Modeling foundation species in food webs

Foundation species are basal species that play an important role in determining community composition by physically structuring ecosystems and modulating ecosystem processes. Foundation species largely operate via non-trophic interactions, presenting a challenge to incorporating them into food web models. Here, we used non-linear, bioenergetic predator-prey models to explore the role of foundation species and their non-trophic effects. We explored four types of models in which the foundation species reduced the metabolic rates of species in a specific trophic position. We examined the outcomes of each of these models for six metabolic rate “treatments” in which the foundation species altered the metabolic rates of associated species by one-tenth to ten times their allometric baseline metabolic rates. For each model simulation, we looked at how foundation species influenced food web structure during community assembly and the subsequent change in food web structure when the foundation species was removed. When a foundation species lowered the metabolic rate of only basal species, the resultant webs were complex, species-rich, and robust to foundation species removals. On the other hand, when a foundation species lowered the metabolic rate of only consumer species, all species, or no species, the resultant webs were species-poor and the subsequent removal of the foundation species resulted in the further loss of species and complexity. This suggests that in nature we should look for foundation species to predominantly facilitate basal species.Organismic and Evolutionary Biolog

Synthesis of spatial and trophic networks and their response to global change

Increasing human demands for production and goods continuously leads to the loss and fragmentation of habitat and eutrophication and threatens biodiversity. Organisms that comprise biodiversity interact with each other and depend on each other and thus, biodiversity is organised in complex interaction network. On the one hand, food-web research has addressed how trophic interactions shape local communities and how global change drivers such as eutrophication affects them. On the other hand, metacommunity research has been focused on spatial distributions and geographic drivers of local and regional biodiversity and how global change drivers such as habitat fragmentation species communities. These two realms have, however, mostly been separate. In this thesis, I present a meta-food-web model that synthesizes local trophic interactions and interpatch dispersal. This model employs species body masses as an interlinking trait that creates food webs and trophic dynamics through predator-prey body mass ratios and spatial networks through species dispersal capacities. With the meta-food-web model, I uncover mechanisms shaping biodiversity that only arise as a consequence of the synthesis of spatial and trophic interactions. The perspective from meta-food-webs reveals that the effect of global change drivers such as eutrophication and habitat fragmentation are highly context dependent and their effect depends on food-web and landscape structures. Furthermore, I show that interacting global change drivers can create non-linearities in biodiversity responses. Thus, this thesis provides a tool and theory derived hypotheses to shed light on consequences of global change and on what may be important to conserve biodiversity

Mutualistic networks: moving closer to a predictive theory

Plant–animal mutualistic networks sustain terrestrial biodiversity and human food security. Global environmental changes threaten these networks, underscoring the urgency for developing a predictive theory on how networks respond to perturbations. Here, I synthesise theoretical advances towards predicting network structure, dynamics, interaction strengths and responses to perturbations. I find that mathematical models incorporating biological mechanisms of mutualistic interactions provide better predictions of network dynamics. Those mechanisms include trait matching, adaptive foraging, and the dynamic consumption and production of both resources and services provided by mutualisms. Models incorporating species traits better predict the potential structure of networks (fundamental niche), while theory based on the dynamics of species abundances, rewards, foraging preferences and reproductive services can predict the extremely dynamic realised structures of networks, and may successfully predict network responses to perturbations. From a theoretician’s standpoint, model development must more realistically represent empirical data on interaction strengths, population dynamics and how these vary with perturbations from global change. From an empiricist’s standpoint, theory needs to make specific predictions that can be tested by observation or experiments. Developing models using short‐term empirical data allows models to make longer term predictions of community dynamics. As more longer term data become available, rigorous tests of model predictions will improve.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/151249/1/ele13279_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/151249/2/ele13279.pd

Biotic Interactions at Species’ Range Limits in a Changing Climate

As the global climate changes, many species are shifting their geographic ranges, often towards the poles or upslope in elevation. The ubiquity of these observation has renewed discussions about the mechanisms that determine species’ range margins. Leading hypotheses state abiotic variables should be the most important factor for setting range limits in environmentally stressful habitats. However, I propose an alternative hypothesis that biotic interactions may still be critically important for setting range limits, even in abiotically stressful habitats. Using a model system of ponds in the Rocky Mountains of Colorado, I developed several field experiments to empirically test the role of biotic interactions, including competition and predation, for setting range limits at across regional elevational gradients and among local habitats. First, I conducted a field experiment spanning an elevational gradient (2800 – 3400 m a.s.l.) to show that biotic interactions can indeed play important roles in maintaining range limits in abiotically stressful habitats. Second, using a field experiment examining a more localized hydroperiod gradient, I show that predation can facilitate the coexistence of competing resident and range-shifting species further supporting the importance of species interactions for maintaining range limits. Third, I show that long-term patterns in species persistence at their range margins are not always correlated with pair-wise interactions, suggesting the importance of considering the entire suite of interactions a species encounters in the ecological communities at their range margins. Finally, I propose a new framework for considering species interactions and range margins in a changing climate. This framework takes a whole food-web approach and integrates the effects of abiotic variables like temperature on the population demographics of and interactions between members of ecological communities. Together these studies highlight the importance of considering both abiotic variables and biotic interactions together if we are to truly understand the effects of climate change on species’ geographic distributio

Multiple stressors effects on community stability

Las actividades antropogénicas ejercen una presión constante sobre los sistemas naturales, amenazando la diversidad, la estabilidad y el funcionamiento de estos en todo el planeta. Además, existe un gran número de factores de estrés antropogénico, como son la eutrofización, la contaminación química y los eventos extremos, que actúan de manera simultánea. En esta tesis se evalúan e implementan nuevos enfoques para comprender los efectos individuales y combinados de los factores de estrés antropogénico sobre la estabilidad de las comunidades y ecosistemas de agua dulce. Esto se hace, en un primer lugar, revisando la literatura disponible sobre los efectos combinados de las olas de calor y los contaminantes químicos, destacando los vacíos de conocimiento y sugiriendo formas eficientes de integrar los eventos extremos en la evaluación del impacto ambiental de los factores de estrés múltiple. Esta tesis se basa también en grandes experimentos de mesocosmos al aire libre para investigar los efectos de los factores de estrés múltiple sobre las comunidades y ecosistemas dulceacuícolas. En estos trabajos se analizan los efectos de tres estresores agrícolas (dos pesticidas y la contaminación por nutrientes) a nivel de población, comunidad y ecosistema, y se estudian sus impactos sobre la estabilidad del ecosistema y la dimensionalidad entre los parámetros que describen dicha estabilidad. Además, se explora el potencial de las redes tróficas para dilucidar los mecanismos que impulsan la disimilitud composicional de las comunidades acuáticas después de la aplicación de una perturbación puntual, y se evalúan los mecanismos que influyen en la aparición de interacciones entre los factores de estrés en el largo plazo. Finalmente, este trabajo analiza los efectos de los eventos extremos, como las olas de calor, sobre la complejidad de los ecosistemas de agua dulce utilizando métricas topológicas y cuantitativas de redes tróficas. En ese sentido, los cambios en la complejidad de la red trófica fueron vinculados con los cuatro componentes que definen la estabilidad del sistema, y que caracterizan la estabilidad funcional, estructural y de los flujos de energía entre las especies que forman la red trófica. En general, esta tesis propone un enfoque general para dilucidar los efectos del cambio global sobre la estabilidad de los ecosistemas, brindando información útil para preservar la estructura y funcionalidad de éstos en condiciones ambientales cambiantes

Thermal tolerance and cadmium susceptibility of amphipods endemic to Lake Baikal

Lake Baikal is affected by global change and regional human activities. The effects of rising temperature and pollution on the unique endemic littoral amphipod fauna of Lake Baikal are unresolved yet. This thesis provides insights into physiological processes determining thermal tolerance and cadmium (Cd) susceptibility in two littoral amphipod species (Eulimnogammarus verrucosus and Eulimnogammarus cyaneus) compared to the related gammarid Gammarus lacustris, which is ubiquitously spread in the Holarctic. Thermal constraints on the oxygen supply system in E. verrucosus, E. cyaneus and G. lacustris may shape the upper temperature limits to the thermal habitats of the species, in line with the theories of allometry of thermal tolerance and systemic to molecular hierarchy of thermal tolerance. Lethal concentrations of Cd were much lower for E. cyaneus and G. lacustris than for E. verrucosus. However, E. verrucosus showed metabolic depression when exposed to Cd concentrations far below lethal ones. These findings underscore the necessity of water management strategies strictly avoiding chemical contamination of Lake Baikal waters

The impact of deleterious mutations on the transition to meiotic sex and the structure of the germline

The accumulation of deleterious mutations predicted by Muller’s ratchet – the progressive increase in mutation load caused by genetic drift – can cause the extinction of asexual populations and is considered one of the forces behind the maintenance of sex, the evolution of sex chromosomes, and the loss of genetic information in inversions. Here, I investigate the extent to which this process has influenced, constrained, and shaped the evolution of life. Using theoretical and computational models, I demonstrate that the need for increased purifying selection played a key role in major evolutionary transitions, focussing on the origin of meiotic sex and the evolution of the female germline. Early models of the origin of sex have generally focussed on the transition from asexual to sexual lifestyle. It is now universally accepted that prokaryotes undergo homologous recombination via lateral gene transfer (LGT), which can prevent the mutational meltdown predicted by Muller’s ratchet. Here, I investigate the origin of sex as part of the transition from prokaryotes to eukaryotes. I develop a theoretical model to investigate the impact of the increase in genome size and density of genomic repeats that took place during eukaryogenesis. My results indicate that these conditions led to the failure of LGT, generating a strong selective pressure for the origin of meiotic sex. But while meiotic sex can facilitate purifying selection on nuclear genes, it cannot prevent the accumulation of mutations in mitochondrial DNA (mtDNA). I demonstrate that the need to preserve mtDNA against Muller’s ratchet caused the evolution of tight mechanisms for mitochondrial quality control, shaping the evolution of the female germline in metazoans. This theoretical framework can be applied to a wide range of biological processes, including bacterial evolution, genome streamlining in organelles and endosymbionts, and the evolution of a two-step meiosis

Transcriptomic and proteomic studies on longevity induced by over-expression of HSP22 in drosophila melanogaster

Le vieillissement est un processus complexe accompagné par une capacité diminuée des cellules à tolérer et répondre aux formes différentes de stress causant des dommages comme l'agrégation de protéine dans les différentes composantes de la cellule. Les chaperons sont des joueurs probablement importants dans le processus de vieillissement en prévenant la dénaturation et l'agrégation des protéines. Chez Drosophila melanogaster, une petite protéine de choc thermique, Hsp22, localisée dans la matrice mitochondriale montre une expression elevée pendant le vieillissement. Sa surexpression chez la mouche augmente la durée moyenne de vie ainsi que la résistance au stress. Bien que Hsp22 montre une activité de chaperon dans des essais in vitro, les mécanismes par lesquels Hsp22 permet d’accroitre la durée de vie in vivo sont toujours inconnus. Une analyse transcriptionelle de tout le génome par microarrays et une analyse comparative du protéome mitochondrial par MALDI-TOF a été entreprise pour dévoiler les différences d’expression entre les mouches surexprimant Hsp22 et les contrôles appropriés. La surexpression générale de Hsp22 en utilisant le système GAL4/UAS dans Drosophila résulte en une augmentation de ~ 30% dans la durée de vie moyenne. L'analyse du transcriptome suggère que Hsp22 joue un rôle dans la détermination de durée de vie en changeant le processus général de vieillissement normal. Effectivement, les mouches surexprimant Hsp22 affichent une surexpression de gènes dont l’expression baisse normalement durant le vieillissement. Les gènes sont impliqués dans la production d'énergie, la biosynthèse des protéines, le taux de renouvellement des protéines et le métabolisme lipidique. L'analyse du protéome mitochondrial soutient aussi un rôle de Hsp22 sur la détermination de la durée de vie en maintenant la fonction mitochondriale et en favorisant la protéolyse. Les présentes données suggèrent l'importance de la maintenance de l’homéostasie protéique durant le vieillissement et discutent des mécanismes potentiels d’extension de la longévitié chez les mouches surexprimant Hsp22.Aging is a complex process accompanied by a decreased capacity of cells to tolerate and respond to various forms of stresses leading to damages such as protein aggregation in various components of the cell. Chaperones are thus likely important players in the aging process by preventing protein denaturation and aggregation. In Drosophila melanogaster, a small heat shock protein Hsp22 localized in the mitochondrial matrix is preferentially up-regulated during aging. Its over-expression results in an extension of lifespan and an increased resistance to stress. Although Hsp22 has been shown to have a chaperone-like activity in vitro, the mechanisms by which it extends lifespan in vivo are still unknown. Genome-wide transcriptional analysis by microarray and comparative mitochondrial proteomic analysis by MALDI-TOF mass analysis have been performed to unveil differences in long-lived Hsp22 over-expressing flies and normal-lived control flies. Ubiquitous over-expression of Hsp22 using the GAL4/UAS system in Drosophila resulted in a ~ 30% increase in mean lifespan. The genomic analysis suggests that Hsp22 plays a role in lifespan determination by altering the regulation of the overall process of normal aging. Indeed, flies over-expressing Hsp22 display an up-regulation of genes normally down-regulated with age and involved in energy production, protein biosynthesis, protein turnover, and lipid metabolism. Mitochondrial proteomic analysis also supports a putative role of Hsp22 on lifespan determination by maintaining mitochondrial function and favoring proteolysis. The present data suggest the importance of the maintenance of protein homeostasis in aging and potential mechanisms of longevity in the Hsp22 over-expressing flies