Collective behavior of biological aggregates

Mención Internacional en el título de doctorThe behavior of living systems can exhibit emergent phenomena that are not present in their individual components. Living systems are far from equilibrium, may lack conservation laws and using tools from statistical physics and thermodynamics is challenging. However, quantitative observations and experiments yield a wealth of data that allow to design models capturing important aspects of the behavior of these systems. This thesis focuses on two topics, the collective behavior of midge swarms and the collective behavior of bacterial biofilms. Prior studies of insect swarms have focused on their formation as an ordering phase transition, which fails to capture many qualitative and quantitative features. In this thesis we study the Vicsek model confined by a harmonic potential. By using dynamical systems and statistical mechanics tools, we have discovered a novel phase transition characterized by scale free chaos, which exhibits power laws and present qualitative features compatible with observations of swarms of male midges in nature and in the laboratory. On the second topic, bacterial biofilms pose a challenge to theorists, who must model elements on different spatial and temporal scales. We present a hybrid model based on an architecture of immersed boundaries with a dynamic energy budget metabolism. The model captures geometric differences between bacteria, being able to reproduce varied patterns depending on their shapes and competence phenomena between different types. We can study antibiotic resistance in biofilms and test cocktails to eradicate them.El comportamiento de los sistemas vivos puede mostrar fenómenos emergentes que no están presentes en sus componentes individuales. Los sistemas vivos están alejados del equilibrio, pueden carecer de leyes de conservación y es todo un reto emplear herramientas de la física estadística y la termodinámica. Experimentos y observaciones cuantitativas producen una gran cantidad de datos que permiten diseñar modelos que expliquen aspectos importantes del comporamiento de estos sistemas. Esta tesis se centra en dos temas, el comportamiento colectivo de los enjambres de insectos voladores como los mosquitos y el comportamiento colectivo de las biopelículas bacterianas. Los estudios previos de enjambres de insectos se han centrado en su formación como una transición orden-desorden, lo que no explica muchos aspectos tanto cualitativos como cuantitativos. En esta tesis estudiamos el modelo de Vicsek confinado por un potencial armónico. Usando herramientas de sistemas dinámicos y de mecánica estadística hemos descubierto una nueva transición de fase caracterizada por caos libre de escalas, que presenta leyes de potencias y tiene rasgos cualitativos compatibles con las observaciones y experimentos de laboratorio de enjambres de dípteros. Por otro lado, las biopelículas bacterianas plantean un reto teórico, pues se debe modelar elementos a diferentes escalas espaciales y temporales. Presentamos un modelo híbrido basado en una arquitectura de fronteras inmersas con un metabolismo de presupuesto de balance energético. El modelo captura las diferencias geométricas entre bacterias, generando patrones diversos según su forma y competencia entre bacterias de distintos tipos. Permite estudiar la resistencia de biopelículas a antibióticos y el diseño de cócteles para erradicarlos.Agradezco el apoyo del Ministerio de Economía y Competitividad de España a través de las ayudas del programa de Formación de Doctores, PRE2018-083807, cofinanciada por el Fondo Social Europeo. También agradezco al apoyo de FEDER /Ministerio de Ciencia, Innovación y Universidades - Agencia Estatal de Investigación por medio de los proyectos MTM2017-84446-C2-1-R y PID2020-112796RB-C21.Programa de Doctorado en Ingeniería Matemática por la Universidad Carlos III de MadridPresidente: Björn Birnir.- Secretaria: Ester Aurora Torrente Orihuela.- Vocal: Antonio Prados Montañ

High Correlated Paternity Leads to Negative Effects on Progeny Performance in Two Mediterranean Shrub Species

Anthropogenic habitat deterioration can promote changes in plant mating systems that subsequently may affect progeny performance, thereby conditioning plant recruitment for the next generation. However, very few studies yet tested mating system parameters other than outcrossing rates; and the direct effects of the genetic diversity of the pollen received by maternal plants (i.e. correlated paternity) has often been overlooked. In this study, we investigated the relation between correlated paternity and progeny performance in two common Mediterranean shrubs, Myrtus communis and Pistacia lentiscus. To do so, we collected open-pollinated progeny from selected maternal plants, calculated mating system parameters using microsatellite genotyping and conducted sowing experiments under greenhouse and field conditions. Our results showed that some progeny fitness components were negatively affected by the high correlated paternity of maternal plants. In Myrtus communis, high correlated paternity had a negative effect on the proportion and timing of seedling emergence in the natural field conditions and in the greenhouse sowing experiment, respectively. In Pistacia lentiscus, seedling emergence time under field conditions was also negatively influenced by high correlated paternity and a progeny survival analysis in the field experiment showed greater mortality of seedlings from maternal plants with high correlated paternity. Overall, we found effects of correlated paternity on the progeny performance of Myrtus communis, a self-compatible species. Further, we also detected effects of correlated paternity on the progeny emergence time and survival in Pistacia lentiscus, an obligate outcrossed species. This study represents one of the few existing empirical examples which highlight the influence that correlated paternity may exert on progeny performance in multiple stages during early seedling growth.España , Ministerio de Ciencia e Innovación CGL2008-00938 and CGL2011-23721

Acerca de la identidad de Helianthemum mathezii y H. pomeridianum (Cistaceae)

The original description of Helianthemum mathezii regarded the species to be a therophyte. However, the detailed observation of the holotype of H. mathezii, as well as newly collected specimens from the type locality, does not support its condition of annual plant. Further study has led to the conclusion that all these plants can readily be identified as H. pomeridianum; the descriptions of H. mathezii and H. pomeridianum are equivalent except for the habit, being the former annual and the latter suffruticose. We show in this study that H. mathezii is to be considered a synonym of H. pomeridianum, and report a new locality of H. pomeridianum in Morocco. Also, we provide the first chromosome count for this species (2n = 22) which emphasizes the close relationship of H. pomeridianum to H. subgen. Plectolobum.En la descripción original de Helianthemum mathezii se considera esta especie como un terofito. Sin embargo, la observación minuciosa de su holotipo, así como de otros especímenes recientemente recolectados en la misma localidad del tipo, sugiere que no se trata de una planta anual. Concluimos que estas plantas pueden ser bien identificadas como H. pomeridianum; las descripciones de H. mathezii y H. pomeridianum son similares excepto en lo referido a su hábito, la primera supuestamente es una planta anual y la segunda sufruticosa. Así pues, aquí recomendamos considerar H. mathezii como sinónimo de H. pomeridianum, y citamos una localidad nueva de esta especie en Marruecos. Además, damos cuenta del primer recuento de cromosomas efectuado para la misma (2n = 22), que demuestra la estrecha afinidad de H. pomeridianum y H. subgen. Plectolobum

On the identity of <em>Helianthemum mathezii</em> and <em>H. pomeridianum</em> (Cistaceae)

The original description of Helianthemum mathezii regarded the species to be a therophyte. However, the detailed observation of the holotype of H. mathezii, as well as newly collected specimens from the type locality, does not support its condition of annual plant. Further study has led to the conclusion that all these plants can readily be identified as H. pomeridianum; the descriptions of H. mathezii and H. pomeridianum are equivalent except for the habit, being the former annual and the latter suffruticose. We show in this study that H. mathezii is to be considered a synonym of H. pomeridianum, and report a new locality of H. pomeridianum in Morocco. Also, we provide the first chromosome count for this species (2n = 22) which emphasizes the close relationship of H. pomeridianum to H. subgen. Plectolobum

Immersed boundary methods for biofilm spread

We propose a computational model to study the growth and spread of bacterial biofilms on surfaces. Bacterial membranes are represented by boundaries immersed in a fluid matrix and subject to interaction forces. Growth, division and death of bacterial cells follow dynamic energy budget rules, in response to variations in environmental concentrations of nutrients, substances released by the cells and toxicants. In this way, we create, enlarge and destroy boundaries, either spherical or rod-shaped. Appropriate forces represent details of the interaction between cells, and the interaction with the environment. Numerical simulations illustrate the evolution of small biofilm seeds. We are able reproduce experimentally observed features such as a tendency of rod-shaped bacteria to align and the formation of inner gaps (due the cell death and reabsorption) which fill with fluid. We calibrated the death parameters to reach a certain aggregate size in the absence of antibiotics, as a result of a balance between dead and newborn cells (as it happens in many tissues). When we add antibiotics small necrotic regions appear at the edges. Resorting to antibiotic cocktails targeting both active cells in the outer regions and dormant cells in the inner core we succeeded in eradicating the biofilm as observed in experiments.Depto. de Análisis Matemático y Matemática AplicadaFac. de Ciencias MatemáticasTRUEsubmitte

Immersed boundary approach to biofilm spread on surfaces

We propose a computational model to study the growth and spread of bacterial biofilms on surfaces. Bacterial membranes are represented by boundaries immersed in a fluid matrix and subject to interaction forces. Growth, division and death of bacterial cells follow dynamic energy budget rules, in response to variations in environmental concentrations of nutrients, substances released by the cells and toxicants. In this way, we create, enlarge and destroy boundaries, either spherical or rod-shaped. Appropriate forces represent details of the interaction between cells, and the interaction with the environment. Numerical simulations illustrate the evolution of small biofilm seeds. We are able reproduce experimentally observed features such as a tendency of rod-shaped bacteria to align and the formation of inner gaps (due the cell death and reabsorption) which fill with fluid. We calibrated the death parameters to reach a certain aggregate size in the absence of antibiotics, as a result of a balance between dead and newborn cells (as it happens in many tissues). When we add antibiotics small necrotic regions appear at the edges. Resorting to antibiotic cocktails targeting both active cells in the outer regions and dormant cells in the inner core we succeeded in eradicating the biofilm as observed in experiments

A phylogenetic hypothesis for Helianthemum (Cistaceae) in the Iberian Peninsula

We have sequenced the nuclear DNA internal transcribed spacer (ITS1+5.8S+ITS2) from samples collected in the field belonging to all taxa of Helianthemum in the Iberian Peninsula and analysed the data matrix by both Bayesian and Maximum Likelihood approaches. The phylogenetic hypothesis that we present here provides strong support for the monophyly of the genus and for the above-species systematics (sections and subgenera) considered in Flora iberica. Nevertheless, most species and subspecies in sections Helianthemum and Pseudocistus clustered in ample polytomies with poor resolution and branch support. This topology is interpreted to be consequence of frequent events of hybridization and introgression and/or rapid adaptive radiation in the genus Helianthemum, the most diversified lineage within the family Cistaceae.En este trabajo presentamos una hipótesis filogenética para el género Helianthemum en la Península Ibérica. Para ello hemos recolectado en el campo material de todos los taxones y analizado las secuencias del marcador nuclear ITS (internal transcribed spacer) completo (ITS1+5.8S+ITS2) tanto con métodos Bayesianos como de Máxima Verosimilitud. Nuestra hipótesis muestra gran apoyo para la monofilia de género y para los taxones supra-específicos considerados en Flora iberica (secciones y subgéneros). En cambio, las especies y subespecies de las secciones más extensas (Helianthemum y Pseudocistus) se han agrupado en amplias politomías con muy bajo apoyo. Interpretamos que esta marcador nuclear tiene baja resolución debido a eventos frecuentes de hibridación e introgresión así como de radiación adaptativa en el género Helianthemum, que es el linaje más diversificado de toda la familia Cistaceae

Extensive pollen flow but few pollen donors and high reproductive variance in an extremely fragmented landscape

Analysing pollen movement is a key to understanding the reproductive system of plant species and how it is influenced by the spatial distribution of potential mating partners in fragmented populations. Here we infer parameters related to levels of pollen movement and diversity of the effective pollen cloud for the wind-pollinated shrub Pistacia lentiscus across a highly disturbed landscape using microsatellite loci. Paternity analysis and the indirect KinDist and Mixed Effect Mating models were used to assess mating patterns, the pollen dispersal kernel, the effective number of males (N(ep)) and their relative individual fertility, as well as the existence of fine-scale spatial genetic structure in adult plants. All methods showed extensive pollen movement, with high rates of pollen flow from outside the study site (up to 73-93%), fat-tailed dispersal kernels and large average pollination distances (δ = 229-412 m). However, they also agreed in detecting very few pollen donors (N(ep) = 4.3-10.2) and a large variance in their reproductive success: 70% of males did not sire any offspring among the studied female plants and 5.5% of males were responsible for 50% of pollinations. Although we did not find reduced levels of genetic diversity, the adult population showed high levels of biparental inbreeding (14%) and strong spatial genetic structure (S(p) = 0.012), probably due to restricted seed dispersal and scarce safe sites for recruitment. Overall, limited seed dispersal and the scarcity of successful pollen donors can be contributing to generate local pedigrees and to increase inbreeding, the prelude of genetic impoverishment

Genetic structure and population differentiation of the Mediterranean pioneer spiny broom Calicotome villosa across the Strait of Gibraltar

The region around the Strait of Gibraltar is considered to be one of the most relevant 'hot spots' of biodiversity in the Mediterranean Basin due to its historical, biogeographical, and ecological features. Prominent among these is its role as a land bridge for the migration and differentiation of species during the Pleistocene, as a consequence of the lowering of sea level and climate changes associated with the Ice Ages. In the present study, we report a multilevel hierarchical investigation of the genetic diversity of Calicotome villosa, a common pioneer legume shrub, at the regional scale. The results of genetic analysis of progeny arrays are consistent with a predominantly outcrossing mating system in all the populations analysed. Geographically, a pattern of population isolation by distance was found, but the Strait accounted for only approximately 2% of the among-population genetic differentiation. Consequently, extensive historical gene flow appears to be the rule for this species in this area. According to the natural history traits of C. villosa (pollination, dispersal, and colonization ability), we hypothesize that gene flow must be strongly influenced by seed dispersal because pollen flow is very limited. Based on the history of trade and land use, cattle and human movements across the Strait must have strongly favoured seed dispersal. We review and discuss these results and compare them with those of other reported studies of genetic and phylogenetic differentiation across the Strait of Gibraltar. It is stressed that colonization ability, which depends upon seed dispersal and life form, can be a more critical factor in gene flow than pollination.Junta de Andalucía PB0551-95, PB1144-98BOS, 2003-07924-CO2-01 to J.A

Scale free chaos in swarms

Swarms are examples of collective behavior of insects, which are singular among manifestations of flocking. Swarms possess strong correlations but no global order and exhibit finite-size scaling with a dynamic critical exponent z ≈ 1. We have discovered a phase transition of the three-dimensional harmonically confined Vicsek model that exists for appropriate noise and small confinement strength. On the critical line of confinement versus noise, swarms are in a state of scale-free chaos that can be characterized by minimal correlation time, correlation length proportional to swarm size and topological data analysis. The critical line separates dispersed single clusters from confined multicluster swarms. Susceptibility, correlation length, dynamic correlation function and largest Lyapunov exponent obey power laws. Their critical exponents agree with those observed in natural midge swarms, unlike values obtained from the order-disorder transition of the standard Vicsek model which confines particles by artificial periodic boundary conditions