New insights in Bayesian Survival Analysis in Ecology

La fauna silvestre está asediada. Y ésta no es solo una frase impactante con la que empezar una tesis, tristemente, es una realidad. En el último siglo, muchas especies han disminuido drásticamente, mientras que otras afrontan su extinción debido, principalmente, a los rápidos cambios (y a gran escala) ocurridos tanto en hábitats como en ecosistemas. El cambio climático, las especies invasoras, la caza ilegal y la sobrepesca son sólo algunas de las principales amenazas que afectan a las poblaciones de animales silvestres en la actualidad. Para abordar este problema, se requiere de un compromiso a todos los niveles, desde las comunidades locales hasta los gobiernos, pasando por los expertos, la educación y la investigación. De hecho, la investigación es una herramienta fundamental para la conservación de las poblaciones silvestres. Entender los factores que afectan a las poblaciones nos permite mejorar su gestión ası́ como su seguimiento, y por lo tanto, su conservación. En las últimas décadas ha habido un gran aumento en la cantidad (y la variedad) de datos recogidos en los sistemas ecológicos, lo que ha conducido al desarrollo de modelos estadı́sticos más complejos. Esta complejidad hace que el proceso inferencial sea difı́cil de llevar a cabo. La perspectiva de la estadı́stica Bayesiana aparece como una buena alternativa para realizar dicho proceso inferencial debido a los avances computacionales ocurridos en las últimas décadas. Además, permite incorporar de manera sencilla la información inicial (si existe y está diponible) ası́ como tiene en cuenta la incertidumbre relativa tanto a los modelos como a los parámetros. En este trabajo investigamos las probabilidades de supervivencia, de recaptura, de recuperación y las probabilidades de migración en el contexto de los modelos de captura-recaptura(-recuperación). Estos modelos tienen en cuenta la detección imperfecta de los individuos, algo muy habitual en los sistemas ecológicos. De hecho, si la detección imperfecta no se tiene en consideración en el modelo puede causar sesgos en las estimaciones de los parámetros. Este trabajo se enmarca en un contexto real, en concreto, el estudio de una colonia de aves marina, el Arao común (Uria aalge). Las aves marinas se consideran centinelas del mar. Los cambios en sus poblaciones reflejan los cambios producidos en el mar, por lo que se consideran bioindicadoras de cambios medioambientales. Asimismo, el cálculo de las probabilidades de supervivencia juvenil en aves marinas es difı́cil debido a la ecologı́a de las especies. Por todo ello, esta tesis no solo supone un reto a nivel estadı́stico sino también a nivel ecológico. Con todo esto en mente, la estructura de la tesis es la siguiente. El Capı́tulo 1 ofrece la motivación ası́ como una revisión general de los métodos de captura-recaptura(-recuperación) y los modelos estadı́sticos asociados. En este Capı́tulo presentamos en detalle los dos modelos utilizados: los modelos de Cormack-Jolly-Seber (CJS) y los modelos de marcaje-recaptura-recuperación (modelos integrados). Además, este capı́tulo ofrece una introducción a la estadı́stica Bayesiana, ası́ como una descripción de uno de los principales métodos para llevarla a cabo, los métodos Markov chain Monte Carlo (MCMC). Por último, concluimos este Capı́tulo con una breve explicación de los dos algoritmos de simulación básicos basados en Métodos Monte Carlo de cadenas de Markov más conocidos (Metropolis-Hastings y Gibbs sampler), junto con una relación de programas y páginas web para la implementación de una gran variedad de modelos de captura-recaptura(-recuperación). El Capı́tulo 2 ofrece el contexto ecológico de esta tesis. Para ello, presentamos la especie objeto de estudio, el Arao común, ası́ como la colonia de estudio, Stora Karlsö (Gotland, Suecia). En este capı́tulo destacamos algunas de sus principales caracterı́sticas ecológicas, caracterı́sticas que necesitaremos conocer para el desarrollo de modelos estadı́sticos biológicamente motivados. La parte principal de este Capı́tulo consiste en una descripción de las dos bases de datos que han motivado el desarrollo metodológico realizado en esta tesis: una base de datos de captura-recaptura y otra de marcaje-recaptura-recuperación. En los Capı́tulos 3, 4 y 5 presentamos los estudios desarrollados a lo largo de esta tesis. En particular, el Capı́tulo 3 ofrece estimaciones fiables de supervivencia juvenil para el Arao común. La novedad de este trabajo radica en que los individuos inmaduros de esta especie (y en general, de las aves marinas) no pueden ser observados debido a que pasan largas temporadas en el mar. Sin embargo, esta colonia tiene una caracterı́stica especial: una elevada proporción de individuos inmaduros son observados, lo que permite obtener dichas estimaciones fiables de supervivencia juvenil. Además, este trabajo representa una primera aproximación al problema del monitoreo parcial, el cual causa sesgos en las estimaciones de los parámetros de interés. Para ello, adoptamos una aproximación subjetiva Bayesiana, de manera que incorporamos información previa acerca de las áreas donde el problema de monitoreo parcial está presente. El Capı́tulo 4 incorpora una metodologı́a comúnmente utilizada en los estudios médicos de supervivencia en el contexto de los modelos de captura-recaptura en ecologı́a. En particular, mostramos cómo las historias de captura se presentan de manera diferente dependiendo de la escala temporal escogida. Además, en este Capı́tulo presentamos cómo el uso de la escala temporal alternativa presentada (la edad) permite una mejor interpretación de los parámetros del modelo cuando la edad es el principal interés en el estudio. Finalmente, en el Capı́tulo 5 ofrecemos un contexto integrado de marcaje-recaptura-recuperación para estudios parcialmente monitorizados. La información suministrada por los datos de anillamiento-recuperación permite corregir los sesgos en las estimaciones de supervivencia obtenidos con datos (solo) de captura-recaptura debido al monitoreo parcial. Además, debido al gran tamaño de la base de datos, el modelo lo presentamos en formulación multinomial, de manera que ofrecemos la expresión explı́cita y eficiente de la verosimilitud ası́ como los estadı́sticos suficientes asociados del modelo integrado propuesto. Tanto la corrección del problema de monitoreo parcial (muy extendido en especies coloniales), como la construcción de las m-arrays integradas y la eficiente verosimilitud suponen un paso adelante en este área, tanto desde un punto de vista aplicado como metodológico. Esta tesis concluye con el Capı́tulo 6, donde se presentan las conclusiones y algunas lı́neas futuras de investigación, seguido de la bibliografı́a utilizada.Wildlife is under siege. And this is not only a fancy sentence to start a thesis, sadly, it is a fact. Over the last century, many wildlife species have seriously declined and many others face their extinction due to rapid and large-scale changes in habitats and ecosystems. Climate change, invasive species, illegal hunting and overfishing are only some of the main threats affecting animal populations nowadays. To address these concerns will require commitment at all levels, from local communities to governments, as well as experts, education and research. Indeed, research is a fundamental tool for conservation. Understanding the factors affecting wildlife populations allow us to improve the management of animal populations and therefore, their conservation. The recently increase in the amount (and variety) of data collected on ecological systems has led to the development of more complex statistical models. This complexity has made the inferential process challenging to perform. The Bayesian approach arises as an alternative to address these issues due to the computational advances occurred in the last decades. Further, prior information (if available) can be easily incorporated as well as this approach takes fuller account of the uncertainties related to models and parameters. In this work we investigate survival, recapture, recovery and migration probabilities in the context of capture-recapture(-recovery) models. These models account for imperfect detection, a common issue in ecological systems. Indeed, if imperfect detection is not taken into account, it may cause biases in estimated demographic parameters of interest. The context of this work is a real one, in particular, a seabird species, the common guillemot (Uria aalge). Seabirds are sentinels of the sea. Their populations reflect conditions over large spatial and long term scales, making them bioindicators of environmental change. Further, the estimation of juvenile survival probabilities in seabirds is far from simple, mainly due to their ecological characteristics. Therefore, this thesis supposes not only a challenge from statistical perspective but also from ecological one. With all this in mind, this thesis is structured as follows. Chapter 1 is devoted to provide the motivation along with an overview of the capture-recapture methods and associated statistical models. After that, we explain in detail the two models used: Cormack-Jolly-Seber (CJS) models and mark-recapture-recovery (MRR) models. Furthermore, we give an introduction of Bayesian inference, before describing the Markov chain Monte Carlo (MCMC) methods. Lastly, we conclude with a brief explanation of the two basic Markov chain simulation algorithms (Metropolis-Hastings and Gibbs sampler), as well as we provide useful software packages and web pages to implement a large variety of capture-recapture(-recovery) models. Chapter 2 takes a brief look at the ecological context of this thesis. To do so, we introduce the species focus of this research, the common guillemot, as well as the study colony, Stora Karlsö (Gotland, Sweden). We briefly provide some of its main ecological characteristics that will be necessary to know in order to fit statistical models biologically motivated. The main part of this Chapter consists in a detailed description of the two data sets that motivated the methodological developments performed in this thesis, a capture-recapture and a mark-recapture- recovery database. Chapters 3, 4 and 5 are dedicated to display the studies performed along this thesis. In particular, Chapter 3 is devoted to provide reliable juvenile survival estimates for common guillemots. The novelty of this work lies in the difficulty on the assessment of juvenile survival due to in this species (and in general, in most seabird species) young birds spend large periods at sea, remaining hence unobservable. However, the study colony has an special feature: a big proportion of immature birds are resighted allowing so to provide those reliable juvenile survival estimates. Further, this work represents a first approximation to the problem of partial monitoring that causes bias in parameter estimates. In particular, we adopt a subjective Bayesian approach so that we incorporate prior information corresponding to the areas where the partial monitoring is affecting. Chapter 4 incorporates a methodology commonly performed in medical survival studies in the context of ecological capture-recapture framework. In particular, we show how differently the capture histories are presented depending on the selected temporal scale. Further, the use of the alternative temporal scale presented (the age) may allow a better interpretation of model parameters when age is the primary interest. Finally, in Chapter 5 we provide an integrated mark-recapture-recovery framework for partially monitored studies. The information gathered by the ring-recovery data allows to correct the bias in survival estimates obtained with only capture-recapture data due to partial monitoring. Moreover, due to the (big) size of the database, we present it in multinomial formulation, so that we provide the explicit efficient likelihood expression along with the associated sufficient statistics of the integrated model proposed. Both the correction of partial monitoring problem (widespread in colonial species) and the construction of the integrated m-arrays along with the efficient likelihood suppose an step forward on this area, either from a practical or methodological perspective. Chapter 6 provides some conclusions and future lines of research, and finally a generic bibliography used along this work is presented

Increased parental effort fails to buffer the cascading effects of warmer seas on common guillemot demographic rates

Research Funding Natural Environment Research Council Award. Grant Number: NE/R016429/1 UK-SCAPE Programme Delivering National Capability Joint Nature Conservation Committee EU ‘The Effect of Large-scale Industrial Fisheries On Non-Target Species’ FP5 Project ‘Interactions between the Marine environment, PREdators and Prey: Implications for Sustainable Sandeel Fisheries’. Grant Numbers: MS21-013, Q5RS-2000-30864 Ministry of Universities-University of ValenciaPeer reviewedPublisher PD

Urinary Arsenic Species and Methylation Efficiency During Pregnancy: Concentrations and Associated Factors in Spanish Pregnant Women

Background: Arsenic (As) is considered to be toxic for humans, the main routes of exposure being through drinking water and the diet. Once ingested, inorganic arsenic can be methylated sequentially to monomethyl and dimethyl arsenicals. Several factors can affect both As exposure and methylation efficiency. Objectives: To describe the urinary concentrations of the different As species and evaluate the methylation effi-ciency during pregnancy, as well as their associated factors in a birth cohort of pregnant Spanish women. Methods: Participants in this cross-sectional study were 1017 pregnant women from two areas of Spain who had taken part in the INMA (Environment and Childhood) project (2003 & ndash;2008). Total As (organic and inorganic compounds) and its main metabolites (monomethylarsonic acid, [MMA], dimethylarsinic acid, [DMA], inorganic As [iAs]) and arsenobetaine [AB]) were measured in urine samples collected during the first trimester. Socio-demographic and dietary information was collected through questionnaires. Multivariate linear regression models were used to explore the association between As species concentrations and covariates. Arsenic methylation efficiency was determined through the percentages of the metabolites and using As methylation phenotypes, obtained from principal component analysis. Results: Median urine concentrations were 33.0, 21.6, 6.5, 0.35 and 0.33 lig/g creatinine for total As, AB, DMA, MMA and iAs, respectively. Daily consumption of rice and seafood during the first trimester of pregnancy were positively associated with the concentration of As species (i.e., beta [CI95%] = 0.36 [0.09, 0.64] for rice and iAs, and 1.06 [0.68, 1.44] for seafood and AB). TAs, AB and iAs concentrations, and DMA and MMA concentrations were associated with legume and vegetable consumption, respectively. The medians of the percentage of As metabolites were 89.7 for %DMA, 5.1 for %MMA and 4.7 for %iAs. Non-smoker women and those with higher body mass index presented a higher methylation efficiency (denoted by a higher %DMA and lower %MMA). Discussion: Certain dietary, lifestyle, and environmental factors were observed to have an influence on both As species concentrations and methylation efficiency in our population. Further birth cohort studies in low exposure areas are necessary to improve knowledge about arsenic exposure, especially to inorganic forms, and its potential health impact during childhood.This study was supported by grants from Instituto de Salud Carlos III, Spain [FIS-FEDER: 07/0314; FIS 11/01007, 13/1944, 16/1288, 19/1338; Miguel Servet-FEDER: CP15/0025, CPII20/00006; FIS-FSE: 17/00260; Miguel Servet-FSE: MS15/0025, MS20/0006; PI06/0867 and FIS-PI18/01142 incl. FEDER funds] , Generalitat Valenciana, Spain BEST/2020/059, Department of Health of the Basque Government, Spain (2005111093) , Provincial Government of Gipuzkoa (DFG06/002) , and annual agreements with the municipalities in the study area (Zumarraga, Urretxu, Legazpi, Azkoitia, Azpeitia and Beasain)

Exploring green gentrification in 28 global North cities : the role of urban parks and other types of greenspaces

Unidad de excelencia María de Maeztu CEX2019-000940-MAlthough cities globally are increasingly mobilizing re-naturing projects to address diverse urban socio-environmental and health challenges, there is mounting evidence that these interventions may also be linked to the phenomenon known as green gentrification. However, to date the empirical evidence on the relationship between greenspaces and gentrification regarding associations with different greenspace types remains scarce. This study focused on 28 mid-sized cities in North America and Western Europe. We assessed improved access to different types of greenspace (i.e. total area of parks, gardens, nature preserves, recreational areas or greenways [i] added before the 2000s or [ii] added before the 2010s) and gentrification processes (including [i] gentrification for the 2000s; [ii] gentrification for the 2010s; [iii] gentrification throughout the decades of the 2000s and 2010s) in each small geographical unit of each city. To estimate the associations, we developed a Bayesian hierarchical spatial model foreach city and gentrification time period (i.e. a maximum of three models per city). More than half of our models showed that parks-together with other factors such as proximity to the city center-are positively associated with gentrification processes, particularly in the US context, except in historically Black disinvested postindustrial cities with lots of vacant land. We also find than in half of our models newly designated nature preserves are negatively associated with gentrification processes, particularly when considering gentrification throughout the 2000s and the 2010s and in the US. Meanwhile, for new gardens, recreational spaces and greenways, our research shows mixed results (some positive, some negative and some no effect associations). Considering the environmental and health benefits of urban re-naturing projects, cities should keep investing in improving park access while simultaneously implementing anti-displacement and inclusive green policies

Crecimiento de pollos de Gaviota de Audouin: el papel de los factores pre y post eclosión

We compared the growth rates of Audouin´s Gull (Larus audouinii) chicks from the Ebro Delta and Columbretes Islands. Chicks from the Columbretes Islands were reared in captivity and fed ad libitum. Wild chicks from the Ebro Delta weighed more than chicks hatched from Columbretes eggs but attained a lower weight at fledging. Chicks from Columbretes eggs hatched with a longer wing length but rates did not differ between samples during the early stages of growth. Eggs from the Ebro Delta were significantly larger than eggs from Columbretes. Hence, differences in growth appeared not to be related to differences in egg size (prehatch factor) but only in parental quality (posthatch factor) through the amount of food delivered to chicks. These differences could be due to the incapacity of parents to provide enough food during the last stages of chick development, in part because of reduced food availability at the Ebro Delta during the study period. Alternatively, differences could be attributed to a trade-off between present and future reproduction. Demographic consequences of reduced food availability for the 1993 Ebro Delta cohort should be explored in future work.Este trabajo compara las tasas de crecimiento de pollos de Gaviota de Audouin (Larus audouinii) procedentes de huevos del delta del Ebro y de las islas Columbretes. Los pollos de las islas Columbretes fueron criados en cautividad y alimentados ad limitum. Los pollos salvajes del delta del Ebro pesaron más que los pollos procedentes de huevos de Columbretes, pero alcanzaron un peso menor en el momento de volar. Los pollos procedentes de huevos de Columbretes eclosionaron con una mayor longitud de ala pero las tasas de crecimiento no difirieron durante las primeras etapas de crecimiento. Los huevos del delta Ebro fueron significativamente más grandes que los huevos de Columbretes. Por tanto, las diferencias en el crecimiento parecieron no estar relacionadas con las diferencias en el tamaño del huevo (factor preeclosión) sino solo de la calidad parental (factor posteclosión), a través de la cantidad de comida suministrada a los pollos. Estas diferencias podrían ser debidas a la incapacidad de los padres de proporcionar suficiente comida durante las últimas fases del desarrollo de los pollos, en parte debido a una disminución en la disponibilidad de alimento en el Delta del Ebro durante el periodo de estudio. Por el contrario, las diferencias se podrían atribuir a un compromiso entre la reproducción presente y futura. Las consecuencias demográficas de la reducción en la disponibilidad de alimento para la cohorte de 1993 de Gaviota de Audouin en el delta del Ebro, deberían ser analizadas en el futuro

Unforeseen effects of ecosystem restoration on yellow-legged gulls in a small western Mediterranean island

A conservation project aimed at ecosystem restoration had several unforeseen effects on a colony of the yellow-legged gull Larus michahellis in a small western Mediterranean island (Benidorm Island). The project included regulation of massive tourist visits to help restore the soil and autochthonous vegetation. However, gulls habituated rapidly to regulation of tourist activities, as nests located either close to or far from the main trail showed a similar hatching success. The quiet conditions produced by regulation seemingly facilitated a rapid colony increase. Partial removal of alien vegetation (Opuntia maxima) showed that gulls had a preference for sites with high vegetation cover because the growth of the colony was proportionally larger in well-vegetated plots. The pricking of a large number of gull eggs surprisingly coincided with a high reproductive success compared to the previous year, although indicators of food availability remained constant between years and the colony had decreased in numbers. Untreated nests were probably more successful because territory size for chicks increased and intraspecific predation decreased. Extreme care must be taken when planning ecosystem-wide management on islands with yellow-legged gull colonies, or other gull species locally considered as pests, to prevent unwanted effects.Partially supported by funding from the LIFE02NATURE/E/8608 programme for the conservation of Audouin’s gull in the Valencian communityPeer Reviewe

Morphometric similarities between central and peripheral populations of the European Shag Phalacrocorax aristotelis

We compared morphometrics and discriminant functions for sexing European Shags Phalacrocorax aristotelis in a central (British) population and a peripheral (northwestern Iberia) population within its distribution range, to account for structural differences between populations and sexes. Overall, British shags were structurally larger than Iberian shags, except in their head and bill length. This north-south cline could be attributable to higher food availability or lower ambient temperatures at higher latitudes. Furthermore, Iberian male shags were structurally larger than females for all variables considered, except for bill length, which was similar for both sexes, as in the British population. This suggests that bill length is a conservative trait in the species, being similar between populations and sexes alike. The most parsimonious discriminant function for sexing Iberian shags included only bill depth, and it correctly sexed 92.6% of the original cases, as was the case among British shags. This suggests that the depth of the bill likely plays a relevant sex-specific role in the species. Applying discriminant functions derived from one population to other populations can be problematic. However, we found that the bill depth discriminant function for British shags correctly sexed 90.2% of Iberian shags, supporting the idea that, although British shags are larger than northwestern Iberian shags, differences between sexes are of the same magnitude.Peer Reviewe