Frederico Mestre

Networks describe nodes connected by links, with numbers of links per node, the degree, forming a range of distributions including random and scale‐free. How network topologies emerge in natural systems still puzzles scientists. Based on previous theoretical simulations, we predict that scale‐free food webs are favourably selected by random disturbances while random food webs are selected by targeted disturbances. We assume that lower human pressures are more likely associated with random disturbances, whereas higher pressures are associated with targeted ones. We examine these predictions using 351 empirical food webs, generally confirming our predictions. Should the topology of food webs respond to changes in the magnitude of disturbances in a predictable fashion, consistently across ecosystems and scales of organisation, it would provide a baseline expectation to understand and predict the consequences of human pressures on ecosystem dynamics.

The aims of the present work are 1) to evaluate the distribution of the Polecat (Mustela putorius) in an area of Southern Portugal, identifying the major environmental descriptors upon which it depends; and 2) to compare the results of two different approaches to model species distribution. Two methods were used; one utilizing presence/absence data in a logistic regression (LR) model, and the other using presence-only data by means of ecological niche factor analysis (ENFA). The results clearly show that, as in other parts of Europe, the Polecat’s presence in Portugal is closely connected to humid habitats and dense vegetation cover. Overall, the environmental descriptors that most infl uence Polecat distribution are main water course length, the number of scrubland patches, the Shannon Wiener landscape diversity index and the number of water surface patches. The two methods we used generated significant differences in their predictions. LR predicts a broader area for the presence o...

This package provides a set of tools to help the ecological de-fragmentation of landscapes divided by linear transportation infrastructures. It works by prioritizing the different sections of these infrastructures (e.g. roads, railways) to increase the available amount of a given resource for widlife

Code and data for the manuscript "<b>Inferring past refugia and demographic history of an Iberian endemic vole through the integration of fossil, niche modelling and genomic data</b>"<br>Frederico Mestre, Soraia Barbosa, José A. Garrido-García, Ricardo Pita, António Mira, Paulo C. Alves, Joana Paupério, Jeremy B. Searle and Pedro Beja<br><b>ENM.zip</b> - R code for the Ecological Niche Modelling<b>genetic_analysis.zip</b> - Demographic genomic modelling, range expansion and spatially explicit refugium inference.<b>shapefiles.zip</b> - Current species occurrence, fossil locations for Last Glacial Maximum and Mid-Holocene<br>

R code for the manuscript "<b>Inferring past refugia and demographic history of an Iberian endemic vole through the integration of fossil, niche modelling and genomic data</b>"<br>Frederico Mestre, Soraia Barbosa, José A. Garrido-García, Ricardo Pita, António Mira, Paulo C. Alves, Joana Paupério, Jeremy B. Searle and Pedro Beja<br><b>ENM.zip</b> - R code for the Ecological Niche Modelling<b>genetic_analysis.zip</b> - Demographic genomic modelling, range expansion and spatially explicit refugium inference.<b>shapefiles.zip</b> - Current species occurrence, fossil locations for Last Glacial Maximum and Mid-Holocene<br>

Food webs represent energy fluxes and nutrient cycling between interacting species, underpinning ecosystem functioning. Whether and how interactions vary over environmental gradients is still largely unknown. We reviewed the literature searching for systematic relationships between structural food-web properties and environmental gradients. Temperature and biotic factors are amongst the most addressed drivers in determining structural food web properties. Most studies are local, replication is often lacking, and regional generalities are difficult to derive. The lack of a consistent theory predicting how food webs change across environmental gradients, the diversity of objectives in food-web studies, and the absence of a standardized methodology for studying them severely limit progress in the field. Moving forward requires the establishment of a core set of testable predictions, agreed standards for data collection and analysis, and the development of geographically distributed exp...

Here we provide the code and datasets for the manuscripts "Human disturbances affect the topology of food webs". Food web matrices were retrieved from online repositories (Ecobase and Globalweb) using the code in https://github.com/FMestre1/fw_package.<br>Data set and Matlab code:<br>FW.m - code to plot the data.catFW.m - code to categorize the food webs.dbaseIndexes.mat - database with the food web information.FWinfo_Real.mat - list of food web interaction matrices.<br>RData versions of the dataset:<br>FW_database_25AJAN2021.RData - database with the food web information.matrix_list_25AJAN2021.RData - list of food web interaction matrices.

R code for the manuscript "<b>Integrating fossil, niche modelling and genetic information to infer past refugia and range shifts in an Iberian endemic vole</b>"<br>by:<br>Frederico Mestre, Soraia Barbosa, José A. Garrido-García, Ricardo Pita, António Mira, Paulo C. Alves, Joana Paupério, Jeremy B. Searle and Pedro Beja<br><b>ENM.r</b> - R code for the Ecological Niche Modelling.<br><b>rangeExpansion.r</b> - R code used for the range expansion analyses.<br><br><b>MC_coords_107samples_OG.csv</b> - Coordinate file for 107 107 Microtus cabrerae and one Microtus agrestis sample, with lat/long, information regarding the four Evolutionarily Significant Units (ESUs) for M. cabrerae (region), population ID (pop) and if the sample was used as outgroup (outgroup).<br><b>MC_GBS_107samples_OG.csv</b> - Genotyping-by-sequencing results for 107 Microtus cabrerae and one Microtus agrestis...

Additional file 1. Additional figures and tables depicting the changes in simulation stability with the number of iterations (Annex 1), an overview of the output post-processing (Annex 2), the full output graphs (Annex 3) and a table with a brief review of the published literature with examples of real species and systems (Annex 4).

Climate change and increasing habitat loss greatly impact species survival, requiring range shifts, phenotypic plasticity and/or evolutionary change for long term persistence, which may not readily occur unaided in threatened species. Therefore, defining conservation actions requires a detailed assessment of evolutionary factors. Existing genetic diversity needs to be thoroughly evaluated and spatially mapped to define conservation units (CUs) in an evolutionary context, and we address that here. We also propose a multidisciplinary approach to determine corridors and functional connectivity between CUs by including genetic diversity in the modelling while controlling for isolation-by-distance and phylogeographic history. We evaluate our approach on a near-threatened Iberian endemic rodent by analysing genotyping-by-sequencing (GBS) genomic data from 107 Cabrera voles (Microtus cabrerae), screening the entire species distribution to define categories of CUs and their connectivity: we defined six management units (MUs) which can be grouped into four evolutionarily significant units (ESUs) and three (putatively) adaptive units (AUs). We demonstrate that the three different categories of CU can be objectively defined using genomic data, and their characteristics and connectivity can inform conservation decision-making. In particular, we show that connectivity of the Cabrera vole is very limited in eastern Iberia, and that the pre-Pyrenean and part of the Betic geographic nuclei contribute the most to the species genetic diversity. We argue that a multidisciplinary framework for CU definition is essential, and that this framework needs a strong evolutionary basis

ABSTRACT O veado, Cervus elaphus é uma das espécies de caça maior de maior importância em termos económicos e sociais, em Portugal. Embora os estudos sobre o veado sejam abundantes, a informação relativa à sua ecologia em habitats mediterrânicos é relativamente escassa, particularmente no que se refere aos biótopos utilizados e à selecção de habitat. A existência desta informação é, contudo, um passo primordial na elaboração de planos de gestão eficazes para as populações desta espécie. 0 presente estudo, visa analisar a existência da selecção de habitat em diferentes fases do ciclo de vida do veado, no Perímetro Florestal da Contenda (PFC), uma área com reduzida intervenção humana, de características eminentemente mediterrânicas, onde esta espécie é sujeita a caça. O Perímetro Florestal da Contenda situa-se no Concelho Moura. Encontra-se dividido pela ribeira do Murtigão em duas regiões principais: Contenda Norte (região plana onde domina o montado de azinho esparso) e Contenda Sul (região com relevos mais acentuados, maior diversidade de biótopos estruturalmente mais densos e complexos como matos, azinhal, sobreiral e florestas de produção). O clima na Contenda e tipicamente mediterrânico com uma época mais seca entre Maio e Setembro onde podemos observar temperaturas mais elevadas e valores de precipitação mais reduzidos. A pluviosidade média anual é de 729,5 mm. Para este estudo foram consideradas três épocas de amostragem, Fevereiro/Marco, Junho e Agosto. Definiu-se um trajecto, com 42 km de comprimento, formado por vários troços, que atravessava os principais habitats existentes na área de estudo. O trajecto, foi percorrido na íntegra, duas vezes (ao nascer e ao pôr-do-sol) em cada época de amostragem Em cada amostragem foram contabilizados apenas os animais observados numa faixa de 250 m para uma lado e outro da linha média do percurso. Para efeitos de tratamento de resultados, os habitats foram agrupados em cinco classes estruturalmente homogéneas: montado de azinho, matos; pinhal bravo/eucaliptal, pinhal manso e sobreiral. A existência de selecção de habitat foi avaliada com base em testes de qui-quadrado e por intervalos de confiança de Bailey. Estes apresentam a vantagem de poder ser aplicados de forma robusta a amostras pequenas. Na época de Fevereiro/Marco o único biótopo evitado foi o montado de azinho, o que provavelmente se terá ficado a dever à utilização desta área pelo gado doméstico, Nas restantes épocas de estudo (quando as necessidades hídricas são mais importantes) a maior afluência de animais a este habitat poderá explicar-se pela elevada disponibilidade de água (existem vários charcos artificiais e pequenos açudes para o gado). Em Fevereiro/Marco o pinhal manso foi procurado bem como o sobreiral. A maior protecção que estes biótopos, estruturalmente mais densos oferecem, e no caso do sobreiral a maior disponibilidade de alimento, poderão estar na origem deste resultado. Em Junho e Agosto, a perturbação causada por acções de desmatação e desbaste em algumas áreas de pinhal bravo, eucaliptal e sobreiral pode ter condicionado os resultados, levando a que estes biótopos fossem por vezes evitados pelos veados. Os matos foram utilizados de forma crescente entre Fevereiro e Agosto, embora só na última época se tivesse observado uma selecção positiva deste biótopo. Esta preferência pode ter-se ficado a dever à procura de áreas menos expostas, face às elevadas temperaturas que caracterizam esta época do ano. Na sua globalidade os nossos resultados demonstram a selectividade do veado em relação aos habitats ocupados nas diferentes épocas do ano. Embora a multiplicidade de factores que potencialmente influenciam esta selecção não nos permitam ser conclusivos quanto às suas causas, os nossos resultados sugerem que as disponibilidades hídricas e de alimento, a termorregulação, a competição com gado e a perturbação humana, serão os factores que isoladamente, ou interactuando entre si, mais influenciam este processo.

El turón es una especie extensamente distribuida a través de Europa, pero es también relativamente desconocido cuando comparado a otros carnívoros europeos, particularmente mediterráneos (Virgós, 2003). El habitat más favorable al turón, según Lodé (1993), son los húmedales y la cubierta densa del bosque. Zabala et al (2005) estudiaron la especie en España y relacionaron su presencia con la ocurrencia de los cursos del agua y con una mayor diversidad del paisaje. La vegetación a longo de los ríos y riberas asume una importancia más alta en paisajes alterados debido a intensificación de la agricultura. Estos habitat llegaron a ser muy importantes para los carnívoros ibéricos, principalmente en áreas con una agricultura más intensa (Virgós, 2001). El turón puede utilizar estos habitats, cerca de los ríos y riberas del área de estudio. No en tanto, si pregunta: lo utilizan porque tienen alivian utilizándolo o, debido al uso intenso de la matriz del paisaje, fueron empujados a estos habitats? El objetivo de este estudio era evaluar los descriptores ambientales que influencian al turón y comparar dos métodos: Ecological Nich Factor Analisys del lugar (ENFA) (Hirzel et al., 2002a) y regresión logística (LR). La diferencia principal entre estos dos acercamientos es el hecho de que la primera utiliza datos de la presencia-solamente mientras que el segundo utiliza datos de presencia y ausencia.

ABSTRACT Rehabilitation is an important part of sea turtle conservation, and post-release tracking of the animals is both a way of obtaining information on their movements and behaviour and, at least temporarily, monitoring the success of the rehabilitation process. Two green turtles, Chelonia mydas, and one loggerhead turtle, Caretta caretta, were rehabilitated after long periods in captivity, and their movements followed by satellite tracking after their release near the south of Portugal. Location data were obtained for an average of 688 days after release. All three animals showed a directional movement and the last observed locations coincided with known feeding areas for both species, near the coasts of Mauritania and the state of Ceará, Brazil, for the green turtles, and near Cuba for the loggerhead. Bathymetry, surface currents, wind, sea surface temperature, chlorophyll-a concentration and geomagnetic field were analysed as spatial and environmental variables potentially affecting movement. Only bathymetry, sea surface temperature and geomagnetic variables showed significant association with the path choice. This project supports the notion that sea turtles have the ability to survive in the wild after long periods in captivity and to return to the species' known feeding areas, justifying the effort in their rehabilitation and post-release tracking.

O presente trabalho foi efectuado no âmbito de um projecto maior, que teve como objectivo monitorizar as populações de várias espécies importantes para a conservação na região de influência da futura albufeira do Pedrógão. Os trabalhos de monitorização decorreram desde finais de 2003 e Novembro de 2004.

Understanding the relationship between spatial patterns of landscape attributes and population presence and abundance is essential for understanding population processes as well as supporting management and conservation strategies. This study evaluates the influence of three factors: environment, habitat management, and season on the presence and abundance of the wild rabbit (Oryctolagus cuniculus), an important prey species for Mediterranean endangered predator species. To address this issue, we estimated wild rabbit presence and abundance by latrine counting in transects located in 45 plots within a 250×250 m grid from June 2007 until June 2009 in a 1,200 ha hunting area in southern Portugal. We then analyzed how wild rabbit presence and abundance correlate with the aforementioned factors. Our results showed that the main variable influencing wild rabbit presence and abundance was the distance to the artificial warrens. North and northeast slope directions were negatively related ...

SUMMARY. — The aims of the present work are 1) to evaluate the distribution of the Polecat (Mustela putorius) in an area of Southern Portugal, identifying the major environmental descriptors upon which it depends; and 2) to compare the results of two different approaches to model species distribution. Two methods were used; one utilizing presence/absence data in a logistic regression (LR) model, and the other using presence-only data by means of ecological niche factor analysis (ENFA). The results clearly show that, as in other parts of Europe, the Polecat’s presence in Portugal is closely connected to humid habitats and dense vegetation cover. Overall, the environmental descriptors that most infl uence Polecat distribution are main water course length, the number of scrubland patches, the Shannon Wiener landscape diversity index and the number of water surface patches. The two methods we used generated signifi cant differences in their predictions. LR predicts a broader area for th...

Climate change and increasing habitat loss greatly impact species survival, requiring range shifts, phenotypic plasticity and/or evolutionary change for long-term persistence, which may not readily occur unaided in threatened species. Therefore, defining conservation actions requires a detailed assessment of evolutionary factors. Existing genetic diversity needs to be thoroughly evaluated and spatially mapped to define conservation units (CUs) in an evolutionary context, and we address that here. We also propose a multidisciplinary approach to determine corridors and functional connectivity between CUs by including genetic diversity in the modelling while controlling for isolation by distance and phylogeographic history. We evaluate our approach on a Near Threatened Iberian endemic rodent by analysing genotyping-by-sequencing (GBS) genomic data from 107 Cabrera voles (Microtus cabrerae), screening the entire species distribution to define categories of CUs and their connectivity: We...

El turón es una especie extensamente distribuida a través de Europa, pero es también relativamente desconocido cuando comparado a otros carnívoros europeos, particularmente mediterráneos (Virgós, 2003). El habitat más favorable al turón, según Lodé (1993), son los húmedales y la cubierta densa del bosque. Zabala et al (2005) estudiaron la especie en España y relacionaron su presencia con la ocurrencia de los cursos del agua y con una mayor diversidad del paisaje. La vegetación a longo de los ríos y riberas asume una importancia más alta en paisajes alterados debido a intensificación de la agricultura. Estos habitat llegaron a ser muy importantes para los carnívoros ibéricos, principalmente en áreas con una agricultura más intensa (Virgós, 2001). El turón puede utilizar estos habitats, cerca de los ríos y riberas del área de estudio. No en tanto, si pregunta: lo utilizan porque tienen alivian utilizándolo o, debido al uso intenso de la matriz del paisaje, fueron empujados a estos habitats? El objetivo de este estudio era evaluar los descriptores ambientales que influencian al turón y comparar dos métodos: Ecological Nich Factor Analisys del lugar (ENFA) (Hirzel et al., 2002a) y regresión logística (LR). La diferencia principal entre estos dos acercamientos es el hecho de que la primera utiliza datos de la presencia-solamente mientras que el segundo utiliza datos de presencia y ausencia.

The red deer  (Cervus elaphus L.) is  the big game species most valuable in Portugal. However, exploitation programs of this species in game reserves are often based on scarce and  inaccurate information on deer population. Reliable estimations of deer densities are needed in order to implement profitable Game Management Programs.
The study was carried out in Perimetro Florestal da Contenda, a 5319 ha State Game Reserve, in Southern Portugal. The main goals were to get strong  estimations of deer density by sex, season, habitat and age class (calves/adults). This information is intended to be used in de development of Game Management Program for the area.
The study site is included at the National List of Sites proposed to be a part of Natura 2000 Network. It is one of the wildest areas in Portugal where some threatened species and Mediterranean habitats can still be found in a highly favourable conservation state.

O veado (Cervus elaphus) é uma espécie com grande implementação a nível nacional uma vez que é a espécie de caça maior com mais importância em termos económicos e sociais. Embora os estudos sobre o veado sejam abundantes, a informação relativa à sua ecologia em habitats mediterrânicos é relativamente escassa, particularmente
no que se refere aos biótopos utilizados e à selecção de habitat. A existência desta informação é, contudo, um passo primordial na elaboração de planos de gestão eficazes para as populações desta espécie. O presente estudo, visa analisar a existência da selecção de habitat em diferentes fases do ciclo de vida do veado, no Perímetro Florestal da Contenda (PFC), uma área com reduzida intervenção humana, de características eminentemente mediterrânicas, onde esta espécie é sujeita a caça.