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Barkley YM, Merkens KPB, Wood M, Oleson EM, Marques TA. Click detection rate variability of central North Pacific sperm whales from passive acoustic towed arrays. J Acoust Soc Am 2024; 155:2627-2635. [PMID: 38629884 DOI: 10.1121/10.0025540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 03/19/2024] [Indexed: 04/19/2024]
Abstract
Passive acoustic monitoring (PAM) is an optimal method for detecting and monitoring cetaceans as they frequently produce sound while underwater. Cue counting, counting acoustic cues of deep-diving cetaceans instead of animals, is an alternative method for density estimation, but requires an average cue production rate to convert cue density to animal density. Limited information about click rates exists for sperm whales in the central North Pacific Ocean. In the absence of acoustic tag data, we used towed hydrophone array data to calculate the first sperm whale click rates from this region and examined their variability based on click type, location, distance of whales from the array, and group size estimated by visual observers. Our findings show click type to be the most important variable, with groups that include codas yielding the highest click rates. We also found a positive relationship between group size and click detection rates that may be useful for acoustic predictions of group size in future studies. Echolocation clicks detected using PAM methods are often the only indicator of deep-diving cetacean presence. Understanding the factors affecting their click rates provides important information for acoustic density estimation.
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Affiliation(s)
- Yvonne M Barkley
- Cooperative Institute for Marine and Atmospheric Research, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, Hawaii 96822, USA
| | | | - Megan Wood
- Saltwater Inc., Anchorage, Alaska 99501, USA
| | - Erin M Oleson
- Pacific Islands Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Honolulu, Hawaii 96818, USA
| | - Tiago A Marques
- Centre for Research into Ecological and Environmental Modelling, The Observatory, University of St Andrews, St Andrews, KY16 9LZ, Scotland
- Departamento de Biologia Animal, Centro de Estatística e Aplicações, Faculdade de Ciências da Universidade de Lisboa, Portugal
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Marques CS, Marques DA, Blackwell SB, Heide-Jørgensen MP, Malinka CE, Marques TA. Narwhal (Monodon monoceros) echolocation click rates to support cue counting passive acoustic density estimation. J Acoust Soc Am 2024; 155:891-900. [PMID: 38310606 DOI: 10.1121/10.0024723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 01/17/2024] [Indexed: 02/06/2024]
Abstract
Estimating animal abundance is fundamental for effective management and conservation. It is increasingly done by combining passive acoustics with knowledge about rates at which animals produce cues (cue rates). Narwhals (Monodon monoceros) are elusive marine mammals for which passive acoustic density estimation might be plausible, but for which cue rates are lacking. Clicking rates in narwhals were investigated using a dataset from sound and movement tag records collected in August 2013-2016 and 2019 in East Greenland. Clicking rates were quantified for ∼1200 one-second-long systematic random samples from 8 different whales. Generalized additive models were used to model (1) the probability of being in a clicking state versus depth and (2) the clicking rate while in a clicking state, versus time and depth. The probability of being in a clicking state increased with depth, reaching ∼1.0 at ∼500 m, while the number of clicks per second (while in a clicking state) increased with depth. The mean cue production rate, weighted by tag duration, was 1.28 clicks per second (se = 0.13, CV = 0.10). This first cue rate for narwhals may be used for cue counting density estimation, but care should be taken if applying it to other geographical areas or seasons, given sample size, geographical, and temporal limitations.
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Affiliation(s)
- Carolina S Marques
- Centro de Estatística e Aplicações, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal
| | - Diana A Marques
- Centro de Estatística e Aplicações, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal
| | - Susanna B Blackwell
- Greeneridge Sciences, Incorporated, 5142 Hollister Avenue, 283, Santa Barbara, California 93111, USA
| | | | - Chloe E Malinka
- Sea Mammal Research Unit Consulting, Scottish Oceans Institute, University of St Andrews, St Andrews, United Kingdom
| | - Tiago A Marques
- Centro de Estatística e Aplicações, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal
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Romagosa M, Nieukirk S, Cascão I, Marques TA, Dziak R, Royer JY, O'Brien J, Mellinger DK, Pereira A, Ugalde A, Papale E, Aniceto S, Buscaino G, Rasmussen M, Matias L, Prieto R, Silva MA. Fin whale song evolution in the North Atlantic. eLife 2024; 13:e83750. [PMID: 38192202 PMCID: PMC10776088 DOI: 10.7554/elife.83750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 12/01/2023] [Indexed: 01/10/2024] Open
Abstract
Animal songs can change within and between populations as the result of different evolutionary processes. When these processes include cultural transmission, the social learning of information or behaviours from conspecifics, songs can undergo rapid evolutions because cultural novelties can emerge more frequently than genetic mutations. Understanding these song variations over large temporal and spatial scales can provide insights into the patterns, drivers and limits of song evolution that can ultimately inform on the species' capacity to adapt to rapidly changing acoustic environments. Here, we analysed changes in fin whale (Balaenoptera physalus) songs recorded over two decades across the central and eastern North Atlantic Ocean. We document a rapid replacement of song INIs (inter-note intervals) over just four singing seasons, that co-occurred with hybrid songs (with both INIs), and a clear geographic gradient in the occurrence of different song INIs during the transition period. We also found gradual changes in INIs and note frequencies over more than a decade with fin whales adopting song changes. These results provide evidence of vocal learning in fin whales and reveal patterns of song evolution that raise questions on the limits of song variation in this species.
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Affiliation(s)
- Miriam Romagosa
- Institute of Marine Sciences - OKEANOS & Institute of Marine Research - IMAR, University of the AzoresHortaPortugal
| | - Sharon Nieukirk
- Cooperative Institute for Marine Ecosystem and Resources Studies, Oregon State UniversityCorvallisUnited States
| | - Irma Cascão
- Institute of Marine Sciences - OKEANOS & Institute of Marine Research - IMAR, University of the AzoresHortaPortugal
| | - Tiago A Marques
- Centre for Research into Ecological and Environmental Modelling, University of St AndrewsSt AndrewsUnited Kingdom
- Centro de Estatística e Aplicações, Departamento de Biologia, Faculdade de Ciências, Universidade de LisboaLisboaPortugal
| | - Robert Dziak
- NOAA Pacific Marine Environmental Laboratory, Hatfield Marine Science CenterCorvallisUnited States
| | - Jean-Yves Royer
- CNRS - UBO - UBS - Ifremer, IUEM - Lab. Geo-OceanPlouzaneFrance
| | - Joanne O'Brien
- Marine and Freshwater Research Centre (MFRC), Atlantic Technological UniversityGalwayIreland
| | - David K Mellinger
- Cooperative Institute for Marine Ecosystem and Resources Studies, Oregon State UniversityCorvallisUnited States
| | - Andreia Pereira
- Instituto Dom Luiz (IDL), Universidade de LisboaLisboaPortugal
| | | | - Elena Papale
- Institute for the Study of Anthropic Impacts and Sustainability in the Marine Environment of the National Research Council of Italy (CNR-IAS)Torretta GranitolaItaly
| | | | - Giuseppa Buscaino
- Institute for the Study of Anthropic Impacts and Sustainability in the Marine Environment of the National Research Council of Italy (CNR-IAS)Torretta GranitolaItaly
| | | | - Luis Matias
- Instituto Dom Luiz (IDL), Universidade de LisboaLisboaPortugal
| | - Rui Prieto
- Institute of Marine Sciences - OKEANOS & Institute of Marine Research - IMAR, University of the AzoresHortaPortugal
| | - Mónica A Silva
- Institute of Marine Sciences - OKEANOS & Institute of Marine Research - IMAR, University of the AzoresHortaPortugal
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Macaulay JDJ, Rojano-Doñate L, Ladegaard M, Tougaard J, Teilmann J, Marques TA, Siebert U, Madsen PT. Implications of porpoise echolocation and dive behaviour on passive acoustic monitoring. J Acoust Soc Am 2023; 154:1982-1995. [PMID: 37782119 DOI: 10.1121/10.0021163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 09/06/2023] [Indexed: 10/03/2023]
Abstract
Harbour porpoises are visually inconspicuous but highly soniferous echolocating marine predators that are regularly studied using passive acoustic monitoring (PAM). PAM can provide quality data on animal abundance, human impact, habitat use, and behaviour. The probability of detecting porpoise clicks within a given area (P̂) is a key metric when interpreting PAM data. Estimates of P̂ can be used to determine the number of clicks per porpoise encounter that may have been missed on a PAM device, which, in turn, allows for the calculation of abundance and ideally non-biased comparison of acoustic data between habitats and time periods. However, P̂ is influenced by several factors, including the behaviour of the vocalising animal. Here, the common implicit assumption that changes in animal behaviour have a negligible effect on P̂ between different monitoring stations or across time is tested. Using a simulation-based approach informed by acoustic biologging data from 22 tagged harbour porpoises, it is demonstrated that porpoise behavioural states can have significant (up to 3× difference) effects on P̂. Consequently, the behavioural state of the animals must be considered in analysis of animal abundance to avoid substantial over- or underestimation of the true abundance, habitat use, or effects of human disturbance.
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Affiliation(s)
- Jamie Donald John Macaulay
- Department of Biology-Zoophysiology, Aarhus University, C. F. Møllers Allé 3, building 1131, 8000 Aarhus C, Denmark
| | - Laia Rojano-Doñate
- Department of Biology-Zoophysiology, Aarhus University, C. F. Møllers Allé 3, building 1131, 8000 Aarhus C, Denmark
| | - Michael Ladegaard
- Department of Biology-Zoophysiology, Aarhus University, C. F. Møllers Allé 3, building 1131, 8000 Aarhus C, Denmark
| | - Jakob Tougaard
- Department of Ecoscience-Marine Mammal Research, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark
| | - Jonas Teilmann
- Department of Ecoscience-Marine Mammal Research, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark
| | - Tiago A Marques
- Centre for Research into Ecological and Environmental Modelling, University of St. Andrews, St. Andrews, Scotland, United Kingdom
| | - Ursula Siebert
- Department of Ecoscience-Marine Mammal Research, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark
| | - Peter Teglberg Madsen
- Department of Biology-Zoophysiology, Aarhus University, C. F. Møllers Allé 3, building 1131, 8000 Aarhus C, Denmark
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Marques TA, Marques CS, Gkikopoulou KC. A sperm whale cautionary tale about estimating acoustic cue rates for deep divers. J Acoust Soc Am 2023; 154:1577-1584. [PMID: 37698440 DOI: 10.1121/10.0020910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 08/22/2023] [Indexed: 09/13/2023]
Abstract
Passive acoustic density estimation has been gaining traction in recent years. Cue counting uses detected acoustic cues to estimate animal abundance. A cue rate, the number of acoustic cues produced per animal per unit time, is required to convert cue density into animal density. Cue rate information can be obtained from animal borne acoustic tags. For deep divers, like beaked whales, data have been analyzed considering deep dive cycles as a natural sampling unit, based on either weighted averages or generalized estimating equations. Using a sperm whale DTAG (sound-and-orientation recording tag) example we compare different approaches of estimating cue rate from acoustic tags illustrating that both approaches used before might introduce biases and suggest that the natural unit of analysis should be the whole duration of the tag itself.
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Affiliation(s)
- Tiago A Marques
- Centre for Research into Ecological and Environmental Modelling, The Observatory, University of St Andrews, St Andrews, KY16 9LZ, Scotland
| | - Carolina S Marques
- Centro de Estatística e Aplicações, Faculdade de Ciências da Universidade de Lisboa, Portugal
| | - Kalliopi C Gkikopoulou
- Centre for Research into Ecological and Environmental Modelling, The Observatory, University of St Andrews, St Andrews, KY16 9LZ, Scotland
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Arranz P, Miranda D, Gkikopoulou KC, Cardona A, Alcazar J, Aguilar de Soto N, Thomas L, Marques TA. Comparison of visual and passive acoustic estimates of beaked whale density off El Hierro, Canary Islands. J Acoust Soc Am 2023; 153:2469. [PMID: 37092951 DOI: 10.1121/10.0017921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 04/06/2023] [Indexed: 05/03/2023]
Abstract
Passive acoustic monitoring (PAM) offers considerable potential for density estimation of cryptic cetaceans, such as beaked whales. However, comparative studies on the accuracy of PAM density estimates from these species are lacking. Concurrent, low-cost drifting PAM, with SoundTraps suspended at 200 m depth, and land-based sightings, were conducted off the Canary Islands. Beaked whale density was estimated using a cue-count method, with click production rate and the probability of click detection derived from digital acoustic recording tags (DTags), and distance sampling techniques, adapted to fixed-point visual surveys. Of 32 870 detections obtained throughout 206 h of PAM recordings, 68% were classified as "certain" beaked whale clicks. Acoustic detection probability was 0.15 [coefficient variation (CV) 0.24] and click production rate was 0.46 clicks s - 1 (CV 0.05). PAM density estimates were in the range of 21.5 or 48.6 whales per 1000 km2 [CV 0.50 or 0.44, 95% confidence interval (CI) 20.7-22.4 or 47-50.9), depending on whether "uncertain" clicks were considered. Density estimates from concurrent sightings resulted in 33.7 whales per 1000 km2 (CV 0.77, 95% CI 8.9-50.5). Cue-count PAM methods under application provide reliable estimates of beaked whale density, over relatively long time periods and in realistic scenarios, as these match the concurrent density estimates obtained from visual observations.
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Affiliation(s)
- P Arranz
- BIOECOMAC, Departamento de Biología Animal, Edafología y Geología. Universidad de La Laguna. Avenida Astrofísico F. Sánchez, s/n. 38206 San Cristóbal de La Laguna, Tenerife, Spain
| | - D Miranda
- BIOECOMAC, Departamento de Biología Animal, Edafología y Geología. Universidad de La Laguna. Avenida Astrofísico F. Sánchez, s/n. 38206 San Cristóbal de La Laguna, Tenerife, Spain
| | - K C Gkikopoulou
- Sea Mammal Research Unit, Scottish Oceans Institute, University of St Andrews, KY16 8LB St Andrews, Scotland
| | - A Cardona
- Sea Mammal Research Unit, Scottish Oceans Institute, University of St Andrews, KY16 8LB St Andrews, Scotland
| | - J Alcazar
- BIOECOMAC, Departamento de Biología Animal, Edafología y Geología. Universidad de La Laguna. Avenida Astrofísico F. Sánchez, s/n. 38206 San Cristóbal de La Laguna, Tenerife, Spain
| | - N Aguilar de Soto
- BIOECOMAC, Departamento de Biología Animal, Edafología y Geología. Universidad de La Laguna. Avenida Astrofísico F. Sánchez, s/n. 38206 San Cristóbal de La Laguna, Tenerife, Spain
| | - L Thomas
- Centre for Research into Ecological and Environmental Modelling, University of St Andrews, KY16 8LB St Andrews, Scotland
| | - T A Marques
- Departamento de Biología Animal, Centro de Estatística e Aplicações, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Campo Grande, Lisboa, Portugal
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Carvalho JS, Stewart FA, Marques TA, Bonnin N, Pintea L, Chitayat A, Ingram R, Moore RJ, Piel AK. Spatio-temporal changes in chimpanzee density and abundance in the Greater Mahale Ecosystem, Tanzania. Ecol Appl 2022; 32:e2715. [PMID: 36178009 PMCID: PMC10078593 DOI: 10.1002/eap.2715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 02/23/2022] [Accepted: 06/16/2022] [Indexed: 06/16/2023]
Abstract
Species conservation and management require reliable information about animal distribution and population size. Better management actions within a species' range can be achieved by identifying the location and timing of population changes. In the Greater Mahale Ecosystem (GME), western Tanzania, deforestation due to the expansion of human settlements and agriculture, annual burning, and logging are known threats to wildlife. For one of the most charismatic species, the endangered eastern chimpanzee (Pan troglodytes schweinfurthii), approximately 75% of the individuals are distributed outside national park boundaries, requiring monitoring and protection efforts over a vast landscape of various protection statuses. These efforts are especially challenging when we lack data on trends in density and population size. To predict spatio-temporal chimpanzee density and abundance across the GME, we used density surface modeling, fitting a generalized additive model to a 10-year time-series data set of nest counts based on line-transect surveys. The chimpanzee population declined at an annual rate of 2.41%, including declines of 1.72% in riparian forests (from this point forward, forests), 2.05% in miombo woodlands (from this point forward, woodlands) and 3.45% in nonforests. These population declines were accompanied by ecosystem-wide declines in vegetation types of 1.36% and 0.32% per year for forests and woodlands, respectively; we estimated an annual increase of 1.35% for nonforests. Our model predicted the highest chimpanzee density in forests (0.86 chimpanzees/km2 , 95% confidence intervals (CIs) 0.60-1.23; as of 2020), followed by woodlands (0.19, 95% CI 0.12-0.30) and nonforests (0.18, 95% CI 0.10-1.33). Although forests represent only 6% of the landscape, they support nearly one-quarter of the chimpanzee population (769 chimpanzees, 95% CI 536-1103). Woodlands dominate the landscape (71%) and therefore support more than a half of the chimpanzee population (2294; 95% CI 1420-3707). The remaining quarter of the landscape is represented by nonforests and supports another quarter of the chimpanzee population (750; 95% CI 408-1381). Given the pressures on the remaining suitable habitat in Tanzania, and the need of chimpanzees to access both forest and woodland vegetation to survive, we urge future management actions to increase resources and expand the efforts to protect critical forest and woodland habitat and promote strategies and policies that more effectively prevent irreversible losses. We suggest that regular monitoring programs implement a systematic random design to effectively inform and allocate conservation actions and facilitate interannual comparisons for trend monitoring, measuring conservation success, and guiding adaptive management.
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Affiliation(s)
- Joana S. Carvalho
- School of Biological and Environmental SciencesLiverpool John Moores UniversityLiverpoolUK
- School of Built and Natural SciencesUniversity of DerbyDerbyUK
| | - Fiona A. Stewart
- School of Biological and Environmental SciencesLiverpool John Moores UniversityLiverpoolUK
- Greater Mahale Ecosystem Research and Conservation ProjectDar es SalaamTanzania
- Department of AnthropologyUniversity College LondonLondonUK
| | - Tiago A. Marques
- School of Mathematics and StatisticsUniversity of St. AndrewsSt. AndrewsUK
- Department of Animal BiologyFaculdade de Ciencias da Universidade de LisboaLisbonPortugal
| | - Noemie Bonnin
- School of Biological and Environmental SciencesLiverpool John Moores UniversityLiverpoolUK
| | - Lilian Pintea
- Department of Conservation ScienceThe Jane Goodall InstituteWashingtonDistrict of ColumbiaUSA
| | - Adrienne Chitayat
- Institute of Biodiversity and Ecosystem DynamicsUniversity of AmsterdamAmsterdamNetherlands
| | - Rebecca Ingram
- Greater Mahale Ecosystem Research and Conservation ProjectDar es SalaamTanzania
| | - Richard J. Moore
- School of Biological and Environmental SciencesLiverpool John Moores UniversityLiverpoolUK
| | - Alex K. Piel
- Greater Mahale Ecosystem Research and Conservation ProjectDar es SalaamTanzania
- Department of AnthropologyUniversity College LondonLondonUK
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Marques TA. Comment on: Premenstrual and menstrual changes reported after COVID-19 vaccination: The EVA project. Womens Health (Lond) 2022; 18:17455057221129395. [PMID: 36217634 PMCID: PMC9551668 DOI: 10.1177/17455057221129395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Tiago A Marques
- Centre for Research into Ecological and
Environmental Modelling, The Observatory, University of St Andrews, St Andrews,
UK,Centro de Estatística e Aplicações,
Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa,
Lisboa, Portugal,Tiago A Marques, Centre for Research into
Ecological and Environmental Modelling, The Observatory, University of St
Andrews, St Andrews KY16 9LZ, UK.
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Schwacke LH, Marques TA, Thomas L, Booth CG, Balmer BC, Barratclough A, Colegrove K, De Guise S, Garrison LP, Gomez FM, Morey JS, Mullin KD, Quigley BM, Rosel PE, Rowles TK, Takeshita R, Townsend FI, Speakman TR, Wells RS, Zolman ES, Smith CR. Modeling population effects of the Deepwater Horizon oil spill on a long-lived species. Conserv Biol 2022; 36:e13878. [PMID: 34918835 PMCID: PMC9545999 DOI: 10.1111/cobi.13878] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 10/22/2021] [Accepted: 12/10/2021] [Indexed: 06/01/2023]
Abstract
The 2010 Deepwater Horizon (DWH) oil spill exposed common bottlenose dolphins (Tursiops truncatus) in Barataria Bay, Louisiana to heavy oiling that caused increased mortality and chronic disease and impaired reproduction in surviving dolphins. We conducted photographic surveys and veterinary assessments in the decade following the spill. We assigned a prognostic score (good, fair, guarded, poor, or grave) for each dolphin to provide a single integrated indicator of overall health, and we examined temporal trends in prognostic scores. We used expert elicitation to quantify the implications of trends for the proportion of the dolphins that would recover within their lifetime. We integrated expert elicitation, along with other new information, in a population dynamics model to predict the effects of observed health trends on demography. We compared the resulting population trajectory with that predicted under baseline (no spill) conditions. Disease conditions persisted and have recently worsened in dolphins that were presumably exposed to DWH oil: 78% of those assessed in 2018 had a guarded, poor, or grave prognosis. Dolphins born after the spill were in better health. We estimated that the population declined by 45% (95% CI 14-74) relative to baseline and will take 35 years (95% CI 18-67) to recover to 95% of baseline numbers. The sum of annual differences between baseline and injured population sizes (i.e., the lost cetacean years) was 30,993 (95% CI 6607-94,148). The population is currently at a minimum point in its recovery trajectory and is vulnerable to emerging threats, including planned ecosystem restoration efforts that are likely to be detrimental to the dolphins' survival. Our modeling framework demonstrates an approach for integrating different sources and types of data, highlights the utility of expert elicitation for indeterminable input parameters, and emphasizes the importance of considering and monitoring long-term health of long-lived species subject to environmental disasters. Article impact statement: Oil spills can have long-term consequences for the health of long-lived species; thus, effective restoration and monitoring are needed.
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Affiliation(s)
| | - Tiago A. Marques
- Centre for Research into Ecological and Environmental Modelling (CREEM), University of St AndrewsThe ObservatoryLondonUK
| | - Len Thomas
- Centre for Research into Ecological and Environmental Modelling (CREEM), University of St AndrewsThe ObservatoryLondonUK
| | - Cormac G. Booth
- SMRU Consulting, Scottish Oceans Institute, East SandsUniversity of St AndrewsSt AndrewsUK
| | - Brian C. Balmer
- National Marine Mammal FoundationJohns IslandSouth CarolinaUSA
| | | | - Kathleen Colegrove
- Zoological Pathology Program, College of Veterinary MedicineUniversity of Illinois at Urbana‐ChampaignBrookfieldIllinoisUSA
| | - Sylvain De Guise
- Department of Pathobiology and Veterinary ScienceUniversity of ConnecticutStorrsConnecticutUSA
| | - Lance P. Garrison
- National Oceanic and Atmospheric Administration, National Marine Fisheries ServiceSoutheast Fisheries Science CenterMiamiFloridaUSA
| | | | | | - Keith D. Mullin
- National Oceanic and Atmospheric Administration, National Marine Fisheries ServiceSoutheast Fisheries Science CenterPascagoulaMississippiUSA
| | | | - Patricia E. Rosel
- National Oceanic and Atmospheric Administration, National Marine Fisheries ServiceSoutheast Fisheries Science CenterLafayetteLouisianaUSA
| | - Teresa K. Rowles
- National Oceanic and Atmospheric Administration, National Marine Fisheries ServiceOffice of Protected ResourcesSilver SpringMarylandUSA
| | - Ryan Takeshita
- National Marine Mammal FoundationJohns IslandSouth CarolinaUSA
| | | | | | - Randall S. Wells
- Chicago Zoological Society's Sarasota Dolphin Research Programc/o Mote Marine LaboratorySarasotaFloridaUSA
| | - Eric S. Zolman
- National Marine Mammal FoundationJohns IslandSouth CarolinaUSA
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Rycyk AM, Berchem C, Marques TA. Estimating Florida manatee (Trichechus manatus latirostris) abundance using passive acoustic methods. JASA Express Lett 2022; 2:051202. [PMID: 36154061 DOI: 10.1121/10.0010495] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Manatees are difficult to detect, particularly cryptic populations that inhabit areas with limited water clarity. The effectiveness of using vocal detections to estimate manatee abundance was evaluated in a clear water spring where manatees congregate seasonally. Vocalizations were extracted by a detection classifier that clustered sounds with similar spectral properties. Vocalization counts from recordings in Blue Spring, FL, USA were strong predictors of manatee abundance. The link between independent visual counts and abundance estimates from passive acoustic monitoring was used to provide an estimate of 1.059 (95% confidence interval 0.963-1.127) vocalizations/manatee/5-min, which might be used elsewhere for cue counting of manatees.
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Affiliation(s)
- Athena M Rycyk
- Division of Natural Sciences, New College of Florida, Sarasota, Florida 34243, USA
| | - Cora Berchem
- Save the Manatee Club, Maitland Florida 32751, USA
| | - Tiago A Marques
- Centre for Research into Ecological and Environmental Modelling, University of St Andrews, St Andrews, KY16 9LZ, Scotland ; ;
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Monteiro S, Rente D, Cunha MV, Marques TA, Cardoso E, Vilaça J, Coelho N, Brôco N, Carvalho M, Santos R. Discrimination and surveillance of infectious severe acute respiratory syndrome Coronavirus 2 in wastewater using cell culture and RT-qPCR. Sci Total Environ 2022; 815:152914. [PMID: 34999067 PMCID: PMC8733236 DOI: 10.1016/j.scitotenv.2022.152914] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/10/2021] [Accepted: 12/31/2021] [Indexed: 05/04/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA has been extensively detected in raw wastewater in studies exploring wastewater-based epidemiology (WBE) for early warning purposes. Nonetheless, only a few limited studies investigated the presence of SARS-CoV-2 in treated wastewaters to determine the potential health risks across the water cycle. The detection of SARS-CoV-2 has been done mostly by RT-qPCR and ddPCR, which only provides information on the presence of nucleic acids rather than information on potential infectivity. In this study, we set to develop and evaluate the use of viability RT-qPCR for the selective discrimination and surveillance of infectious SARS-CoV-2 in secondary-treated wastewater. Enzymatic (nuclease) and viability dye (Reagent D) pretreatments were applied to infer infectivity through RT-qPCR using porcine epidemic diarrhea virus (PEDV) as a CoV surrogate. Infectivity tests were first performed on PEDV purified RNA, then on infectious and heat-inactivated PEDV, and finally on heat inactivated PEDV spiked in concentrated secondary-treated wastewater. The two viability RT-qPCR methods were then applied to 27 secondary-treated wastewater samples positive for SARS-CoV-2 RNA at the outlet of five large urban wastewater treatment plants in Portugal. Reagent D pretreatment showed similar behavior to cell culture for heat-inactivated PEDV and both viability RT-qPCR methods performed comparably to VERO E6 cell culture for SARS-CoV-2 present in secondary-treated wastewater, eliminating completely the RT-qPCR signal. Our study demonstrated the lack of infectious SARS-CoV-2 viral particles on secondary-treated wastewater through the application of two pretreatment methods for the rapid inference of infectivity through RT-qPCR, showing their potential application in environmental screening. This study addressed a knowledge gap on the public health risks of SARS-CoV-2 across the water cycle.
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Affiliation(s)
- Silvia Monteiro
- Laboratorio de Análises, Tecnico Lisboa, Universidade de Lisboa, Lisboa, Portugal.
| | - Daniela Rente
- Laboratorio de Análises, Tecnico Lisboa, Universidade de Lisboa, Lisboa, Portugal
| | - Mónica V Cunha
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal; Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Tiago A Marques
- Centre for Research into Ecological and Environmental Modelling, The Observatory, University of St Andrews, St Andrews KY16 9LZ, Scotland; Centro de Estatística e Aplicações, Departamento de Biologia Ambiental, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Eugénia Cardoso
- Águas do Tejo Atlântico, Fábrica de Águas de Alcântara, Avenida de Ceuta, 1300-254 Lisboa, Portugal
| | - João Vilaça
- SIMDOURO, ETAR de Gaia Litoral, 4400-356 Canidelo, Portugal
| | | | - Nuno Brôco
- AdP VALOR, Serviços Ambientais, S.A., Rua Visconde de Seabra, 3, 1700-421 Lisboa, Portugal
| | - Marta Carvalho
- AdP VALOR, Serviços Ambientais, S.A., Rua Visconde de Seabra, 3, 1700-421 Lisboa, Portugal
| | - Ricardo Santos
- Laboratorio de Análises, Tecnico Lisboa, Universidade de Lisboa, Lisboa, Portugal
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12
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Monteiro S, Rente D, Cunha MV, Marques TA, Cardoso E, Álvaro P, Vilaça J, Ribeiro J, Silva M, Coelho N, Brôco N, Carvalho M, Santos R. Recovery of SARS-CoV-2 from large volumes of raw wastewater is enhanced with the inuvai R180 system. J Environ Manage 2022; 304:114296. [PMID: 34923418 PMCID: PMC8673751 DOI: 10.1016/j.jenvman.2021.114296] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 12/06/2021] [Accepted: 12/11/2021] [Indexed: 05/06/2023]
Abstract
Wastewater-based epidemiology (WBE) for severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) is a powerful tool to complement syndromic surveillance. Although detection of SARS-CoV-2 in raw wastewater may be prompted with good recoveries during periods of high community prevalence, in the early stages of population outbreaks concentration procedures are required to overcome low viral concentrations. Several methods have become available for the recovery of SARS-CoV-2 from raw wastewater, generally involving filtration. However, these methods are limited to small sample volumes, possibly missing the early stages of virus circulation, and restrained applicability across different water matrices. The aim of this study was thus to evaluate the performance of three methods enabling the concentration of SARS-CoV-2 from large volumes of wastewater: i) hollow fiber filtration using the inuvai R180, with an enhanced elution protocol and polyethylene glycol (PEG) precipitation; ii) PEG precipitation; and iii) skimmed milk flocculation. The performance of the three approaches was evaluated in wastewater from multiple wastewater treatment plants (WWTP) with distinct singularities, according to: i) effective volume; ii) percentage of recovery; iii) extraction efficiency; iv) inhibitory effect; and v) the limits of detection and quantification. The inuvai R180 system had the best performance, with detection of spiked control across all samples, with average recovery percentages of 68% for porcine epidemic diarrhea virus (PEDV), with low variability. Mean recoveries for PEG precipitation and skimmed milk flocculation were 9% and 14%, respectively. The inuvai R180 enables the scalability of volumes without negative impact on the costs, time for analysis, and recovery/inhibition. Moreover, hollow fiber ultrafilters favor the concentration of different microbial taxonomic groups. Such combined features make this technology attractive for usage in environmental waters monitoring.
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Affiliation(s)
- Silvia Monteiro
- Laboratorio de Análises, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal.
| | - Daniela Rente
- Laboratorio de Análises, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Mónica V Cunha
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisboa, Portugal; Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisboa, Portugal
| | - Tiago A Marques
- Centre for Research Into Ecological and Environmental Modelling, The Observatory, University of St Andrews, St Andrews, KY16 9LZ, Scotland, UK; Centro de Estatística e Aplicações, Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisboa, Portugal
| | - Eugénia Cardoso
- Águas Do Tejo Atlântico, Fábrica de Águas de Alcântara, Avenida de Ceuta, 1300-254, Lisboa, Portugal
| | - Pedro Álvaro
- Águas Do Tejo Atlântico, Fábrica de Águas de Alcântara, Avenida de Ceuta, 1300-254, Lisboa, Portugal
| | - João Vilaça
- SIMDOURO, ETAR de Gaia Litoral, 4400-356, Canidelo, Portugal
| | - Jorge Ribeiro
- SIMDOURO, ETAR de Gaia Litoral, 4400-356, Canidelo, Portugal
| | - Marco Silva
- Águas Do Norte, Lugar de Gaído, 4755-045, Barcelos, Portugal
| | - Norberta Coelho
- Águas Do Norte, Lugar de Gaído, 4755-045, Barcelos, Portugal
| | - Nuno Brôco
- AdP VALOR, Serviços Ambientais, S.A., Rua Visconde de Seabra, 3, 1700-421, Lisboa, Portugal
| | - Marta Carvalho
- AdP VALOR, Serviços Ambientais, S.A., Rua Visconde de Seabra, 3, 1700-421, Lisboa, Portugal
| | - Ricardo Santos
- Laboratorio de Análises, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
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Grilo ML, Amaro G, Chambel L, Marques CS, Marques TA, Gil F, Sousa-Santos C, Robalo JI, Oliveira M. Aeromonas spp. Prevalence, Virulence, and Antimicrobial Resistance in an Ex Situ Program for Threatened Freshwater Fish—A Pilot Study with Protective Measures. Animals (Basel) 2022; 12:ani12040436. [PMID: 35203144 PMCID: PMC8868083 DOI: 10.3390/ani12040436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/31/2022] [Accepted: 02/07/2022] [Indexed: 01/27/2023] Open
Abstract
Simple Summary Knowledge regarding best practices to prevent bacterial disease and antimicrobial resistance acquisition in aquatic ex situ programs is limited. This pilot study aimed to investigate the role of protective measures in the prevalence, antimicrobial resistance profiles, and virulence signatures of Aeromonas spp. in Portuguese nase (Iberochondrostoma lusitanicum) kept in an ex situ program. Fish were randomly divided into two tanks (i.e., with and without protective measures). Bacterial sampling was performed weekly for 5 weeks, and Aeromonas spp. prevalence, antimicrobial resistance, and virulence signatures were compared. We observed an increase in antimicrobial resistance among collected isolates over the experiment duration, with a trend of Aeromonas spp. prevalence and virulence decreasing when using protective measures. This pilot study sheds light on Aeromonas spp. prevalence, antimicrobial resistance, and virulence dynamics in aquatic ex situ programs, while constituting a first approach in the determination of the potential use of protective measures in such settings. Abstract Ex situ breeding programs are important conservation tools for endangered freshwater fish. However, developing husbandry techniques that decrease the likelihood of disease, antimicrobial resistance, and virulence determinants acquisition during this process is challenging. In this pilot study, we conducted a captivity experiment with Portuguese nase (Iberochondrostoma lusitanicum), a critically endangered leuciscid species, to investigate the influence of simple protective measures (i.e., material disinfection protocols and animal handling with gloves) on the dynamics of a potential pathogenic genus, Aeromonas, as well as its virulence profiles and antimicrobial resistance signatures. Our findings show that antimicrobial resistance in Aeromonas spp. collected from I. lusitanicum significantly increased during the extent of the assay (5 weeks), with all isolates collected at the end of the study classified as multidrug-resistant. Additionally, humans handling fishes without protective measures were colonized by Aeromonas spp. The use of protective measures suggested a decreasing trend in Aeromonas spp. prevalence in I. lusitanicum, while bacterial isolates displayed significantly lower virulence index values when virulence phenotypical expression was tested at 22 °C. Despite this study representing an initial trial, which needs support from further research, protective measures tested are considered a simple tool to be applied in ex situ breeding programs for aquatic animals worldwide. Furthermore, current results raise concern regarding antimicrobial resistance amplification and zoonotic transmission of Aeromonas spp. in aquatic ex situ programs.
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Affiliation(s)
- Miguel L. Grilo
- CIISA—Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, 1300-477 Lisbon, Portugal;
- MARE—Marine and Environmental Sciences Centre, ISPA—Instituto Universitário de Ciências Psicológicas, Sociais e da Vida, 1149-041 Lisbon, Portugal; (C.S.-S.); (J.I.R.)
- Correspondence: (M.L.G.); (M.O.)
| | - Guadalupe Amaro
- CIISA—Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, 1300-477 Lisbon, Portugal;
| | - Lélia Chambel
- BioISI—Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal;
| | - Carolina S. Marques
- Departamento de Biologia Animal, Centro de Estatística e Aplicações, Universidade de Lisboa, 1749-016 Lisbon, Portugal; (C.S.M.); (T.A.M.)
| | - Tiago A. Marques
- Departamento de Biologia Animal, Centro de Estatística e Aplicações, Universidade de Lisboa, 1749-016 Lisbon, Portugal; (C.S.M.); (T.A.M.)
- Centre for Research into Ecological & Environmental Modelling, University of St Andrews, St Andrews KY16 9LZ, UK
| | - Fátima Gil
- Aquário Vasco da Gama, 1495-718 Cruz Quebrada-Dafundo, Portugal;
| | - Carla Sousa-Santos
- MARE—Marine and Environmental Sciences Centre, ISPA—Instituto Universitário de Ciências Psicológicas, Sociais e da Vida, 1149-041 Lisbon, Portugal; (C.S.-S.); (J.I.R.)
| | - Joana I. Robalo
- MARE—Marine and Environmental Sciences Centre, ISPA—Instituto Universitário de Ciências Psicológicas, Sociais e da Vida, 1149-041 Lisbon, Portugal; (C.S.-S.); (J.I.R.)
| | - Manuela Oliveira
- CIISA—Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, 1300-477 Lisbon, Portugal;
- Correspondence: (M.L.G.); (M.O.)
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14
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Monteiro S, Rente D, Cunha MV, Gomes MC, Marques TA, Lourenço AB, Cardoso E, Álvaro P, Silva M, Coelho N, Vilaça J, Meireles F, Brôco N, Carvalho M, Santos R. A wastewater-based epidemiology tool for COVID-19 surveillance in Portugal. Sci Total Environ 2022; 804:150264. [PMID: 34798759 PMCID: PMC8432975 DOI: 10.1016/j.scitotenv.2021.150264] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/06/2021] [Accepted: 09/06/2021] [Indexed: 05/20/2023]
Abstract
The presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in wastewater produced interest in its use for sentinel surveillance at a community level and as a complementary approach to syndromic surveillance. With this work, we set the foundations for wastewater-based epidemiology (WBE) in Portugal by monitoring the trends of SARS-CoV-2 RNA circulation in the community, on a nationwide perspective during different epidemiological phases of the pandemic. The Charité assays (E_Sarbecco, RdRP, and N_Sarbecco) were applied to monitor, over 32-weeks (April to December 2020), the dynamics of SARS-CoV-2 RNA at the inlet of five wastewater treatment plants (WWTP), which together serve more than two million people in Portugal. Raw wastewater from three Coronavirus disease 2019 (COVID-19) reference hospitals was also analyzed during this period. In total, more than 600 samples were tested. For the first weeks, detection of SARS-CoV-2 RNA was sporadic, with concentrations varying from 103 to 105 genome copies per liter (GC/L). Prevalence of SARS-CoV-2 RNA increased steeply by the end of May into late June, mainly in Lisboa e Vale do Tejo region (LVT), during the reopening phase. After the summer, with the reopening of schools in mid-September and return to partial face-to-face work, a pronounced increase of SARS-CoV-2 RNA in wastewater was detected. In the LVT area, SARS-CoV-2 RNA load agreed with reported trends in hotspots of infection. Synchrony between trends of SARS-CoV-2 RNA in raw wastewater and daily new COVID-19 cases highlights the value of WBE as a surveillance tool, particularly after the phasing out of the epidemiological curve and when hotspots of disease re-emerge in the population which might be difficult to spot based solely on syndromic surveillance and contact tracing. This is the first study crossing several epidemiological stages highlighting the long-term use of WBE for SARS-CoV-2.
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Affiliation(s)
- Sílvia Monteiro
- Laboratorio de Análises, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal.
| | - Daniela Rente
- Laboratorio de Análises, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Mónica V Cunha
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal; Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Manuel Carmo Gomes
- Departamento de Biologia Vegetal, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Tiago A Marques
- Centre for Research into Ecological and Environmental Modelling, The Observatory, University of St Andrews, St Andrews KY16 9LZ, Scotland, United Kingdom; Centro de Estatística e Aplicações, Departamento de Biologia Ambiental, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Artur B Lourenço
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Eugénia Cardoso
- Águas do Tejo Atlântico, Fábrica de Águas de Alcântara, Avenida de Ceuta, 1300-254 Lisboa, Portugal
| | - Pedro Álvaro
- Águas do Tejo Atlântico, Fábrica de Águas de Alcântara, Avenida de Ceuta, 1300-254 Lisboa, Portugal
| | - Marco Silva
- Águas do Norte, Lugar de Gaído, 4755-045 Barcelos, Portugal
| | | | - João Vilaça
- SIMDOURO, ETAR de Gaia Litoral, 4400-356 Canidelo, Portugal
| | | | - Nuno Brôco
- AdP VALOR, Serviços Ambientais, S.A., Rua Visconde de Seabra, 3, 1700-421 Lisboa, Portugal
| | - Marta Carvalho
- AdP VALOR, Serviços Ambientais, S.A., Rua Visconde de Seabra, 3, 1700-421 Lisboa, Portugal
| | - Ricardo Santos
- Laboratorio de Análises, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
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15
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Hilário RR, Carvalho WD, Gheler-Costa C, Rosalino LMC, Marques TA, Adania CH, Paulino JS, Almeida PM, Mustin K. Drivers of human-wildlife impact events involving mammals in Southeastern Brazil. Sci Total Environ 2021; 794:148600. [PMID: 34198085 DOI: 10.1016/j.scitotenv.2021.148600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 06/16/2021] [Accepted: 06/18/2021] [Indexed: 06/13/2023]
Abstract
Annually millions of animals are killed as a result of human-wildlife impacts. Each year the NGO Associação Mata Ciliar (NGOMC), in Southeastern Brazil, receives and rehabilitates thousands of animals. We evaluated how natural and anthropogenic characteristics affect the risk of different types of human-wildlife impacts for mammals that arrive at the NGOMC; and explore the relationship between both the animal's size and the type of human-wildlife impact event, survival rates and the likelihood that these animals can be fully rehabilitated. To test our hypotheses regarding the drivers and consequences of the total number of human-wildlife impact events, traffic collisions, electrocutions, and requested removals, we used records of the mammals that arrived at the NGOMC between 2012 and 2018, and obtained data on environmental attributes and anthropogenic factors at the municipality level, as well as species weights. The total number of human-wildlife impact events and of requested removals were both positively correlated with deforestation rate and urban area. The number of traffic collisions was positively related to the number of fires. Municipalities with larger urban areas were more likely to have at least one electrocuted mammal. Temporally, the number of fires two months before was positively correlated with the number of human-wildlife impact events. Traffic collisions and electrocutions more frequently resulted in the death of the animal, than did other events. Animals that died were heavier on average than those that remained in captivity or were successfully released back into the wild. We conclude that human-wildlife impact event rates should decline with lower rates of deforestation, less anthropogenic fires and the adoption of other specific measures to avoid both traffic collisions with fauna and electrocutions.
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Affiliation(s)
- R R Hilário
- Postgraduate Program in Tropical Biodiversity, Federal University of Amapá, Macapá, AP, Brazil; Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal.
| | - W D Carvalho
- Postgraduate Program in Tropical Biodiversity, Federal University of Amapá, Macapá, AP, Brazil; Postgraduate Program in Environment and Biodiversity, Federal University of Grande Dourados, Dourados, MS, Brazil; Associação Mata Ciliar, Jundiaí, SP, Brazil
| | | | - L M C Rosalino
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - T A Marques
- Centre for Research into Ecological and Environmental Modelling & Centro de Estatística e Aplicações, Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Portugal
| | - C H Adania
- Associação Mata Ciliar, Jundiaí, SP, Brazil
| | | | | | - K Mustin
- Postgraduate Program in Animal Biology, Federal University of Pelotas, Pelotas, RS, Brazil
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Grilo ML, Chambel L, Marques TA, Sousa-Santos C, Robalo JI, Oliveira M. Sympatric threatened Iberian leuciscids exhibit differences in Aeromonas diversity and skin lesions' prevalence. PLoS One 2021; 16:e0255850. [PMID: 34352027 PMCID: PMC8341478 DOI: 10.1371/journal.pone.0255850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 07/23/2021] [Indexed: 11/18/2022] Open
Abstract
Assessments regarding health aspects of Iberian leuciscids are limited. There is currently an information gap regarding effects of infectious diseases on these populations and their role as a possible conservation threat. Moreover, differences in susceptibility to particular agents, such as Aeromonas spp., by different species/populations is not clear. To understand potential differences in Aeromonas diversity and load, as well as in the prevalence and proportion of skin lesions, in fishes exposed to similar environmental conditions, an observational study was implemented. Using a set of 12 individuals belonging to two sympatric Iberian leuciscid species (Squalius pyrenaicus and Iberochondrostoma lusitanicum), the skin lesion score in each individual was analyzed. Furthermore, a bacterial collection of Aeromonas spp. isolated from each individual was created and isolates' load was quantified by plate counting, identified at species level using a multiplex-PCR assay and virulence profiles established using classical phenotypic methods. The similarity relationships of the isolates were evaluated using a RAPD analysis. The skin lesion score was significantly higher in S. pyrenaicus, while the Aeromonas spp. load did not differ between species. When analyzing Aeromonas species diversity between fishes, different patterns were observed. A predominance of A. hydrophila was detected in S. pyrenaicus individuals, while I. lusitanicum individuals displayed a more diverse structure. Similarly, the virulence index of isolates from S. pyrenaicus was higher, mostly due to the isolated Aeromonas species. Genomic typing clustered the isolates mainly by fish species and skin lesion score. Specific Aeromonas clusters were associated with higher virulence indexes. Current results suggest potential differences in susceptibility to Aeromonas spp. at the fish species/individual level, and constitute important knowledge for proper wildlife management through the signalization of at-risk fish populations and hierarchization of conservation measures.
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Affiliation(s)
- Miguel L. Grilo
- CIISA–Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Lisbon, Portugal
- MARE–Marine and Environmental Sciences Centre, ISPA–Instituto Universitário de Ciências Psicológicas, Sociais e da Vida, Lisbon, Portugal
- * E-mail: (MLG); (MO)
| | - Lélia Chambel
- BioISI–Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Tiago A. Marques
- Departamento de Biologia Animal, Centro de Estatística e Aplicações, Universidade de Lisboa, Lisbon, Portugal
- Centre for Research into Ecological & Environmental Modelling, University of St Andrews, St Andrews, United Kingdom
| | - Carla Sousa-Santos
- MARE–Marine and Environmental Sciences Centre, ISPA–Instituto Universitário de Ciências Psicológicas, Sociais e da Vida, Lisbon, Portugal
| | - Joana I. Robalo
- MARE–Marine and Environmental Sciences Centre, ISPA–Instituto Universitário de Ciências Psicológicas, Sociais e da Vida, Lisbon, Portugal
| | - Manuela Oliveira
- CIISA–Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Lisbon, Portugal
- * E-mail: (MLG); (MO)
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17
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Romagosa M, Pérez-Jorge S, Cascão I, Mouriño H, Lehodey P, Pereira A, Marques TA, Matias L, Silva MA. Food talk: 40-Hz fin whale calls are associated with prey biomass. Proc Biol Sci 2021; 288:20211156. [PMID: 34229495 PMCID: PMC8261222 DOI: 10.1098/rspb.2021.1156] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 06/09/2021] [Indexed: 11/12/2022] Open
Abstract
Animals use varied acoustic signals that play critical roles in their lives. Understanding the function of these signals may inform about key life-history processes relevant for conservation. In the case of fin whales (Balaenoptera physalus), that produce different call types associated with different behaviours, several hypotheses have emerged regarding call function, but the topic still remains in its infancy. Here, we investigate the potential function of two fin whale vocalizations, the song-forming 20-Hz call and the 40-Hz call, by examining their production in relation to season, year and prey biomass. Our results showed that the production of 20-Hz calls was strongly influenced by season, with a clear peak during the breeding months, and secondarily by year, likely due to changes in whale abundance. These results support the reproductive function of the 20-Hz song used as an acoustic display. Conversely, season and year had no effect on variation in 40-Hz calling rates, but prey biomass did. This is the first study linking 40-Hz call activity to prey biomass, supporting the previously suggested food-associated function of this call. Understanding the functions of animal signals can help identifying functional habitats and predict the negative effects of human activities with important implications for conservation.
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Affiliation(s)
- Miriam Romagosa
- Okeanos – Instituto de Investigação em Ciências do Mar, Universidade dos Açores & IMAR – Instituto do Mar, Horta, Portugal
| | - Sergi Pérez-Jorge
- Okeanos – Instituto de Investigação em Ciências do Mar, Universidade dos Açores & IMAR – Instituto do Mar, Horta, Portugal
| | - Irma Cascão
- Okeanos – Instituto de Investigação em Ciências do Mar, Universidade dos Açores & IMAR – Instituto do Mar, Horta, Portugal
| | - Helena Mouriño
- Centro de Matemática, Aplicações Fundamentais e Investigação Operacional, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Patrick Lehodey
- Collecte Localisation Satellite (CLS), Ramonville St Agne, France
| | - Andreia Pereira
- Instituto Dom Luiz (IDL), Universidade de Lisboa, Lisboa, Portugal
| | - Tiago A. Marques
- Centro de Estatística e Aplicações, Departamento de Biologia, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
- Centre for Research into Ecological and Environmental Modelling, University of St Andrews, St Andrews, UK
| | - Luís Matias
- Instituto Dom Luiz (IDL), Universidade de Lisboa, Lisboa, Portugal
| | - Mónica A. Silva
- Okeanos – Instituto de Investigação em Ciências do Mar, Universidade dos Açores & IMAR – Instituto do Mar, Horta, Portugal
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Grilo ML, Isidoro S, Chambel L, Marques CS, Marques TA, Sousa-Santos C, Robalo JI, Oliveira M. Molecular Epidemiology, Virulence Traits and Antimicrobial Resistance Signatures of Aeromonas spp. in the Critically Endangered Iberochondrostoma lusitanicum Follow Geographical and Seasonal Patterns. Antibiotics (Basel) 2021; 10:759. [PMID: 34206643 PMCID: PMC8300795 DOI: 10.3390/antibiotics10070759] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 06/15/2021] [Accepted: 06/20/2021] [Indexed: 11/24/2022] Open
Abstract
Despite the fact that freshwater fish populations are experiencing severe declines worldwide, our knowledge on the interaction between endangered populations and pathogenic agents remains scarce. In this study, we investigated the prevalence and structure of Aeromonas communities isolated from the critically endangered Iberochondrostoma lusitanicum, a model species for threatened Iberian leuciscids, as well as health parameters in this species. Additionally, we evaluated the virulence profiles, antimicrobial resistance signatures and genomic relationships of the Aeromonas isolates. Lesion prevalence, extension and body condition were deeply affected by location and seasonality, with poorer performances in the dry season. Aeromonas composition shifted among seasons and was also different across river streams. The pathogenic potential of the isolates significantly increased during the dry season. Additionally, isolates displaying clinically relevant antimicrobial resistance phenotypes (carbapenem and fluroquinolone resistance) were detected. As it inhabits intermittent rivers, often reduced to disconnected pools during the summer, the dry season is a critical period for I. lusitanicum, with lower general health status and a higher potential of infection by Aeromonas spp. Habitat quality seems a determining factor on the sustainable development of this fish species. Also, these individuals act as reservoirs of important antimicrobial resistant bacteria with potential implications for public health.
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Affiliation(s)
- Miguel L. Grilo
- CIISA—Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, 1300-477 Lisbon, Portugal;
- MARE—Marine and Environmental Sciences Centre, ISPA—Instituto Universitário de Ciências Psicológicas, Sociais e da Vida, 1149-041 Lisbon, Portugal; (C.S.-S.); (J.I.R.)
| | - Sara Isidoro
- CIISA—Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, 1300-477 Lisbon, Portugal;
| | - Lélia Chambel
- BioISI—Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal;
| | - Carolina S. Marques
- Departamento de Biologia Animal, Centro de Estatística e Aplicações, Universidade de Lisboa, 1749-016 Lisbon, Portugal; (C.S.M.); (T.A.M.)
| | - Tiago A. Marques
- Departamento de Biologia Animal, Centro de Estatística e Aplicações, Universidade de Lisboa, 1749-016 Lisbon, Portugal; (C.S.M.); (T.A.M.)
- Centre for Research into Ecological & Environmental Modelling, University of St Andrews, St Andrews KY16 9LZ, UK
| | - Carla Sousa-Santos
- MARE—Marine and Environmental Sciences Centre, ISPA—Instituto Universitário de Ciências Psicológicas, Sociais e da Vida, 1149-041 Lisbon, Portugal; (C.S.-S.); (J.I.R.)
| | - Joana I. Robalo
- MARE—Marine and Environmental Sciences Centre, ISPA—Instituto Universitário de Ciências Psicológicas, Sociais e da Vida, 1149-041 Lisbon, Portugal; (C.S.-S.); (J.I.R.)
| | - Manuela Oliveira
- CIISA—Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, 1300-477 Lisbon, Portugal;
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Blackwell SB, Thode AM, Conrad AS, Ferguson MC, Berchok CL, Stafford KM, Marques TA, Kim KH. Estimating acoustic cue rates in bowhead whales, Balaena mysticetus, during their fall migration through the Alaskan Beaufort Sea. J Acoust Soc Am 2021; 149:3611. [PMID: 34241095 DOI: 10.1121/10.0005043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 05/05/2021] [Indexed: 06/13/2023]
Abstract
Eight years of passive acoustic data (2007-2014) from the Beaufort Sea were used to estimate the mean cue rate (calling rate) of individual bowhead whales (Balaena mysticetus) during their fall migration along the North Slope of Alaska. Calls detected on directional acoustic recorders (DASARs) were triangulated to provide estimates of locations at times of call production, which were then translated into call densities (calls/h/km2). Various assumptions were used to convert call density into animal cue rates, including the time for whales to cross the arrays of acoustic recorders, the population size, the fraction of the migration corridor missed by the localizing array system, and the fraction of the seasonal migration missed because recorders were retrieved before the end of the migration. Taking these uncertainties into account in various combinations yielded up to 351 cue rate estimates, which summarize to a median of 1.3 calls/whale/h and an interquartile range of 0.5-5.4 calls/whale/h.
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Affiliation(s)
- Susanna B Blackwell
- Greeneridge Sciences, Inc., 5266 Hollister Avenue, Santa Barbara, California 93111, USA
| | - Aaron M Thode
- Marine Physical Laboratory, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, USA
| | - Alexander S Conrad
- Greeneridge Sciences, Inc., 5266 Hollister Avenue, Santa Barbara, California 93111, USA
| | - Megan C Ferguson
- Marine Mammal Laboratory, Alaska Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 7600 Sand Point Way Northeast, Seattle, Washington 98115, USA
| | - Catherine L Berchok
- Marine Mammal Laboratory, Alaska Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 7600 Sand Point Way Northeast, Seattle, Washington 98115, USA
| | - Kathleen M Stafford
- Applied Physics Laboratory, University of Washington, Seattle, Washington 98105, USA
| | - Tiago A Marques
- Centre for Research into Ecological and Environmental Modelling, School of Mathematics and Statistics, University of St Andrews, The Observatory, Buchanan Gardens, St Andrews, Fife KY16 9LZ, Scotland
| | - Katherine H Kim
- Greeneridge Sciences, Inc., 5266 Hollister Avenue, Santa Barbara, California 93111, USA
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20
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Affiliation(s)
- Bárbara Cartagena‐Matos
- cE3c‐ Centre for Ecology Evolution and Environmental Changes Faculty of Sciences University of Lisbon Portugal
| | - Klervi Lugué
- Oceanic Observatory of Madeira (OOM) Funchal Portugal
| | - Paulo Fonseca
- cE3c‐ Centre for Ecology Evolution and Environmental Changes Faculty of Sciences University of Lisbon Portugal
| | - Tiago A. Marques
- Centre for Research into Ecological and Environmental Modelling University of St Andrews St Andrews UK
- Departamento de Biologia Animal Centro de Estatística e Aplicações Faculdade de Ciências da Universidade de Lisboa Lisboa Portugal
| | - Rui Prieto
- MARE – Marine and Environmental Sciences Centre of Azores Institute of Marine Research (IMAR) University of the AzoresPortugal
| | - Filipe Alves
- Oceanic Observatory of Madeira (OOM) Funchal Portugal
- MARE – Marine and Environmental Sciences Centre/ARDITI, Madeira Portugal
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21
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Gonçalves L, Turkman MAA, Geraldes C, Marques TA, Sousa L. COVID-19: Nothing is Normal in this Pandemic. J Epidemiol Glob Health 2021; 11:146-149. [PMID: 33605119 PMCID: PMC8242106 DOI: 10.2991/jegh.k.210108.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 12/12/2020] [Indexed: 01/12/2023] Open
Abstract
This manuscript brings attention to inaccurate epidemiological concepts that emerged during the COVID-19 pandemic. In social media and scientific journals, some wrong references were given to a “normal epidemic curve” and also to a “log-normal curve/distribution”. For many years, textbooks and courses of reputable institutions and scientific journals have disseminated misleading concepts. For example, calling histogram to plots of epidemic curves or using epidemic data to introduce the concept of a Gaussian distribution, ignoring its temporal indexing. Although an epidemic curve may look like a Gaussian curve and be eventually modelled by a Gauss function, it is not a normal distribution or a log-normal, as some authors claim. A pandemic produces highly-complex data and to tackle it effectively statistical and mathematical modelling need to go beyond the “one-size-fits-all solution”. Classical textbooks need to be updated since pandemics happen and epidemiology needs to provide reliable information to policy recommendations and actions.
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Affiliation(s)
- Luzia Gonçalves
- Global Health and Tropical Medicine, Unidade de Saúde Pública Internacional e Bioestatística, Instituto de Higiene e Medicina Tropical, Universidade NOVA de Lisboa, Rua da Junqueira 100, Lisboa 1349-008, Portugal.,CEAUL - Centro de Estatística e Aplicações, Faculdade de Ciências, Universidade de Lisboa, Portugal
| | | | - Carlos Geraldes
- CEAUL - Centro de Estatística e Aplicações, Faculdade de Ciências, Universidade de Lisboa, Portugal.,ISEL - Instituto Superior de Engenharia de Lisboa - Instituto Politécnico de Lisboa, Portugal
| | - Tiago A Marques
- CEAUL - Centro de Estatística e Aplicações, Faculdade de Ciências, Universidade de Lisboa, Portugal.,Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Portugal.,Centre for Research into Ecological and Environmental Modelling, The Observatory, University of St Andrews, Scotland
| | - Lisete Sousa
- CEAUL - Centro de Estatística e Aplicações, Faculdade de Ciências, Universidade de Lisboa, Portugal.,Departamento de Estatística e Investigação Operacional, Faculdade de Ciências, Universidade de Lisboa, Portugal
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22
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Carvalho C, Peste F, Marques TA, Knight A, Vicente LM. The Contribution of Rat Studies to Current Knowledge of Major Depressive Disorder: Results From Citation Analysis. Front Psychol 2020; 11:1486. [PMID: 32765345 PMCID: PMC7381216 DOI: 10.3389/fpsyg.2020.01486] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 06/03/2020] [Indexed: 12/28/2022] Open
Abstract
Major depressive disorder (MDD) is the most severe depression type and one of the leading causes of morbidity worldwide. Animal models are widely used to understand MDD etiology, pathogenesis, and treatment, but the efficacy of this research for patients has barely been systematically evaluated. Such evaluation is important given the resource consumption and ethical concerns incurred by animal use. We used the citation tracking facilities within Web of Science and Scopus to locate citations of original research papers on rats related to MDD published prior to 2013—to allow adequate time for citations—identified in PubMed and Scopus by relevant search terms. Resulting citations were thematically coded in eight categories, and descriptive statistics were calculated. 178 publications describing relevant rat studies were identified. They were cited 8,712 times. More than half (4,633) of their citations were by other animal studies. 794 (less than 10%) were by human medical papers. Citation analysis indicates that rat model research has contributed very little to the contemporary clinical understanding of MDD. This suggests a misuse of limited funding hence supporting a change in allocation of research and development funds targeting this disorder to maximise benefits for patients.
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Affiliation(s)
- Constança Carvalho
- Centro de Filosofia das Ciências da Universidade de Lisboa (CFCUL), Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal
| | - Filipa Peste
- Centre for Environmental and Marine Studies, Departamento de Biologia, Universidade de Aveiro, Aveiro, Portugal
| | - Tiago A Marques
- Centre for Research into Ecological and Environmental Modelling, Departamento de Biologia Animal, Centro de Estatística e Aplicações, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Andrew Knight
- Centre for Animal Welfare, University of Winchester, Winchester, United Kingdom
| | - Luís M Vicente
- Centro de Filosofia das Ciências da Universidade de Lisboa (CFCUL), Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal
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Carvalho C, Varela SAM, Marques TA, Knight A, Vicente L. Are in vitro and in silico approaches used appropriately for animal-based major depressive disorder research? PLoS One 2020; 15:e0233954. [PMID: 32579547 PMCID: PMC7313753 DOI: 10.1371/journal.pone.0233954] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 05/11/2020] [Indexed: 11/18/2022] Open
Abstract
The current paradigm for biomedical research and drug testing postulates that in vitro and in silico data inform animal studies that will subsequently inform human studies. Recent evidence points out that animal studies have made a poor contribution to current knowledge of Major Depressive Disorder, whereas the contribution of in vitro and in silico studies to animal studies- within this research area- is yet to be properly quantified. This quantification is important since biomedical research and drug discovery and development includes two steps of knowledge transferability and we need to evaluate the effectiveness of both in order to properly implement 3R principles (Replacement, Reduction and Refinement). Here, we used the citation tracking facility within Web of Science to locate citations of original research papers on in vitro and in silico related to MDD published identified in PubMed by relevant search terms. 67 publications describing target papers were located. Both in vitro and in silico papers are more cited by human medical papers than by animal papers. The results suggest that, at least concerning MDD research, the current two steps of knowledge transferability are not being followed, indicating a poor compliance with the 3R principles.
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Affiliation(s)
- Constança Carvalho
- Faculdade de Ciências, Centro de Filosofia das Ciências, Universidade de Lisboa, Lisboa, Portugal
- * E-mail:
| | - Susana A. M. Varela
- Faculdade de Ciências, cE3c – Centre for Ecology, Evolution and Environmental Changes, Universidade de Lisboa, Lisboa, Portugal
| | - Tiago A. Marques
- Centre for Research into Ecological and Environmental Modelling, University of St Andrews, St Andrews, Scotland
- Departamento de Biologia Animal, Faculdade de Ciências, Centro de Estatística e Aplicações, Universidade de Lisboa, Lisboa, Portugal
| | - Andrew Knight
- Centre for Animal Welfare, University of Winchester, Winchester, United Kingdom
| | - Luís Vicente
- Faculdade de Ciências, Centro de Filosofia das Ciências, Universidade de Lisboa, Lisboa, Portugal
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24
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Romagosa M, Baumgartner M, Cascão I, Lammers MO, Marques TA, Santos RS, Silva MA. Author Correction: Baleen whale acoustic presence and behaviour at a Mid-Atlantic migratory habitat, the Azores Archipelago. Sci Rep 2020; 10:6087. [PMID: 32242074 PMCID: PMC7118157 DOI: 10.1038/s41598-020-63117-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Miriam Romagosa
- Institute of Marine Research (IMAR) and Okeanos R & D Centre, University of the Azores, Horta, Portugal.
| | - Mark Baumgartner
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Irma Cascão
- Institute of Marine Research (IMAR) and Okeanos R & D Centre, University of the Azores, Horta, Portugal
| | - Marc O Lammers
- NOAA's Hawaiian Island Humpback Whale National Marine Sanctuary, Kihei, HI, USA and Oceanwide Science Institute, Honolulu, HI, USA
| | - Tiago A Marques
- Centre for Research into Ecological and Environmental Modelling, University of St. Andrews, St. Andrews, UK and Centro de Estatística e Aplicações, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
| | - Ricardo S Santos
- Institute of Marine Research (IMAR) and Okeanos R & D Centre, University of the Azores, Horta, Portugal
| | - Mónica A Silva
- Institute of Marine Research (IMAR) and Okeanos R & D Centre, University of the Azores, Horta, Portugal
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25
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Vacquié-Garcia J, Lydersen C, Marques TA, Andersen M, Kovacs KM. First abundance estimate for white whales Delphinapterus leucas in Svalbard, Norway. ENDANGER SPECIES RES 2020. [DOI: 10.3354/esr01016] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The Svalbard Archipelago (Norway) is experiencing rapid declines in the seasonal duration and extent of sea-ice cover, and local tidewater glaciers are melting. These environmental changes represent a threat to ice-associated species in the region, including white whales Delphinapterus leucas. However, no estimates of stock size or trends are available for this stock. An aerial survey was conducted during the summer of 2018, covering the coastlines of all major islands in Svalbard, as well fjords and open ocean areas. A total count was attempted for the coastlines, while coverage of the fjords and open ocean areas was designed as distance-sampling line transects. In total, 265 white whales were detected in 22 groups along the 4965 km of coastline coverage. No whales were observed on fjord (1481 km) or open ocean transects (535 km). After correcting for surface availability using behavioural data from the same area (in summer) and making adjustments for small areas not flown during the survey, the stock size was estimated to be 549 individuals (95% CI: 436%%CONV_ERR%%723). This estimate is surprisingly low given that this species is one of the most frequently observed cetaceans in the area, but it confirms suspicions based on difficulties in finding animals when operating white whale tagging programmes over the past decade. This first population estimate is important in the context of the rapid environmental change taking place in the Arctic and for providing a baseline for comparison with future estimates.
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Affiliation(s)
| | - C Lydersen
- Norwegian Polar Institute, Fram Centre, 9296 Tromsø, Norway
| | - TA Marques
- Centre for Research into Ecological & Environmental Modelling (Scottish Oceans Institute), Buchanan Gardens, St Andrews, KY16 9LY, UK
- Departamento de Biologia Animal, Centro de Estatística e Aplicações da Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - M Andersen
- Norwegian Polar Institute, Fram Centre, 9296 Tromsø, Norway
| | - KM Kovacs
- Norwegian Polar Institute, Fram Centre, 9296 Tromsø, Norway
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Carvalho C, Varela SA, Bastos LF, Orfão I, Beja V, Sapage M, Marques TA, Knight A, Vicente L. The Relevance ofIn Silico,In Vitroand Non-human Primate Based Approaches to Clinical Research on Major Depressive Disorder. Altern Lab Anim 2019; 47:128-139. [DOI: 10.1177/0261192919885578] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Major depressive disorder (MDD) is the most severe form of depression and the leading cause of disability worldwide. When considering research approaches aimed at understanding MDD, it is important that their effectiveness is evaluated. Here, we assessed the effectiveness of original studies on MDD by rating their contributions to subsequent medical papers on the subject, and we compared the respective contribution of findings from non-human primate (NHP) studies and from human-based in vitro or in silico research approaches. For each publication, we conducted a quantitative citation analysis and a systematic qualitative analysis of the citations. In the majority of cases, human-based research approaches (both in silico and in vitro) received more citations in subsequent human research papers than did NHP studies. In addition, the human-based approaches were considered to be more relevant to the hypotheses and/or to the methods featured in the citing papers. The results of this study suggest that studies based on in silico and in vitro approaches are taken into account by medical researchers more often than are NHP-based approaches. In addition, these human-based approaches are usually cheaper and less ethically contentious than NHP studies. Therefore, we suggest that the traditional animal-based approach for testing medical hypotheses should be revised, and more opportunities created for further developing human-relevant innovative techniques.
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Affiliation(s)
- Constança Carvalho
- Centro de Filosofia das Ciências da Universidade de Lisboa, Lisboa, Portugal
| | - Susana A.M. Varela
- cE3c—Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
- Instituto Gulbenkian de Ciência (IGC), Oeiras, Portugal
| | - Luísa Ferreira Bastos
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Instituto de Engenharia Biomédica (INEB), Porto, Portugal
| | - Inês Orfão
- Centro de Filosofia das Ciências da Universidade de Lisboa, Lisboa, Portugal
- cE3c—Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Vanda Beja
- Independent Consultant, Clinical Psychologist, Lisboa, Portugal
| | - Manuel Sapage
- cE3c—Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Tiago A. Marques
- Centre for Research into Ecological and Environmental Modelling, University of St Andrews, St Andrews, Scotland, UK
- Departamento de Biologia Animal, Centro de Estatística e Aplicações, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Andrew Knight
- Centre for Animal Welfare, University of Winchester, Winchester, UK
| | - Luís Vicente
- Centro de Filosofia das Ciências da Universidade de Lisboa, Lisboa, Portugal
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Dias FS, Wenceslau JFC, Marques TA, Miller DL. Density and distribution of western chimpanzees around a bauxite deposit in the Boé Sector, Guinea-Bissau. Am J Primatol 2019; 81:e23047. [PMID: 31520454 DOI: 10.1002/ajp.23047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 07/21/2019] [Accepted: 07/24/2019] [Indexed: 11/08/2022]
Abstract
The Boé sector in southeast Guinea-Bissau harbors a population of western chimpanzees (Pan troglodytes verus) that inhabits a mosaic of forest and savanna. The Boé sector contains a substantial bauxite deposit in a region called Ronde Hill, and there are plans for the construction of a mine, which may endanger the chimpanzee population. In 1-week survey in May 2013, we used the standing crop nest counts method to obtain the number of chimpanzee nests and from that estimate the density and abundance of chimpanzees. We carried out five 1-km line transects that covered the bauxite deposit and surrounding valleys. We used density surface modeling to analyze habitat preferences, then predicted chimpanzee nest density and distribution based on environmental variables. We found the projected location of the mine partially coincides with an area of high predicted abundances of chimpanzee nests and is surrounded by highly suitable areas for chimpanzees (northeast and southwest). We conclude the mine could have significant direct and indirect effects on this population of chimpanzees whose impacts must be carefully considered and properly mitigated if the mine is built.
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Affiliation(s)
- Filipe S Dias
- Centre for Applied Ecology "Prof. Baeta Neves" (CEABN-InBIO), School of Agriculture, University of Lisbon, Tapada da Ajuda, Lisbon, Portugal.,Laboratório Associado, CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal.,Laboratório Associado, CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, Lisbon, Portugal
| | | | - Tiago A Marques
- Centre for Research into Ecological & Environmental Modelling and School of Mathematics & Statistics, University of St Andrews, St Andrews, Scotland, United Kingdom.,Departamento de Biologia Animal, Centro de Estatística e Aplicações da Universidade de Lisboa, Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
| | - David L Miller
- Departamento de Biologia Animal, Centro de Estatística e Aplicações da Universidade de Lisboa, Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
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García-Barón I, Cortés-Avizanda A, Verburg PH, Marques TA, Moreno-Opo R, Pereira HM, Donázar JA. Front Cover. DIVERS DISTRIB 2018. [DOI: 10.1111/ddi.12794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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29
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García-Barón I, Cortés-Avizanda A, Verburg PH, Marques TA, Moreno-Opo R, Pereira HM, Donázar JA. How to fit the distribution of apex scavengers into land-abandonment scenarios? The Cinereous vulture in the Mediterranean biome. DIVERS DISTRIB 2018. [DOI: 10.1111/ddi.12743] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Isabel García-Barón
- Department of Conservation Biology; Estación Biológica de Doñana (CSIC); Sevilla Spain
- AZTI; Pasaia Spain
| | - Ainara Cortés-Avizanda
- Department of Conservation Biology; Estación Biológica de Doñana (CSIC); Sevilla Spain
- Animal Ecology and Demography Group, IMEDEA (CSIC-UIB); Esporles Spain
- Infraestruturas de Portugal Biodiversity Chair, InBio; Vairão Portugal
| | - Peter H. Verburg
- Environmental Geography Group; Institute for Environmental Studies; VU University Amsterdam; Amsterdam The Netherlands
- Swiss Federal Research Institute WSL; Birmensdorf Switzerland
| | - Tiago A. Marques
- Research Unit for Wildlife Population Assessment; Centre for Research into Ecological and Environmental Modelling; University of St Andrews; St Andrews UK
- Centro de Estatística e Aplicações; Faculdade de Ciências; Universidade de Lisboa; Lisboa Portugal
| | - Rubén Moreno-Opo
- Evolution and Conservation Biology Research Group; University Complutense of Madrid; Madrid Spain
| | - Henrique M. Pereira
- Infraestruturas de Portugal Biodiversity Chair, InBio; Vairão Portugal
- CEABN/InBio; Centro de Ecologia Aplicada “Professor Baeta Neves”; Instituto Superior de Agronomia; Universidade de Lisboa; Lisboa Portugal
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig; Leipzig Germany
- Institute of Biology; Martin Luther University Halle-Wittenberg; Halle, Saale Germany
| | - José A. Donázar
- Department of Conservation Biology; Estación Biológica de Doñana (CSIC); Sevilla Spain
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Verfuss UK, Gillespie D, Gordon J, Marques TA, Miller B, Plunkett R, Theriault JA, Tollit DJ, Zitterbart DP, Hubert P, Thomas L. Comparing methods suitable for monitoring marine mammals in low visibility conditions during seismic surveys. Mar Pollut Bull 2018; 126:1-18. [PMID: 29421075 DOI: 10.1016/j.marpolbul.2017.10.034] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 10/06/2017] [Accepted: 10/16/2017] [Indexed: 06/08/2023]
Abstract
Loud sound emitted during offshore industrial activities can impact marine mammals. Regulations typically prescribe marine mammal monitoring before and/or during these activities to implement mitigation measures that minimise potential acoustic impacts. Using seismic surveys under low visibility conditions as a case study, we review which monitoring methods are suitable and compare their relative strengths and weaknesses. Passive acoustic monitoring has been implemented as either a complementary or alternative method to visual monitoring in low visibility conditions. Other methods such as RADAR, active sonar and thermal infrared have also been tested, but are rarely recommended by regulatory bodies. The efficiency of the monitoring method(s) will depend on the animal behaviour and environmental conditions, however, using a combination of complementary systems generally improves the overall detection performance. We recommend that the performance of monitoring systems, over a range of conditions, is explored in a modelling framework for a variety of species.
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Affiliation(s)
- Ursula K Verfuss
- SMRU Consulting, Europe, New Technology Centre, North Haugh, St Andrews, Fife KY16 9SR, UK.
| | - Douglas Gillespie
- Sea Mammal Research Unit, Scottish Oceans Institute, University of St Andrews, Fife KY16 8LB, UK
| | - Jonathan Gordon
- Marine Ecological Research, 7 Beechwood Terrace West, Newport-On-Tay, Fife DD6 8JH, UK
| | - Tiago A Marques
- Centre for Research into Ecological and Environmental Modelling, The Observatory, University of St Andrews, St Andrews, Fife KY16 9LZ, UK
| | - Brianne Miller
- SMRU Consulting, North America, 1529 W 6th Ave, Vancouver, BC V6J 1R1, Canada
| | - Rachael Plunkett
- SMRU Consulting, Europe, New Technology Centre, North Haugh, St Andrews, Fife KY16 9SR, UK
| | - James A Theriault
- Ocean Environmental Consulting, 9 Ravine Park Cres, Halifax B3M 4S6, NS, Canada
| | - Dominic J Tollit
- SMRU Consulting, North America, 1529 W 6th Ave, Vancouver, BC V6J 1R1, Canada
| | - Daniel P Zitterbart
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
| | - Philippe Hubert
- Prove Systems Ltd, Unit 1 Mill court, Mill lane, Tayport, Fife DD6 9EL, UK
| | - Len Thomas
- Centre for Research into Ecological and Environmental Modelling, The Observatory, University of St Andrews, St Andrews, Fife KY16 9LZ, UK
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Marques TA, Thomas L, Kéry M, Buckland ST, Borchers DL, Rexstad E, Fewster RM, MacKenzie DI, Royle JA, Guillera-Arroita G, Handel CM, Pavlacky DC, Camp RJ. Model-based approaches to deal with detectability: a comment on Hutto (2016a). Ecol Appl 2017; 27:1694-1698. [PMID: 28376252 DOI: 10.1002/eap.1553] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 03/08/2017] [Accepted: 03/29/2017] [Indexed: 06/07/2023]
Affiliation(s)
- Tiago A Marques
- Centre for Research into Ecological and Environmental Modelling, The Observatory, University of St. Andrews, St. Andrews, KY16 9LZ, United Kingdom
- Centro de Estatística e Aplicações da Universidade de Lisboa, Bloco C6-Piso 4, Campo Grande, 1749-016, Lisboa, Portugal
| | - Len Thomas
- Centre for Research into Ecological and Environmental Modelling, The Observatory, University of St. Andrews, St. Andrews, KY16 9LZ, United Kingdom
| | - Marc Kéry
- Swiss Ornithological Institute, Seerose 1, 6204, Sempach, Switzerland
| | - Stephen T Buckland
- Centre for Research into Ecological and Environmental Modelling, The Observatory, University of St. Andrews, St. Andrews, KY16 9LZ, United Kingdom
| | - David L Borchers
- Centre for Research into Ecological and Environmental Modelling, The Observatory, University of St. Andrews, St. Andrews, KY16 9LZ, United Kingdom
| | - Eric Rexstad
- Centre for Research into Ecological and Environmental Modelling, The Observatory, University of St. Andrews, St. Andrews, KY16 9LZ, United Kingdom
| | - Rachel M Fewster
- Department of Statistics, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Darryl I MacKenzie
- Proteus Wildlife Research Consultants, P.O. Box 7, Outram, 9062, New Zealand
| | - J Andrew Royle
- Patuxent Wildlife Research Center, U.S. Geological Survey, Laurel, Maryland, 20708, USA
| | | | - Colleen M Handel
- Alaska Science Center, U.S. Geological Survey, Anchorage, Alaska, 99508, USA
| | - David C Pavlacky
- Bird Conservancy of the Rockies, 14500 Lark Bunting Lane, Brighton, Colorado, 80603, USA
- Department of Fish, Wildlife, and Conservation Biology, Colorado State University, Fort Collins, Colorado, 80523, USA
| | - Richard J Camp
- Hawai`i Cooperative Studies Unit, University of Hawai`i at Hilo, Hawai`i National Park, Hawaii, 96718, USA
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Warren VE, Marques TA, Harris D, Thomas L, Tyack PL, Aguilar de Soto N, Hickmott LS, Johnson MP. Spatio-temporal variation in click production rates of beaked whales: Implications for passive acoustic density estimation. J Acoust Soc Am 2017; 141:1962. [PMID: 28372060 DOI: 10.1121/1.4978439] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Passive acoustic monitoring has become an increasingly prevalent tool for estimating density of marine mammals, such as beaked whales, which vocalize often but are difficult to survey visually. Counts of acoustic cues (e.g., vocalizations), when corrected for detection probability, can be translated into animal density estimates by applying an individual cue production rate multiplier. It is essential to understand variation in these rates to avoid biased estimates. The most direct way to measure cue production rate is with animal-mounted acoustic recorders. This study utilized data from sound recording tags deployed on Blainville's (Mesoplodon densirostris, 19 deployments) and Cuvier's (Ziphius cavirostris, 16 deployments) beaked whales, in two locations per species, to explore spatial and temporal variation in click production rates. No spatial or temporal variation was detected within the average click production rate of Blainville's beaked whales when calculated over dive cycles (including silent periods between dives); however, spatial variation was detected when averaged only over vocal periods. Cuvier's beaked whales exhibited significant spatial and temporal variation in click production rates within vocal periods and when silent periods were included. This evidence of variation emphasizes the need to utilize appropriate cue production rates when estimating density from passive acoustic data.
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Affiliation(s)
- Victoria E Warren
- Centre for Research into Ecological and Environmental Modelling, The Observatory, Buchanan Gardens, University of St Andrews, St Andrews, Fife, KY16 9LZ, Scotland
| | - Tiago A Marques
- Centre for Research into Ecological and Environmental Modelling, The Observatory, Buchanan Gardens, University of St Andrews, St Andrews, Fife, KY16 9LZ, Scotland
| | - Danielle Harris
- Centre for Research into Ecological and Environmental Modelling, The Observatory, Buchanan Gardens, University of St Andrews, St Andrews, Fife, KY16 9LZ, Scotland
| | - Len Thomas
- Centre for Research into Ecological and Environmental Modelling, The Observatory, Buchanan Gardens, University of St Andrews, St Andrews, Fife, KY16 9LZ, Scotland
| | - Peter L Tyack
- Sea Mammal Research Unit, Scottish Oceans Institute, University of St Andrews, Fife, KY16 8LB, Scotland
| | - Natacha Aguilar de Soto
- Centre for Research into Ecological and Environmental Modelling, The Observatory, Buchanan Gardens, University of St Andrews, St Andrews, Fife, KY16 9LZ, Scotland
| | - Leigh S Hickmott
- Sea Mammal Research Unit, Scottish Oceans Institute, University of St Andrews, Fife, KY16 8LB, Scotland
| | - Mark P Johnson
- Sea Mammal Research Unit, Scottish Oceans Institute, University of St Andrews, Fife, KY16 8LB, Scotland
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Vacquié-Garcia J, Lydersen C, Marques TA, Aars J, Ahonen H, Skern-Mauritzen M, Øien N, Kovacs KM. Late summer distribution and abundance of ice-associated whales in the Norwegian High Arctic. ENDANGER SPECIES RES 2017. [DOI: 10.3354/esr00791] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Frasier KE, Wiggins SM, Harris D, Marques TA, Thomas L, Hildebrand JA. Delphinid echolocation click detection probability on near-seafloor sensors. J Acoust Soc Am 2016; 140:1918. [PMID: 27914405 DOI: 10.1121/1.4962279] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The probability of detecting echolocating delphinids on a near-seafloor sensor was estimated using two Monte Carlo simulation methods. One method estimated the probability of detecting a single click (cue counting); the other estimated the probability of detecting a group of delphinids (group counting). Echolocation click beam pattern and source level assumptions strongly influenced detectability predictions by the cue counting model. Group detectability was also influenced by assumptions about group behaviors. Model results were compared to in situ recordings of encounters with Risso's dolphin (Grampus griseus) and presumed pantropical spotted dolphin (Stenella attenuata) from a near-seafloor four-channel tracking sensor deployed in the Gulf of Mexico (25.537°N 84.632°W, depth 1220 m). Horizontal detection range, received level and estimated source level distributions from localized encounters were compared with the model predictions. Agreement between in situ results and model predictions suggests that simulations can be used to estimate detection probabilities when direct distance estimation is not available.
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Affiliation(s)
- Kaitlin E Frasier
- Scripps Institution of Oceanography, 9500 Gilman Drive, La Jolla, California 92093-0205, USA
| | - Sean M Wiggins
- Scripps Institution of Oceanography, 9500 Gilman Drive, La Jolla, California 92093-0205, USA
| | - Danielle Harris
- Centre for Research into Ecological and Environmental Modelling, University of St Andrews, The Observatory, Buchanan Gardens, Fife KY16 9LZ, United Kingdom
| | - Tiago A Marques
- Centre for Research into Ecological and Environmental Modelling, University of St Andrews, The Observatory, Buchanan Gardens, Fife KY16 9LZ, United Kingdom
| | - Len Thomas
- Centre for Research into Ecological and Environmental Modelling, University of St Andrews, The Observatory, Buchanan Gardens, Fife KY16 9LZ, United Kingdom
| | - John A Hildebrand
- Scripps Institution of Oceanography, 9500 Gilman Drive, La Jolla, California 92093-0205, USA
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Valente AM, Marques TA, Fonseca C, Torres RT. A new insight for monitoring ungulates: density surface modelling of roe deer in a Mediterranean habitat. EUR J WILDLIFE RES 2016. [DOI: 10.1007/s10344-016-1030-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Kidney D, Rawson BM, Borchers DL, Stevenson BC, Marques TA, Thomas L. An Efficient Acoustic Density Estimation Method with Human Detectors Applied to Gibbons in Cambodia. PLoS One 2016; 11:e0155066. [PMID: 27195799 PMCID: PMC4873237 DOI: 10.1371/journal.pone.0155066] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 04/24/2016] [Indexed: 11/23/2022] Open
Abstract
Some animal species are hard to see but easy to hear. Standard visual methods for estimating population density for such species are often ineffective or inefficient, but methods based on passive acoustics show more promise. We develop spatially explicit capture-recapture (SECR) methods for territorial vocalising species, in which humans act as an acoustic detector array. We use SECR and estimated bearing data from a single-occasion acoustic survey of a gibbon population in northeastern Cambodia to estimate the density of calling groups. The properties of the estimator are assessed using a simulation study, in which a variety of survey designs are also investigated. We then present a new form of the SECR likelihood for multi-occasion data which accounts for the stochastic availability of animals. In the context of gibbon surveys this allows model-based estimation of the proportion of groups that produce territorial vocalisations on a given day, thereby enabling the density of groups, instead of the density of calling groups, to be estimated. We illustrate the performance of this new estimator by simulation. We show that it is possible to estimate density reliably from human acoustic detections of visually cryptic species using SECR methods. For gibbon surveys we also show that incorporating observers' estimates of bearings to detected groups substantially improves estimator performance. Using the new form of the SECR likelihood we demonstrate that estimates of availability, in addition to population density and detection function parameters, can be obtained from multi-occasion data, and that the detection function parameters are not confounded with the availability parameter. This acoustic SECR method provides a means of obtaining reliable density estimates for territorial vocalising species. It is also efficient in terms of data requirements since since it only requires routine survey data. We anticipate that the low-tech field requirements will make this method an attractive option in many situations where populations can be surveyed acoustically by humans.
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Affiliation(s)
- Darren Kidney
- Centre for Research into Ecological and Environmental Modelling, University of St Andrews, St Andrews, United Kingdom
| | | | - David L. Borchers
- Centre for Research into Ecological and Environmental Modelling, University of St Andrews, St Andrews, United Kingdom
| | - Ben C. Stevenson
- Centre for Research into Ecological and Environmental Modelling, University of St Andrews, St Andrews, United Kingdom
| | - Tiago A. Marques
- Centro de Estatística e Aplicações da Universidade de Lisboa, Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
| | - Len Thomas
- Centre for Research into Ecological and Environmental Modelling, University of St Andrews, St Andrews, United Kingdom
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Marques TA. A Comment on Horcajada-Sánchez and Barja (2015): A Cautionary Tale about Left Truncation and Density Gradients in Distance Sampling. ANN ZOOL FENN 2016. [DOI: 10.5735/086.053.0204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Anderson AS, Marques TA, Shoo LP, Williams SE. Detectability in Audio-Visual Surveys of Tropical Rainforest Birds: The Influence of Species, Weather and Habitat Characteristics. PLoS One 2015; 10:e0128464. [PMID: 26110433 PMCID: PMC4482497 DOI: 10.1371/journal.pone.0128464] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 04/27/2015] [Indexed: 11/17/2022] Open
Abstract
Indices of relative abundance do not control for variation in detectability, which can bias density estimates such that ecological processes are difficult to infer. Distance sampling methods can be used to correct for detectability, but in rainforest, where dense vegetation and diverse assemblages complicate sampling, information is lacking about factors affecting their application. Rare species present an additional challenge, as data may be too sparse to fit detection functions. We present analyses of distance sampling data collected for a diverse tropical rainforest bird assemblage across broad elevational and latitudinal gradients in North Queensland, Australia. Using audio and visual detections, we assessed the influence of various factors on Effective Strip Width (ESW), an intuitively useful parameter, since it can be used to calculate an estimate of density from count data. Body size and species exerted the most important influence on ESW, with larger species detectable over greater distances than smaller species. Secondarily, wet weather and high shrub density decreased ESW for most species. ESW for several species also differed between summer and winter, possibly due to seasonal differences in calling behavior. Distance sampling proved logistically intensive in these environments, but large differences in ESW between species confirmed the need to correct for detection probability to obtain accurate density estimates. Our results suggest an evidence-based approach to controlling for factors influencing detectability, and avenues for further work including modeling detectability as a function of species characteristics such as body size and call characteristics. Such models may be useful in developing a calibration for non-distance sampling data and for estimating detectability of rare species.
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Affiliation(s)
- Alexander S Anderson
- Centre for Tropical Biodiversity and Climate Change, College of Marine & Environmental Sciences, James Cook University, Townsville, Queensland, Australia
| | - Tiago A Marques
- Research Unit for Wildlife Population Assessment, Centre for Research into Ecological and Environmental Modeling, University of St Andrews, The Observatory, Buchanan Gardens, St Andrews, Scotland
| | - Luke P Shoo
- School of Biological Sciences, The University of Queensland, St. Lucia, Queensland, Australia
| | - Stephen E Williams
- Centre for Tropical Biodiversity and Climate Change, College of Marine & Environmental Sciences, James Cook University, Townsville, Queensland, Australia
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Borchers DL, Stevenson BC, Kidney D, Thomas L, Marques TA. A Unifying Model for Capture-Recapture and Distance Sampling Surveys of Wildlife Populations. J Am Stat Assoc 2015; 110:195-204. [PMID: 26063947 PMCID: PMC4440664 DOI: 10.1080/01621459.2014.893884] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Revised: 02/01/2014] [Indexed: 12/05/2022]
Abstract
A fundamental problem in wildlife ecology and management is estimation of population size or density. The two dominant methods in this area are capture–recapture (CR) and distance sampling (DS), each with its own largely separate literature. We develop a class of models that synthesizes them. It accommodates a spectrum of models ranging from nonspatial CR models (with no information on animal locations) through to DS and mark-recapture distance sampling (MRDS) models, in which animal locations are observed without error. Between these lie spatially explicit capture–recapture (SECR) models that include only capture locations, and a variety of models with less location data than are typical of DS surveys but more than are normally used on SECR surveys. In addition to unifying CR and DS models, the class provides a means of improving inference from SECR models by adding supplementary location data, and a means of incorporating measurement error into DS and MRDS models. We illustrate their utility by comparing inference on acoustic surveys of gibbons and frogs using only capture locations, using estimated angles (gibbons) and combinations of received signal strength and time-of-arrival data (frogs), and on a visual MRDS survey of whales, comparing estimates with exact and estimated distances. Supplementary materials for this article are available online.
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Affiliation(s)
- Christophe Laplanche
- Université de Toulouse INP UPS EcoLab (Laboratoire Ecologie Fonctionnelle et Environnement) ENSAT Avenue de l‘Agrobiopole 31326 Castanet Tolosan France
- ECOLAB CNRS 31326 Castanet Tolosan France
| | - Tiago A. Marques
- Centre for Research into Ecological and Environmental Modelling, The Observatory, Buchanan Gardens University of St Andrews St Andrews KY16 9LZ Scotland UK
| | - Len Thomas
- Centre for Research into Ecological and Environmental Modelling, The Observatory, Buchanan Gardens University of St Andrews St Andrews KY16 9LZ Scotland UK
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Affiliation(s)
- Mary Louise Burt
- Centre for Research into Environmental and Ecological Modelling; University of St Andrews; The Observatory, Buchanan Gardens, St Andrews, KY16 9LZ UK
| | - David L. Borchers
- Centre for Research into Environmental and Ecological Modelling; University of St Andrews; The Observatory, Buchanan Gardens, St Andrews, KY16 9LZ UK
| | - Kurt J. Jenkins
- USGSF-Forest and Rangeland Ecosystem Science Center; Olympic Field Station, Port Angeles; WA 98362 USA
| | - Tiago A. Marques
- Centre for Research into Environmental and Ecological Modelling; University of St Andrews; The Observatory, Buchanan Gardens, St Andrews, KY16 9LZ UK
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Carvalho JS, Meyer CFJ, Vicente L, Marques TA. Where to nest? Ecological determinants of chimpanzee nest abundance and distribution at the habitat and tree species scale. Am J Primatol 2014; 77:186-99. [PMID: 25224379 DOI: 10.1002/ajp.22321] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Revised: 07/07/2014] [Accepted: 07/11/2014] [Indexed: 11/06/2022]
Abstract
Conversion of forests to anthropogenic land-uses increasingly subjects chimpanzee populations to habitat changes and concomitant alterations in the plant resources available to them for nesting and feeding. Based on nest count surveys conducted during the dry season, we investigated nest tree species selection and the effect of vegetation attributes on nest abundance of the western chimpanzee, Pan troglodytes verus, at Lagoas de Cufada Natural Park (LCNP), Guinea-Bissau, a forest-savannah mosaic widely disturbed by humans. Further, we assessed patterns of nest height distribution to determine support for the anti-predator hypothesis. A zero-altered generalized linear mixed model showed that nest abundance was negatively related to floristic diversity (exponential form of the Shannon index) and positively with the availability of smaller-sized trees, reflecting characteristics of dense-canopy forest. A positive correlation between nest abundance and floristic richness (number of plant species) and composition indicated that species-rich open habitats are also important in nest site selection. Restricting this analysis to feeding trees, nest abundance was again positively associated with the availability of smaller-sized trees, further supporting the preference for nesting in food tree species from dense forest. Nest tree species selection was non-random, and oil palms were used at a much lower proportion (10%) than previously reported from other study sites in forest-savannah mosaics. While this study suggests that human disturbance may underlie the exclusive arboreal nesting at LCNP, better quantitative data are needed to determine to what extent the construction of elevated nests is in fact a response to predators able to climb trees. Given the importance of LCNP as refuge for Pan t. verus our findings can improve conservation decisions for the management of this important umbrella species as well as its remaining suitable habitats.
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Affiliation(s)
- Joana S Carvalho
- Centre for Environmental and Marine Studies (CESAM), Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
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Mieiro CL, Dolbeth M, Marques TA, Duarte AC, Pereira ME, Pacheco M. Mercury accumulation and tissue-specific antioxidant efficiency in the wild European sea bass (Dicentrarchus labrax) with emphasis on seasonality. Environ Sci Pollut Res Int 2014; 21:10638-10651. [PMID: 24875309 DOI: 10.1007/s11356-014-3053-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 05/16/2014] [Indexed: 06/03/2023]
Abstract
The main goal of this study was to assess both mercury (Hg) accumulation and organs' specific oxidative stress responses of gills, liver and kidney of Dicentrarchus labrax with emphasis on seasonality. Fish were collected in cold and warm periods in three stations: reference, moderated and highly contaminated sites. Our results showed that seasonal factors slightly influenced Hg accumulation between year periods (cold and warm) and strongly affected organs' response basal levels. In contrast, seasonality seemed not to influence oxidative stress responses, since similar response patterns were obtained for both year periods, and moderate degree of antioxidant responses was obtained. Moreover, the oxidative stress profile may be attributed to Hg contamination degree, which showed organ-specific response and accumulation patterns. Hence, gills showed to be able to adapt to Hg contamination, and in opposition, kidney and liver demonstrated some vulnerability to Hg toxicity. The critical Hg concentrations indicated specific threshold limits for each organ. Overall, seasonality should be taken into account in monitoring programmes, helping to characterize the individuals' reference values of response and thus to discriminate between the effects induced by natural causes or by contamination.
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Affiliation(s)
- C L Mieiro
- CESAM and Department of Chemistry, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal,
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Valente AM, Fonseca C, Marques TA, Santos JP, Rodrigues R, Torres RT. Living on the edge: roe deer (Capreolus capreolus) density in the margins of its geographical range. PLoS One 2014; 9:e88459. [PMID: 24533091 PMCID: PMC3922805 DOI: 10.1371/journal.pone.0088459] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Accepted: 01/07/2014] [Indexed: 11/29/2022] Open
Abstract
Over the last decades roe deer (Capreolus capreolus) populations have increased in number and distribution throughout Europe. Such increases have profound impacts on ecosystems, both positive and negative. Therefore monitoring roe deer populations is essential for the appropriate management of this species, in order to achieve a balance between conservation and mitigation of the negative impacts. Despite being required for an effective management plan, the study of roe deer ecology in Portugal is at an early stage, and hence there is still a complete lack of knowledge of roe deer density within its known range. Distance sampling of pellet groups coupled with production and decay rates for pellet groups provided density estimates for roe deer in northeastern Portugal (Lombada National Hunting Area - LNHA, Serra de Montesinho – SM and Serra da Nogueira – SN; LNHA and SM located in Montesinho Natural Park). The estimated roe deer density using a stratified detection function was 1.23/100 ha for LNHA, 4.87/100 ha for SM and 4.25/100 ha in SN, with 95% confidence intervals (CI) of 0.68 to 2.21, 3.08 to 7.71 and 2.25 to 8.03, respectively. For the entire area, the estimated density was about 3.51/100 ha (95% CI - 2.26–5.45). This method can provide estimates of roe deer density, which will ultimately support management decisions. However, effective monitoring should be based on long-term studies that are able to detect population fluctuations. This study represents the initial phase of roe deer monitoring at the edge of its European range and intends to fill the gap in this species ecology, as the gathering of similar data over a number of years will provide the basis for stronger inferences. Monitoring should be continued, although the study area should be increased to evaluate the accuracy of estimates and assess the impact of management actions.
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Affiliation(s)
- Ana M. Valente
- CESAM, Departamento de Biologia, Universidade de Aveiro, Aveiro, Portugal
| | - Carlos Fonseca
- CESAM, Departamento de Biologia, Universidade de Aveiro, Aveiro, Portugal
- Universidade Lúrio, Campus de Marrere, Nampula, Mozambique
| | - Tiago A. Marques
- Centre for Research into Ecological and Environmental Modelling, The Observatory, University of St Andrews, St Andrews, Scotland
| | - João P. Santos
- CESAM, Departamento de Biologia, Universidade de Aveiro, Aveiro, Portugal
- Instituto de Investigación en Recursos Cinegéticos, Ciudad Real, Spain
| | - Rogério Rodrigues
- Departamento de Conservação da Natureza e Florestas do Norte, Parque Florestal, Vila Real, Portugal
| | - Rita Tinoco Torres
- CESAM, Departamento de Biologia, Universidade de Aveiro, Aveiro, Portugal
- * E-mail:
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Kun-Rodrigues C, Salmona J, Besolo A, Rasolondraibe E, Rabarivola C, Marques TA, Chikhi L. New density estimates of a threatened sifaka species (Propithecus coquereli) in Ankarafantsika National Park. Am J Primatol 2014; 76:515-28. [PMID: 24443250 DOI: 10.1002/ajp.22243] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2013] [Revised: 11/10/2013] [Accepted: 11/13/2013] [Indexed: 11/11/2022]
Abstract
Propithecus coquereli is one of the last sifaka species for which no reliable and extensive density estimates are yet available. Despite its endangered conservation status [IUCN, 2012] and recognition as a flagship species of the northwestern dry forests of Madagascar, its population in its last main refugium, the Ankarafantsika National Park (ANP), is still poorly known. Using line transect distance sampling surveys we estimated population density and abundance in the ANP. Furthermore, we investigated the effects of road, forest edge, river proximity and group size on sighting frequencies, and density estimates. We provide here the first population density estimates throughout the ANP. We found that density varied greatly among surveyed sites (from 5 to ∼100 ind/km2) which could result from significant (negative) effects of road, and forest edge, and/or a (positive) effect of river proximity. Our results also suggest that the population size may be ∼47,000 individuals in the ANP, hinting that the population likely underwent a strong decline in some parts of the Park in recent decades, possibly caused by habitat loss from fires and charcoal production and by poaching. We suggest community-based conservation actions for the largest remaining population of Coquerel's sifaka which will (i) maintain forest connectivity; (ii) implement alternatives to deforestation through charcoal production, logging, and grass fires; (iii) reduce poaching; and (iv) enable long-term monitoring of the population in collaboration with local authorities and researchers.
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Marques JT, Ramos Pereira MJ, Marques TA, Santos CD, Santana J, Beja P, Palmeirim JM. Optimizing sampling design to deal with mist-net avoidance in Amazonian birds and bats. PLoS One 2013; 8:e74505. [PMID: 24058579 PMCID: PMC3776857 DOI: 10.1371/journal.pone.0074505] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Accepted: 08/02/2013] [Indexed: 11/25/2022] Open
Abstract
Mist netting is a widely used technique to sample bird and bat assemblages. However, captures often decline with time because animals learn and avoid the locations of nets. This avoidance or net shyness can substantially decrease sampling efficiency. We quantified the day-to-day decline in captures of Amazonian birds and bats with mist nets set at the same location for four consecutive days. We also evaluated how net avoidance influences the efficiency of surveys under different logistic scenarios using re-sampling techniques. Net avoidance caused substantial declines in bird and bat captures, although more accentuated in the latter. Most of the decline occurred between the first and second days of netting: 28% in birds and 47% in bats. Captures of commoner species were more affected. The numbers of species detected also declined. Moving nets daily to minimize the avoidance effect increased captures by 30% in birds and 70% in bats. However, moving the location of nets may cause a reduction in netting time and captures. When moving the nets caused the loss of one netting day it was no longer advantageous to move the nets frequently. In bird surveys that could even decrease the number of individuals captured and species detected. Net avoidance can greatly affect sampling efficiency but adjustments in survey design can minimize this. Whenever nets can be moved without losing netting time and the objective is to capture many individuals, they should be moved daily. If the main objective is to survey species present then nets should still be moved for bats, but not for birds. However, if relocating nets causes a significant loss of netting time, moving them to reduce effects of shyness will not improve sampling efficiency in either group. Overall, our findings can improve the design of mist netting sampling strategies in other tropical areas.
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Affiliation(s)
- João Tiago Marques
- Departamento de Biologia Animal, Centro de Biologia Ambiental, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
- Instituto de Desenvolvimento Sustentável Mamirauá, Tefé, Amazonas, Brazil
- * E-mail:
| | - Maria J. Ramos Pereira
- Instituto de Desenvolvimento Sustentável Mamirauá, Tefé, Amazonas, Brazil
- Departamento de Biologia e Centro de Estudos do Ambiente e do Mar, Universidade de Aveiro, Campus Universitário de Santiago, Aveiro, Portugal
| | - Tiago A. Marques
- Centre for Research into Ecological and Environmental Modelling, University of St Andrews, The Observatory, Buchanan Gardens, Fife, United Kingdom
| | - Carlos David Santos
- Departamento de Biologia e Centro de Estudos do Ambiente e do Mar, Universidade de Aveiro, Campus Universitário de Santiago, Aveiro, Portugal
- Department of Migration and Immuno-ecology, Max Planck Institute for Ornithology, Radolfzell, Germany
- ERENA, SA, Lisboa, Portugal
| | | | - Pedro Beja
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
| | - Jorge M. Palmeirim
- Departamento de Biologia Animal, Centro de Biologia Ambiental, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
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Langrock R, Marques TA, Baird RW, Thomas L. Modeling the Diving Behavior of Whales: A Latent-Variable Approach with Feedback and Semi-Markovian Components. JABES 2013. [DOI: 10.1007/s13253-013-0158-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Carvalho JS, Marques TA, Vicente L. Population status of Pan troglodytes verus in Lagoas de Cufada Natural Park, Guinea-Bissau. PLoS One 2013; 8:e71527. [PMID: 23940766 PMCID: PMC3737107 DOI: 10.1371/journal.pone.0071527] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Accepted: 06/28/2013] [Indexed: 11/19/2022] Open
Abstract
The western chimpanzee, Pan troglodytes verus, has been classified as Endangered on the IUCN Red List since 1988. Intensive agriculture, commercial plantations, logging, and mining have eliminated or degraded the habitats suitable for P. t. verus over a large part of its range. In this study we assessed the effect of land-use change on the population size and density of chimpanzees at Lagoas de Cufada Natural Park (LCNP), Guinea-Bissau. We further explored chimpanzee distribution in relation to landscape-level proxies of human disturbance. Nest count and distance-sampling methods were employed along 11 systematically placed linear transects in 2010 and 2011. Estimated nest decay rate was 293.9 days (%CV = 58.8). Based on this estimate of decay time and using the Standing-Crop Nest Count Method, we obtained a habitat-weighted average chimpanzee density estimate for 2011 of 0.22 nest building chimpanzees/km(2) (95% CI 0.08-0.62), corresponding to 137 (95% CI 51.0-390.0) chimpanzees for LCNP. Human disturbance had a negative influence on chimpanzee distribution as nests were built farther away from human settlements, roads, and rivers than if they were randomly distributed, coinciding with the distribution of the remaining patches of dense canopy forest. We conclude that the continuous disappearance of suitable habitat (e.g. the replacement of LCNP's dense forests by monocultures of cashew plantations) may be compromising the future of one of the most threatened Guinean coastal chimpanzee populations. We discuss strategies to ensure long-term conservation in this important refuge for this chimpanzee subspecies at its westernmost margin of geographic distribution.
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Affiliation(s)
- Joana S Carvalho
- Centre for Environmental and Marine Studies, Department of Biology, Lisbon University, Campo Grande C2, Lisboa, Portugal.
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Marques TA, Thomas L, Martin SW, Mellinger DK, Ward JA, Moretti DJ, Harris D, Tyack PL. Estimating animal population density using passive acoustics. Biol Rev Camb Philos Soc 2012. [PMID: 23190144 PMCID: PMC3743169 DOI: 10.1111/brv.12001] [Citation(s) in RCA: 220] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Reliable estimation of the size or density of wild animal populations is very important for effective wildlife management, conservation and ecology. Currently, the most widely used methods for obtaining such estimates involve either sighting animals from transect lines or some form of capture-recapture on marked or uniquely identifiable individuals. However, many species are difficult to sight, and cannot be easily marked or recaptured. Some of these species produce readily identifiable sounds, providing an opportunity to use passive acoustic data to estimate animal density. In addition, even for species for which other visually based methods are feasible, passive acoustic methods offer the potential for greater detection ranges in some environments (e.g. underwater or in dense forest), and hence potentially better precision. Automated data collection means that surveys can take place at times and in places where it would be too expensive or dangerous to send human observers. Here, we present an overview of animal density estimation using passive acoustic data, a relatively new and fast-developing field. We review the types of data and methodological approaches currently available to researchers and we provide a framework for acoustics-based density estimation, illustrated with examples from real-world case studies. We mention moving sensor platforms (e.g. towed acoustics), but then focus on methods involving sensors at fixed locations, particularly hydrophones to survey marine mammals, as acoustic-based density estimation research to date has been concentrated in this area. Primary among these are methods based on distance sampling and spatially explicit capture-recapture. The methods are also applicable to other aquatic and terrestrial sound-producing taxa. We conclude that, despite being in its infancy, density estimation based on passive acoustic data likely will become an important method for surveying a number of diverse taxa, such as sea mammals, fish, birds, amphibians, and insects, especially in situations where inferences are required over long periods of time. There is considerable work ahead, with several potentially fruitful research areas, including the development of (i) hardware and software for data acquisition, (ii) efficient, calibrated, automated detection and classification systems, and (iii) statistical approaches optimized for this application. Further, survey design will need to be developed, and research is needed on the acoustic behaviour of target species. Fundamental research on vocalization rates and group sizes, and the relation between these and other factors such as season or behaviour state, is critical. Evaluation of the methods under known density scenarios will be important for empirically validating the approaches presented here.
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Affiliation(s)
- Tiago A Marques
- Centre for Research into Ecological and Environmental Modelling, University of St Andrews, The Observatory, Buchanan Gardens, Fife, KY16 9LZ, UK.
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Bispo R, Marques TA, Pestana D. Statistical power of goodness-of-fit tests based on the empirical distribution function for type-I right-censored data. J STAT COMPUT SIM 2012. [DOI: 10.1080/00949655.2011.624519] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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