' responses to management effort enhances cost-effectiveness of conservation decisions

Cattarino, Lorenzo / Virgilio Hermoso / Lindsay W. Bradford / Josie Carwardine / Kerrie A. Wilson / Mark J. Kennard / Simon Linke

Elsevier Ltd. Biological conservation. 2016 May, v. 197

2016

Abstract: Limited resources available for conservation require prioritizing location and level of conservation management efforts to abate threats to species. Ideally, the optimal level of management effort to allocate to an action should be informed by the ... ...

Abstract	Limited resources available for conservation require prioritizing location and level of conservation management efforts to abate threats to species. Ideally, the optimal level of management effort to allocate to an action should be informed by the species' responses to actions. This would enhance cost-effectiveness of conservation recommendations. How continuous species' responses to varying levels of management effort (‘species response curves’) affect the cost of abating threats to species is poorly understood, but critical for cost-effective threat management.We developed an optimization approach to prioritize management efforts based on varying species' response curves. We tested our framework in the Mitchell River catchment, northern Australia, to find the optimal level of effort to allocate to restoration of river connectivity and riparian revegetation to improve persistence of freshwater fish species. We compared the results of our analysis against a traditional approach, which assumes that (1) an action is either fully implemented or not; and (2) when the action is fully implemented the species persists; when the action is not implemented, the species goes locally extinct.We showed that by using species response curves we can abate threats to species at budgets up to 20% lower than when applying the traditional approach. Our approach can aid identifying how much effort (i.e., area managed, timeframe of management or budget invested) to allocate to multiple actions, and where, to cost-effectively abate threats to species. This has the potential to significantly improve biodiversity outcomes when resources are limited, by improving precision of on-ground conservation decisions.
Keywords	biodiversity ; cost effectiveness ; freshwater fish ; land restoration ; natural resources conservation ; rivers ; watersheds ; Australia
Language	English
Dates of publication	2016-05
Size	p. 116-123.
Publishing place	Elsevier Ltd
Document type	Article
ISSN	0006-3207
DOI	10.1016/j.biocon.2016.02.030
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Article: Land‐use drivers of forest fragmentation vary with spatial scale

Cattarino, Lorenzo / McAlpine, Clive A / Rhodes, Jonathan R

Global ecology and biogeography. 2014 Nov., v. 23, no. 11

2014

Abstract: AIM: Improving our understanding of the drivers of forest fragmentation is fundamental to mitigating the consequences of anthropogenic fragmentation for biodiversity. Moreover, the impacts of fragmentation on biodiversity depend on the spatial scale at ... ...

Abstract	AIM: Improving our understanding of the drivers of forest fragmentation is fundamental to mitigating the consequences of anthropogenic fragmentation for biodiversity. Moreover, the impacts of fragmentation on biodiversity depend on the spatial scale at which fragmentation occurs. Therefore, understanding how the effect of land use on fragmentation patterns varies across scales is critical to ensure that fragmentation is managed at scales relevant to the ecology of target species or to land management. Here, we quantified the influence of land use on patterns of forest fragmentation at different scales using Queensland, Australia, as a case study. LOCATION: North‐eastern Australia. METHODS: We combined fractal analysis with piecewise linear regression to measure patterns of forest fragmentation across a range of scales in 5309 landscapes of c. 50 km², with different proportions of land used for cropping and grazing. A significant change in fragmentation patterns occurred at approximately 1 km². We used beta regression to quantify the impact of land use on the degree of fragmentation at scales finer and coarser than 1 km². RESULTS: The use of land for grazing tended to create more fragmented forest patterns than use of land for cropping. This difference was more pronounced at coarser than finer scales. MAIN CONCLUSIONS: Our finding suggests that the choice of land use where conservation actions, such as revegetation and retention of forest patches, are to be prioritized depends on the scale at which we measure fragmentation. This information contributes to reducing the risk of mismatches between the scale at which fragmentation is managed and the scale at which fragmentation is measured, which is often dictated by the scale of species movements or the scale of land management. Our finding also improves our capacity to discern between fragmentation patterns that are typical of land‐sharing and land‐sparing conservation strategies, as spatial scale varies, thus aiding the implementation of land sparing and land sharing at scales relevant to biodiversity conservation and land management.
Keywords	biodiversity ; case studies ; forests ; grazing ; grazing lands ; habitat fragmentation ; land restoration ; land use ; landscapes ; linear models ; risk ; Queensland
Language	English
Dates of publication	2014-11
Size	p. 1215-1224.
Publishing place	Blackwell Science
Document type	Article
ZDB-ID	2021283-5
ISSN	1466-8238 ; 1466-822X ; 0960-7447
ISSN (online)	1466-8238
ISSN	1466-822X ; 0960-7447
DOI	10.1111/geb.12187
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