Ecology

Mathematical Biology Mathematics for Health
Data Knowledge
Ecology
Care and Ageing Big Data 
Epidemiology

 

 Machine Learning
Evolution & Genetics  

EcologyProjects:

  • Ecology
    • Models for species distribution
    • Estimation of mortality of birds and bats due to collision with human infrastructures
    • Modeling the risk of fire
  • Conservation Biology
    • Identification of priority areas for conservation
  • Ocean Sciences
    • Animal Population Dynamics and Abundance Estimation, Preferential Sampling
    • Climate change

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Project: Models for species distribution

Description: Development of mathematical tools to address issues related to the estimate the niche of species (i.e., a hypervolume discriminating suitability as a function of environmental conditions).

Methods: Optimization | Multivariate statistics

CMA Researchers: Jorge Orestes Cerdeira

Funding:

  • Project PTDC/AAC-AMB/113394/2009: “Species Performance Modeling Algorithm (S-PerforMA)” (2011-2014).
  • Project PTDC/AGR-FOR/1756/2014: “Alterações climáticas e seu impacto em florestas de pinheiro ao longo da costa oeste portuguesa: o caso de duas pragas recentemente emergidas” (2018-2021).

Supervision:

  • One Ph.D. (Forestry Engineering, co-supervisor) at ISA, Univ of Lisbon, 2016.
  • One Pós-Doc (FCT Grant SFRH/BPD/115057/2016), 2017 - 2020.

Publications:

  • JO Cerdeira, T Monteiro-Henriques, MJ Martins, PC Silva, D Alagador, AMA Franco, ML Campagnolo, P Arsénio, FC Aguiar, M Cabeza, Revisiting niche fundamentals with Tukey depth, Methods in Ecology and Evolution, online.
  • P Clemente, M Calvache, P Antunes, R Santos, JO Cerdeira, MJ Martins, Combining social media photographs and species distribution models to map cultural ecosystem services: the case of a natural park in Portugal, Ecological Indicators 96 (2019) 59-58.
  • T Monteiro-Henriques, MJ Martins, JO Cerdeira, PC Silva, P Arsénio, A Silva, A Bellu, JC Costa, Bioclimatological mapping tackling uncertainty propagation: application to mainland Portugal International Journal of Climatology 36 (2016) 400-411.
  • FS Dias, MN Bugalho, PM Rodríguez-González, A Albuquerque, JO Cerdeira, Effects of forest certification on the ecological condition of Mediterranean streams, Journal of Applied Ecology 52 (2015) 190-198.
  • PC Silva, JO Cerdeira, MJ Martins and T Monteiro Henriques Data depth for the uniform distribution, Environmental and Ecological Statistics 21 (2014) 27-39.
  • JO Cerdeira, T Monteiro-Henriques, MJ Martins, PC Silva, D Alagador and A Franco, Mathematical contributions to link biota with environment, Journal of Vegetation Science 25 (2014) 1148-1153.
  • R Heleno, C Garcia, P Jordano, A Traveset, JM Gómez, N Blüthgen, J Memmott, M Moora, JO Cerdeira, S Rodríguez-Echeverría, H Freitas, JM Olesen, Ecological networks: delving into the architecture of biodiversity, Biology Letters 10 (2014) 20131000.
  • F Aguiar, JO Cerdeira, MJ Martins and MT Ferreira, Riparian forests of Southwest Europe: are functional trait and species composition assemblages constrained by environment?, Journal of Vegetation Science 24 (2013) 628-638.

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Project: Estimation of mortality of birds and bats due to collision with human infrastructures

Description: The human influence on the environment is today a consensual matter of concern. For decades humans used the natural resources with little concern for the negative consequences on the environment. That led to many situations of clear degradation of natural resources. Today, the consequences on biodiversity are well known. Threats are directly linked to the loss of habitats due to the destruction, modification, and fragmentation of ecosystems and direct mortality. This project aims to model wildlife mortality due to collision with obstacles such as power lines, wind turbines, solar panels.

Methods: GLMM | Spatial-temporal modelling | Meta-analysis

CMA Researchers: Regina Bispo

Publications:

  • Paula, J., Bispo, R., Leite, A., Pereira, P., Costa, H., Fonseca, C., Marcarenhas, M. & Bernardino, J. (2015) Camera-trapping as a methodology to assess the persistence of wildlife carcasses resulting from collisions with human-made structures. Wildlife Research, 41(8):717-725
  • Bernardino, J., Bispo, R., Costa, H. & Mascarenhas, M. (2013) Estimating bird and bat fatality at wind farms: a practical overview of estimators, their assumptions and limitations. New Zealand Journal of Zoology, 40:63-74
  • Marques, T.A., Buckland, S.T., Bispo, R. & Howland, B. (2013) Accounting for animal density gradients using independent information in distance sampling surveys. Statistical Methods & Applications, 22:67-80.
  • Bispo, R., Bernardino, J., Marques, T. A. & Pestana, D. (2013) Modeling carcass removal time for avian mortality assessment in wind farms using survival analysis. Environmental and Ecological Statistics, 20:147-165.

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Project: Modeling the risk of fire

Description: Describing and modeling the risk of fire in Portugal, taking into consideration that several factors may explain ignition and spread of forest fires, such as fuel characteristics, climate ignition sources, vegetation, topography and others. Joint modeling of the probability of ignition and fire sizes through hierarchical space-time models in a Bayesian framework.

Methods: Generalized linear models | Bayesian statistics

CMA Researchers: Isabel Natário

Publications:

  • Natário I, Oliveira MM, Marques S (2014). Using INLA to Estimate a Highly Dimensional Spatial Model for Forest Fires in Portugal. In New Advances in Statistical Modeling and Applications - Studies in Theoretical and Applied Statistics. Editors: António Pacheco, Rui Santos, Maria do Rosário Oliveira, Carlos Daniel Paulino. Pp. 239-247. Springer. DOI: 10.1007/978-3-319-05323-3_23
  • Oliveira MM, Natário I, Marques S, Garcia-Gonzalo J, Botequim B, Borges JG, Tomé M, Pereira JM, Tomé J, Demétrio CGB (2013). Aplicações Estatísticas em Análise de Catástrofes Naturais. In Matemática do Planeta Terra, Edts Fernando Pestana da Costa, João Teixeira Pinto, Jorge Buescu. IST Press. Lisboa.

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Project: Identification of priority areas for conservation

Description: Combinatorial optimization tools (arising from different areas such as flow theory, variants of Steiner tree problems on graphs, connectivity and covers) are developed and turned to algorithms used to identify priority areas for species mitigating fragmentation of habitats and coping with climate change.

Methods: Combinatorial optimization | Graphs

CMA Researchers: Jorge Orestes Cerdeira

Funding: Project PTDC/AAG-GLO/3979/2014: “Biodiversity Conservation, Global Change and Uncertainties: Reconciling Biodiversity Persistence and Human Development upon Dynamic Environments (RECONCILE)” (2016-2019).

Supervision:

  • One PhD (Applied Math, Variants of the Steiner tree problem with applications to Conservation Biology) at ISEG, Univ of Lisbon, 2013.
  • One Pós-Doc (FCT Grant SFRH/BPD/104077/2014), 2016 - 2018.

Publications:

  •  D Alagador, JO Cerdeira, Introducing Spatio-Temporal Conservation Units: Models for Flexible Optimization of Species Persistence Under Climate Change, in Handbook of Climate Change and Biodiversity, Sringer, Cham (2019) 243-258.
  • D Alagador, JO Cerdeira, A quantitative analysis on the effects of critical factors limiting the effectiveness of species conservation in future time, Ecology and Evolution 8 (2018) 3457-3467.
  • D Alagador, JO Cerdeira, Meeting species persistence targets under climate change: a spatially-explicit conservation planning model, Diversity and Distribution 23 (2017) 703-713.
  • D Alagador, JO Cerdeira, MB Araujo, Climate change, species range shifts and dispersal corridors: an evaluation of spatial conservation models, Methods in Ecology and Evolution 7 (2016) 853-866.
  • FS Dias, DL Miller, TA Marques, J Marcelino, MC Caldeira, JO Cerdeira, MN Bugalho, Conservation zones promote oak regeneration and shrub diversity in certified Mediterranean oak woodlands, Biological Conservation 195 (2016) 214-223.
  • MN Bugalho, FS Dias, B Brinas, and JO Cerdeira, Using the high conservation value forest concept and Pareto optimization to identify areas maximizing biodiversity and ecosystem services in cork oak landscapes, Agroforestry Systems, 90 (2016) 35–44.
  • R Brás, JO Cerdeira, Computational comparison of algorithms for a generalization of the node-weighted Steiner tree and forest problems, in Operations Research, CIM Series in Mathematical Sciences 4, 67-83, 2015, Switzerland: Springer International Publishing
  • D Alagador, JO Cerdeira, A model to minimize costs and promote species persistence under climate change, in Operations Research and Big Data - IO2015-XVII Congress of Portuguese Association of Operational Research, 1-8, 2015, Switzerland: Springer International Publishing.
  • D Alagador, JO Cerdeira, MB Araujo, Shifting protected areas: scheduling spatial priorities under climate change, Journal of Applied Ecology 51 (2014) 703-713.
  • R Brás, JO Cerdeira, D Alagador and MB Araújo, Linking habitats for multiple species, Environmental Modelling & Software 40 (2013) 336-339.
  • F Dias, MN Bugalho, JO Cerdeira, MJ Martins, Is forest certification targeting areas of high biodiversity in cork oak savannas?, Biodiversity and Conservation 22 (2013) 93-112.

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Project: Animal Population Dynamics and Abundance Estimation, Preferential Sampling

Description: Development of statistical methods for accessing the dynamics and abundance estimation of the black scabbardfish in NE Atlantic. It resulted in a benchmark model, based on state space models, for the WKDEEP of the International Council for the Exploration of the Sea (ICES), the global organization that develops science and counseling to support the sustainable use of the oceans. This model, that was accepted after a critical review, being used since then for providing counseling on the fishery of the black scabbardfish, an important fishing resource for Portugal; Evaluation of the exploration state of the UNDULATA ray in the Portuguese continental waters; Development of statistical methodologies for considering in the modeling process the sampling schemes used for fishery data, strongly relying on commercial vessels, the preferential sampling.

Methods: State Space Models | Hierarchical models | Geostatistics | Space Point Processes

CMA Researchers: Isabel Natário, Paula Simões (recently)

Projects:

  • Participation in project UNDULATA, Estudo para o conhecimento da dinâmica populacional da espécie raia curva Raja undulata, na costa continental Portuguesa, PROMAR UNDULATA -Nº 31-03-01-FEP-0186.
  • Participation in project DEEPFISHMAN, EU Seventh framework programme, from 1st April 2009 to 30 March 2012, as a consultant PTDC/MAT-STA/28243/2017: PREFERENTIAL: Improving spatial estimation and survey design through preferential sampling in fishery and biological applications

Publications:

  • Figueiredo I, Natário I, Moura T, Carvalho ML (2013). Modelling the dynamics of the deep-water shark Centroscymnus coelolepis off mainland Portugal. Aquatic Living Resources, 26: 355- 364.
  • Natário, I., Figueiredo, I., Carvalho, M.L. (2015). A State Space Model Approach for Modelling the Population Dynamics of Black Scabbardfish in Portuguese Mainland Waters. In Dynamics Games and Science. Edts: Bourguignon, Jean-Pierre and Jeltsch, Rolf and Pinto, Alberto Adrego and Viana, Marcelo. CIM Series in Mathematical Sciences Volume 1: 499-512.

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Project: Climate change

Description:

Methods: Generalized linear models | Multivariate Statistics

CMA Researchers: Regina Bispo

Publications:

  • Faleiro, F., Pimentel, M., Pegado. M. R., Bispo, R., Lopes, A.R., Diniz, M. & Rosa, R. (206). Small pelagics in a changing ocean: biological responses of sardine early stages to warming. Conservation Physiology.
  • Pimentel, M., Faleiro, F., Marques, T. A., Bispo, R, Dionísio, G., Faria, A. M., Machado, J., Peck, M. A., Portner, H., Gonçalves, E., Pousão-Ferreira, P. & Rosa, R. (2016) Foraging behaviour, swimming performance and malformations of early stages of commercially important fishes under ocean acidification and warming. Climatic Change.