Understanding the life history response of animal populations to environmental selection pressure is a central research theme in evolutionary ecology and conservation biology. Our current knowledge of life history traits in animal populations is, however, mostly based on studies conducted on temperate systems, contrasting with the fact that a large number of species live in the tropics. The roseate tern (Sterna dougallii) is a oceanic seabird showing mainly a tropical distribution with a relatively fragile conservation status, making it an interesting case study. In this thesis, ten years of data (1998-2007) were used to determine the main demographic traits of the tropical roseate tern population breeding on Aride Island, Seychelles (western Indian Ocean), and to explore their relation with environmental factors. We focused on the estimation of reproductive success, age at first reproduction (sexual maturation) and age-specific survival probabilities in relation to both oceanography of the study area (food availability) and quality of the breeding habitat. By using chlorophyll concentrations as a proxy measure of marine fish stocks, we showed that the overall low reproductive success in this population (range 0.0 0.57 chick/pair) is mainly dictated by the strong inter-annual fluctuations in local food supply conditions around Aride Island. Reproductive success was also found to be related to the spatial variation in vegetation characteristics of the nesting (woodland) habitat used by the terns. Birds nesting in densely-vegetated areas with a closed canopy cover had higher chick mortalities, presumably through a high level of parasitism by ticks, when compared to those breeding in more open areas such as forest clearings. By relying on capture-mark-recapture methods, age of first reproduction was estimated at 3-4 years and age-specific survival probabilities at 0.62, 0.77 and 0.81 in juveniles (1-year), immature individuals (2-years), and breeding adults (3-years and older), respectively. Most of these demographic parameters were also found to be influenced by oceanographic conditions (e.g. Indian ocean Dipole) and the levels of tick infestation during the chick-growing period. We further show how these vital rates can be incorporated into a simple population viability analysis in order to model population dynamics (i.e. population growth rate) and, ultimately, to provide local managers with conservation measures. Finally, the contribution of this work to the global knowledge of tropical seabird life histories is discussed through a comparison with demographic parameters of temperate roseate tern populations.

Near the beginning of the last century, R. A. Fisher and Sewall Wright devised an elegant, mathematically tractable model of gene reproduction and replacement that laid the foundation for contemporary population genetics. The Wright-Fisher model and its extensions have given biologists powerful tools of statistical inference that enabled the quantification of genetic drift and selection. Given the utility of these tools, we often forget that their model - for reasons of mathematical tractability - makes assumptions that are violated in many real-world populations. In particular, the classical models assume fixed population sizes, held constant by (unspecified) sampling mechanisms. Here, we consider an alternative framework that merges Moran’s continuous time Markov chain model of allele frequencies in haploid populations of fixed size with the density dependent models of ecological competition of Lotka, Volterra, Gause, and Kolmogorov. This allows for haploid populations of stochastically varying – but bounded – size. Populations are kept finite by resource limitation. We show the existence of limits that naturally generalize the weak and strong selection regimes of classical population genetics, which allow the calculation of fixation times and probabilities, as well as the long-term stationary allele frequency distribution.

Range expansion events of the Humboldt squid reveal our inadequate understanding of populations of this species. Despite recent hatching, reproductive, tagging, genetic and dietary studies of Dosidicus gigas, much speculation remains concerning geographic migration, stock assessment and habitat preferences. This study provides evidence that statolith trace elemental variations can be useful in distinguishing among geographic populations. Specimens were collected from the Galapagos Islands, southern California, and Washington State. A dissection method was recorded and published. By using laser ablation methods, discrete measurements of 10 elements were collected at 6 to 7 ablation sites covering embryonic, paralarval, juvenile and adult stages. Analysis of Variance revealed important ontogenic elemental variations among ablation locations. Multivariate Analysis of Variance, ordination techniques and discriminant function analysis with permutation testing were all utilized to compare and characterize the variations found in elemental concentrations. Significant ontogenic variations were found for 8 out of the 10 focus elements; this is the first report for 5 of these elements for this species. The geographic populations were effectively classified as distinct group for the first time using these methods. Elemental fingerprint signatures were found to be significantly different at multiple ontogenic growth regions of the statolith. Seattle and California paralarvae exhibited similar elemental signatures despite significant differences in those found in the embryonic core and juvenile regions of the statolith. These methods are a useful tool in providing stock assessment and can be improved for use in future population dynamics models.

The central objective of this thesis is to better understand early life history dynamics of salmonids in large regulated rivers. I studied spawning, incubating, and age-0 life stages of rainbow trout in the Lee’s Ferry reach of the Colorado River below Glen Canyon Dam, AZ. My first objective was to evaluate the effects of hourly fluctuations in flow on nearshore habitat use and growth of age-0 trout. Catch rates in nearshore areas were at least 2- to 4-fold higher at the daily minimum flow compared to the daily maximum and indicated that most age-0 trout do not maintain their position within immediate shoreline areas during the day when flows are high. Otolith growth increased by 25% on Sundays in one year of study, because it was the only day of the week when flows did not fluctuate. My second objective was to evaluate the effects of flow fluctuations on survival from fertilization to a few months from emergence (early survival). Fluctuations were predicted to result in incubation mortality rates of 24% in 2003 and 50% in 2004, when flow was experimentally manipulated to reduce trout abundance, compared to 5% in 2006 and 11% in 2007 under normal operations. Early survival increased by over 6-fold in 2006 when egg deposition decreased by at least 10-fold. Because of this strong compensatory dynamic, flow-dependent incubation mortality in experimental years was likely not large enough to reduce the abundance of age-0 trout. My final objective was to determine how flow, fish size and density effects habitat use, growth, and survival of age-0 trout. Apparent survival rates from July to November were 0.18 (2004), 0.19 (2006), and 0.32 (2007). A stock synthesis model was developed to jointly estimate parameters describing early life history dynamics, and indicated that early survival was lower for cohorts fertilized during the first half of the spawning period and was negatively correlated with egg deposition, that movement of age-0 trout from low- to high-angle shorelines increased with fish size, and that survival varied by habitat type and over time in response to flow changes from Glen Canyon Dam.

En aquesta tesi es té en compte un model no lineal de creixement de població de cèl·lules que s'estructuren pel seu contingut de ciclina i cinases depenents de ciclina (CDK). Aquest model condueix a un sistema no lineal d'equacions en derivades parcials de primer ordre amb termes no locals. Per estudiar aquest sistema utilitzem la teoria de semigrups lineals positius i la formulació semilineal, que són eines molt poderoses per fer front a l'anàlisi d'aquest tipus de models, tant des del punt de vista del problema de valor inicial, com de l'existència i l'estabilitat d'estats estacionaris. El model que es considera a la tesi descriu la següent situació biològica: les cèl·lules s'estructuren en relació amb el contingut d'un determinat grup de proteïnes anomenades ciclines i CDK i es divideixen en dos tipus: proliferants i quiescents. Les cèl·lules proliferants creixen i es divideixen, donant a lloc al final del cicle cel·lular a noves cèl·lules, o bé van cap al compartiment de les quiescents, mentre que les cèl·lules quiescents no envelleixen ni es divideixen, ni canvien el seu contingut de ciclina, però o tornen cap al compartiment de proliferació o bé romanen en l’estat de repòs. D'altra banda, tant les cèl·lules proliferants com les quiescents poden experimentar l'apoptosi, la mort cel·lular programada. L'únic terme no lineal en el model és un terme de reclutament de cèl·lules quiescents cap a la fase de proliferació. En aquest treball demostrem l'existència global, unicitat i positivitat de les solucions del problema de valor inicial. Reescrivint el nostre sistema en una forma abstracta podem demostrar que un cert operador lineal és el generador infinitesimal d'un semigrup positiu fortament continu. D'altra banda s'utilitza la formulació semilineal estàndard per a l’equació no lineal abstracta i obtenim una única solució global positiva per a qualsevol condició inicial positiva a L1. També es prova l'existència i unicitat d'un estat estacionari no trivial del nostre sistema sota hipòtesis adequades. Com es fa sovint en situacions similars, el problema és relacionat amb provar l'existència (i unicitat) d'un vector propi positiu normalitzat. Això correspon als vectors propis del valor propi dominant d'un determinat operador lineal positiu parametritzat pel valor de la variable de feedback. L'existència tant del valor propi dominant i de (l’únic) vector propi positiu està donat per una versió del teorema de Perron- Frobenius en dimensió infinita. També s’inclouen simulacions numèriques basades en la integració al llarg de les línies característiques. Amb l'ajuda d'aquestes simulacions numèriques trobem inestabilitat de l'estat estacionari per a valors de paràmetres compatibles amb els que donen inestabilitat en el model de dimensió finita. També s'inclou la demostració de l'existència de solucions independents del contingut de ciclina per a una elecció molt particular dels valors dels paràmetres i funcions que defineixen el model. Finalment s'utilitza la formulació anomenada cumulativa (o en retard) de la dinàmica de poblacións estructurades. En particular s'ha considerat una versió diferent del model estudiat abans, on es suposa que el pas de proliferants a quiescents només pot ocórrer una sola vegada, enfocament oposat al primer model on aquestes transicions poden ocórrer infinites vegades. A més a més, també suposem que hi ha un valor particular x del contingut de ciclina que separa les cèl·lules que encara no es poden dividir de les altres que sí que poden dividir-se. L'equació del model resulta ser una equació amb retard que relaciona els valors actuals d'aquestes variables amb la seva història (el seu valor en el passat). Fent servir aquest enfocament, es pot provar l'existència i unicitat de solucions del problema de valor inicial, i el principi d'estabilitat lineal a través d'una formulació semilineal en el marc dels semigrups duals. / In this thesis we consider a nonlinear cell population model where cells are structured with respect to the content of cyclin and cyclin dependent kinases (CDK). This model leads to a first order nonlinear partial differential equations system with non local terms. To study this system we use the theory of positive linear semigroups and the semilinear formulation, which are very powerful tools to deal with the analysis of this kind of models, both from the point of view of the initial value problem as well as the existence and stability of steady states. The model considered in the thesis describes the following biological situation: cells are structured with respect to the content of a certain group of proteins called cyclin and CDK and are distributed into two types: proliferating and quiescent cells. The proliferating cells grow and divide, giving birth at the end of the cell cycle to new cells, or else transit to the quiescent compartment, whereas quiescent cells do not age nor divide nor change their cyclin content but either transit back to the proliferating compartment or else stay in the quiescent compartment. Moreover, both proliferating and quiescent cells may experiment apoptosis, i.e. programmed cell death. The only nonlinear term is a recruitment term of quiescent cells going back to the proliferating phase. In this work we start proving global existence, uniqueness and positiveness of the solutions of the initial value problem. We rewrite our system in an abstract form and show that some linear operator is the infinitesimal generator of a positive strongly continuous semigroup. On the other hand we use the standard semilinear formulation for the nonlinear (abstract) equation and obtain a unique global positive solution for any positive initial condition in L1. We also prove the existence and uniqueness of a nontrivial steady state of our system under suitable hypotheses. As it is often done in similar situations, the problem is related to proving the existence (and uniqueness) of a positive normalized eigenvector. This eigenvector corresponds to the dominant eigenvalue of a certain positive linear operator parameterized by the value of the (one dimensional) feedback variable G. The existence of both dominant eigenvalue and (unique) positive eigenvector is given by a version of the infinite dimensional Perron-Frobenius theorem. We include numerical simulations based on the integration along characteristic lines. With the help of these numerical simulations we find instability of the steady state for parameter values compatible with the ones which give instability in the finite dimensional model. We also include a computation showing the existence of cyclin-independent solutions for a very particular choice of the parameter values and functions defining the model. Finally we use the so-called cumulative or delayed formulation of the structured population dynamics. In particular we have considered a different version of the model studied before, where one assumes that proliferating cells can become quiescent only once opposed to the other approach where these transitions can occur infinitely many times and moreover, we also assume that there is a particular value x of the cyclin content that separates cells which still cannot divide from the others which are able to divide. The model equation turns out to be a delay equation relating the current values of these variables with their history (their value in the past). Using this approach, one can prove existence and uniqueness of solutions of the initial value problem, and the linear stability principle by means of a semi-linear formulation in the framework of dual semigroups.

Cerithium zonatum is a dominate species in an intertidal zone of Shi-Lang, Green Island. This study aimed to characterize the population dynamics, reproduction and trophic ecology of C. zonatum in this intertidal zone. Results indicated C. zonatum in rocky habitat had high density, high growth rate and small shell length. In seagrass bed it was low in population density and large in shell length. The reproductive season of C. zonatum was from spring to summer, with indirect development and short planktonic period. The C. zonatum was a primary consumer with £_13C values of -6.97 - -6.26‰ and £_15N values of 3.65 - 5.13‰. They fed on seagrass detritus and periphyton including microalgae and filamentous green algae. The major food was seagrass detritus and filamentous green algae in the seagrass beds. In the rocky and sand habitats, the major food was microalgae and filamentous green algae. The population dynamics and food sources of C. zonatum were different among seagrass bed, rocky and sand habitats. In general, the C. zonatum was an opportunistic feeder with low mobility. And, the high population density and growth rate of C. zonatum in rocky habitat might result from abundant food sources in the area.

The goal of my dissertation was to describe the dynamics of a group of Houston toads located at the Griffith League Ranch (GLR), Bastrop County, Texas. My research included using statistical modeling to predict activity and abundance, mark-recapture techniques to estimate survivorship, and simulation modeling to explore the impacts of the difference in age at first reproduction and to project the future dynamics of the population at the GLR. From 2001 – 2005, 225 individual Houston toads (199 M : 26 F) were captured using two methods: breeding pond surveys and drift fences. Houston toads were neither caught equally among capture methods, nor across years. Toad activity was mostly confined within their breeding season, and activity was not continuous. A logistic regression indicated activity depended on time of year, mean precipitation, mean minimum daily temperature, and mean percent lunation as well as two-way interactions with moon-phase and other variables. Abundance depended on time of year, current precipitation, minimum temperature, and two-way interactions between time of year and the other two variables. Twenty-one of the 199 males (10.5%) and no females were recaptured among years. The probability of male survival was estimated using program MARK. Eight of 16 candidate models were supported and all but one contained precipitation as a covariate, indicating precipitation is important for Houston toad survival. Survivorship estimates varied from 0.1 to 0.41. The sex ratio was significantly male-biased. The odds of catching females in traps were 3.5 greater than capturing females in a pond, while the odds of capturing males in a trap were 0.28 compared to ponds. Results from a simulation model indicated the sex ratio is biased because of the difference in maturation times between males and females, coupled with high juvenile mortality. Results from an individual-based, spatially-explicit, stochastic simulation model, indicated a relatively low probability (~ 0.013) of B. houstonensis going extinct at the GLR within the next 10 years. Emergent properties of the model were similar to results observed in the field or reported in the literature. The model also identified that dispersal of Houston toads should be a future research priority.

The population dynamics and the feeding of the scyphomedusa Aurelia aurita in Tapeng Bay, southwestern Taiman, were investigated from April, 1999 to April, 2000 and May, 2001 to April, 2002. A. aurita distributed mainly in the inner water of the Bay. The average abundance of A. aurita was 71¡Ó256 ind.100m¡Ð3, with higher abundance in winter and spring than in summer and autumn. The abundance of A. aurita showed no significant correlation with hydrographic features, but it seems to have one or two month¡¦s time lag with the seasonal distribution pattern of copepods. The main reproduction period of A. aurita was form autumn to next spring. The occurrence of ephyra was mainly in winter and spring, with maximum abundance of 328 ind./100m3. The average bell diameter of A. aurita was 13.9¡Ó4.2 cm. The size of bell diameter varied seasonally, generally had larger size in autumn and smaller size in spring. Seventeen zooplankton taxa were found in the stomach contents of A. aurita, copepods were the most dominant (70.3%), followed by copepods nauplius (20.1%), bivalve larva (3.0%) and fish eggs (2.3%). The average ingestion rate of A. aurita was 2165¡Ó2673 prey ind.-1 day-1 , the feeding impact of A. aurita on zooplankton was 14.69 % ~ 40.84 % %, with no significant difference among sizes.

Many insects form symbioses with maternally inherited, intracellular bacteria, which can have major effects on the ecology and evolution of the insect host. Here I investigated the interaction between a global agricultural pest, Bemisia tabaci (the sweetpotato whitefly), and a Rickettsia bacterial symbiont. Rickettsia had previously been tracked sweeping through field populations of B. tabaci in the southwestern USA and had been shown to dramatically increase whitefly fitness under laboratory conditions. In contrast, the Rickettsia present in whiteflies in Israel has few observable fitness effects and is declining in frequency in field populations. I explored the population dynamics of Rickettsia in B. tabaci field populations in the USA and Israel, and assessed the genetic diversity of the Rickettsia in these populations. In laboratory experiments, there was no observable effect of Rickettsia on the heat shock or constant temperature tolerance of USA B. tabaci. Instead, whitefly genetic background appears to influence the effects of Rickettsia. Lastly, analysis of the genome sequence of Rickettsia provided insights into the mechanism of the fitness benefit and evolutionary history of the bacterium. Taken together, these integrated ecological, physiological and genomic studies provide some explanation for the contrasting and wide-ranging phenotypes associated with whitefly Rickettsia, and provide support for the hypothesis that the fitness benefit provided by Rickettsia is context dependent. The Rickettsia symbiosis exhibits geographically distinct population dynamics, is affected by whitefly genotype, and may involve manipulation of host plants and/or defense against pathogens rather than nutritional supplementation. Overall, these results highlight the important role that microbial symbionts may play in the adaptation of invasive species to changing environments.

The central objective of this thesis is to better understand early life history dynamics of salmonids in large regulated rivers. I studied spawning, incubating, and age-0 life stages of rainbow trout in the Lee’s Ferry reach of the Colorado River below Glen Canyon Dam, AZ. My first objective was to evaluate the effects of hourly fluctuations in flow on nearshore habitat use and growth of age-0 trout. Catch rates in nearshore areas were at least 2- to 4-fold higher at the daily minimum flow compared to the daily maximum and indicated that most age-0 trout do not maintain their position within immediate shoreline areas during the day when flows are high. Otolith growth increased by 25% on Sundays in one year of study, because it was the only day of the week when flows did not fluctuate. My second objective was to evaluate the effects of flow fluctuations on survival from fertilization to a few months from emergence (early survival). Fluctuations were predicted to result in incubation mortality rates of 24% in 2003 and 50% in 2004, when flow was experimentally manipulated to reduce trout abundance, compared to 5% in 2006 and 11% in 2007 under normal operations. Early survival increased by over 6-fold in 2006 when egg deposition decreased by at least 10-fold. Because of this strong compensatory dynamic, flow-dependent incubation mortality in experimental years was likely not large enough to reduce the abundance of age-0 trout. My final objective was to determine how flow, fish size and density effects habitat use, growth, and survival of age-0 trout. Apparent survival rates from July to November were 0.18 (2004), 0.19 (2006), and 0.32 (2007). A stock synthesis model was developed to jointly estimate parameters describing early life history dynamics, and indicated that early survival was lower for cohorts fertilized during the first half of the spawning period and was negatively correlated with egg deposition, that movement of age-0 trout from low- to high-angle shorelines increased with fish size, and that survival varied by habitat type and over time in response to flow changes from Glen Canyon Dam.