Les pêcheries de thonidés représentent 7.9% de la production mondiale de produits de la mer. La plupart des stocks de thons sont pleinement exploités, et certains surexploités, et tous font face à une pression de pêche croissante. En raison de l'extension des zones de pêche, les évaluations des stocks dépendent en grande partie des captures commerciales. Toutefois, les données commerciales peuvent varier au cours du temps étant donné que les pêcheurs peuvent investir dans des engins de pêche et de l'équipement, s'établir au large des côtes, ou commencer à pêcher dans de nouvelles zones. Peu d'attention a été portée à la réponse des pêcheurs aux mesures de gestion ou aux conséquences de l'investissement technologique. L'objectif de la présente thèse est d'étudier les effets de stratégies de pêche et les réponses adaptatives des flottes de senneurs sur les thons tropicaux et la faune associée dans l'Océan Atlantic Est et dans l'Océan Pacifique Est. Dans un premier temps, nous montrons comment l'introduction de nouvelles technologies a eu un effet direct en augmentant la puissance de pêche, et un effet indirect en entraînant une modification des zones pêche. Nous étudions les effets de deux fermetures spatio-temporelles sur la dynamique de la flotte de senneurs européens. La première mesure de gestion a diminué les jours où des captures sont réalisées, les carrés avec capture à l'intérieur de la zone partiellement fermée, tandis que la pêche sur DCP a été redistribuée à l'extérieur de la zone et aucun changement n'a pas été enregistré pour la pêche sur banc libre. La seconde fermeture de pêche a entraîné une augmentation de toutes les activités de pêche en dehors de la zone. Dans l'Océan Pacifique Est, la flotte de senneurs mexicains a réagit à la fermeture d'une saison de pêche en diminuant le nombre de jours passés à quai. Par conséquent, le nombre de calées sur bancs associés aux dauphins a augmenté, et les niveaux de capture observés avant la mesure de gestion ont été maintenues. Nous analysons les effets des stratégies de senneurs de l'Union Européenne sur les prises accessoires. Nous mettons en évidence que la composition des espèces de requins capturés sous DCP et les raies capturées sur bancs libres ont changé au cours du temps. Nous estimons également que plusieurs types d'espèces peuvent être capturés par mode de pêche. / Tuna and tuna-like fisheries represent 7.9% of the global production of marine capture fisheries. Most tuna stocks are fully exploited and some overexploited, facing growing fishing pressures. Due to the extent of fishing grounds, stock assessments depend largely in commercial data, which vary over time because fishermen may invest in fishing technology, expand offshore, or start fishing in different areas. However, little attention has received the responses of fishermen facing management regulations or the effects resulting from technological investment. For these reasons the aim of this study was to investigate the effects of fishing strategies developed by purse seine fleets on tropical tunas and on associated fauna in the eastern Atlantic and eastern Pacific oceans. The continuous introduction of new fishing technology in the French fleet in the 1980s and the 1990s evidenced a direct increase in fishing power when large yellowfin in free-swimming school is targeted and likely an indirect effect by modifying the fishing grounds characterizing FAD-fishing on small size categories. The consequences of the two time-area closures on the spatio-temporal dynamics of the European Union fleet were investigated. The regulation on FADs resulted in a decrease in the days with catch and successful squares inside the restricted area, reallocating FAD-fishing outside the area while no change in free-swimming school fishing was observed. The no-take time-area increased all fishing activities outside the restricted area with apparently no gain in terms of protection of juveniles. In the eastern Pacific as a response to a closed season the Mexican fleet reduced days in port and consequently the number of sets on dolphin-associated schools increased, maintaining the catch levels observed before the regulation. The study of the effects of the EU fleet fishing strategies on bycatch over two time periods showed that the species composition of sharks caught on FADs and may be for rays caught on free-swimming schools changed over time. We also estimated the total number of species that can be potentially be caught by fishing mode.

<p>Sea turtles are long lived marine species that are currently endangered because their life history and population dynamics hinder them from withstanding modern anthropogenic threats. Worldwide, fisheries bycatch in on the major threats to the survival of sea turtles and that is also the case in the Eastern Pacific. To establish regional conservation priorities for the mitigation of bycatch, it is essential to first obtain a comprehensive picture of the regional sea turtle bycatch situation. This comprehensive analysis was lacking for the Eastern Pacific; therefore one component of this dissertation (the first chapter) is focused on delivering a regional bycatch analysis for the Eastern Pacific. A literature review was conducted to obtain numbers of turtles captured, frequencies, bycatch and mortality rates per species and country in trawl, longline, and gillnet fisheries, and to compile results of mitigation measures. Moreover, estimates for current annual capture rates in trawl fisheries were obtained and compared with population numbers. </p><p>This regional bycatch used all the information compiled and synthesized to give conservation priorities at the regional level. The review underlines the high bycatch rates in trawls for Costa Rica, Guatemala, and El Salvador and the detrimental impact that these captures could have specially for hawksbill Eretmochelys imbricata due to its reduced population numbers and for green turtle Chelonia mydas due to its highest mortality rate. It also emphasizes the continuous lack of use of TEDs as a bycatch mitigation measure. In longline fisheries, the review identifies the high bycatch rates in pelagic longline fisheries of Costa Rica, Ecuador, and Nicaragua in a global context but given that olive ridley Lepidochelys olivacea is the most common species captured in these countries, it highlights the capture of loggerhead Caretta caretta and leatherback Dermochelys coriacea off Peru and Chile due to their small population numbers. Bottom longlines have high mortality rates compared with pelagic longlines in the region and the review identifies a need for further research in this area due to the scarce information but high mortality rates. The review also noted that some mitigation measures for pelagic longlines like circle hooks and hooks with appendages could bring improvements in the mitigation of bycatch in longline fisheries in the region, there is still considerable work to be done in technology transfer, sea turtle handling, and estimates of post-release mortality rates. </p><p>For gillnet fisheries, the most important highlight is how little information exists for the region given the high rates of bycatch for sea turtles in this gear. However, the difficulties of studying bycatch in highly dynamic and artisanal fisheries are recognized as the major impediment for this situation. Nevertheless, the high bycatch rates in areas where sea turtles congregate in high numbers like in foraging grounds for loggerhead in Baja California, Mexico and for greens in Paracas and Sechura, Peru, calls for either gear modifications (which has not been that successful), change of gear, or areas closed for gillnets. </p><p>The second half of the dissertation is focused on foraging ecology of oceanic sea turtles in the Southeast Pacific Ocean. Sea turtles in the oceanic stage are the least known stage due to the difficulty of accessing these individuals. However, it is a very important stage in the life cycle and can be critical for the population dynamics of sea turtles as some population models have shown. Therefore, this dissertation is filling a gap in the life cycle of sea turtle populations in the Eastern Pacific. </p><p>To study foraging ecology, we used Stable Isotope Analysis (SIA) of turtle tissues as well as potential prey items from the oceanic realm. SIA is a great tool because it gives an integrated view, from days to weeks, of prey from a consumer tissue. SIA also can be used to link consumers to habitats when elements that have spatial trends are used. In chapter two, we investigate the foraging ecology of three species of sea turtles to compare trophic status and to observe if spatial patterns were shown in the SIA signatures of sea turtles. To our knowledge this is the first study employing SIA to research the ecology of three species of sea turtles from the same time and space. Our results show that spatial patterns in delta15N and delta13C were observed in sea turtle's tissues as correlations with latitude. We also found that loggerhead's signatures differed significantly from green and olive ridleys, especially in terms of delta15N. Loggerheads had higher values of delta15N and also a wider nitrogen trophic niche. Greens and olive ridleys were similar in isotopic nitrogen values but they were significantly different in carbon. When analyzing a smaller group of animals captured in a more restricted area, nitrogen differences were not found which suggests that latitudinal spatial patterns play an important role in the nitrogen signature. On the contrary, carbon signatures still differed among turtles in the restricted area which suggest that the inshore-offshore trend is strong and made us conclude that loggerheads are restricted to oceanic areas but that greens and olive ridleys could be using both coastal and oceanic areas.</p><p>In chapter three, we conduct a mixing model analysis using the Bayesian program SIAR to identify the most important prey items for green, olive ridley, and loggerhead off Peru. Also, we wanted to identify the contribution of longline baits in the diet of oceanic turtles. The analysis was restricted to the central zone of our study area to avoid spatial trends in nitrogen. To use as sources in the model, we collected potential prey items offshore Peru during trips on longline fishing vessels and obtained their stable isotope signatures. Results from our mixing models show that for greens and olive ridleys, crustaceans, mollusks, and coastal Ulva (indicator of coastal prey) were the only important food items. In the case of greens, crustaceans had a very high proportional contribution and due to the fact that nitrogen values of crustaceans were the lowest ones among the sources it seems that greens would be eating in a lower trophic level. The importance of coastal Ulva for greens and olive ridleys is a confirmation of our findings from chapter two where we suggest that these two species could be using oceanic as well as coastal areas. </p><p>Results for loggerheads showed cnidarians, mollusks, mackerel and squid bait as foraging items and highlights the differences among this species and the other two. The lack of importance of coastal Ulva again suggests that loggerheads remain only in oceanic areas off Peru. Moreover, the importance of mackerel and squid, the most common longline baits, suggests this species is the one interacting the most with longline fisheries and that cumulative effect of multiple interactions could have a detrimental effect in this population.</p> / Dissertation

<div>Inferring genetic population structure in endangered, highly migratory species such as sea turtles is a necessary but difficult task in order to design conservation and management plans. Genetically discrete populations are not obvious in highly migratory species, yet require unique conservation planning due to unique spatial and behavioral life-history characteristics. Population structure may be inferred using slowly evolving mitochondrial DNA (mtDNA), but some populations may have diverged recently and are difficult to detect using mtDNA. In these cases, rapidly evolving nuclear microsatellites may better elucidate population structuring. Bayesian inference and ordination may be useful for assigning individuals to inferred populations when populations are unknown. It is important to carefully examine population inference results to detect hierarchical population structuring, and to use multiple, mathematically diverse methods when inferring and describing population structure from genetic data. Here I use Bayesian inference, ordination, and multiple genetic analyses to investigate population structure in Olive ridley sea turtles (ORs; Lepidochelys olivacea) nesting in northwestern Costa Rica (NWCR) and across the entire Eastern Tropical Pacific (ETP). Mitochondrial DNA did not show structure within NWCR, and existing data from prior studies are not appropriately published to compare NWCR to Mexican ORs. In NWCR, Bayesian inference suggested one population, but ordination suggested four moderately structured populations with high internal relatedness, and moderate to high levels of connectivity. In the ETP, Bayesian inference suggested a Mexican and Central American population, but hierarchical analysis revealed a third subpopulation within Mexico. Ordination revealed nine cryptic clusters across the ETP that primarily corresponded to Mexican and Central American populations but contained individuals from both populations, some from other, distant nesting sites. The subpopulation within Mexico was well-defined after ordination, and all clusters displayed high 10 internal relatedness and moderate genetic differentiation. Bottlenecks were detected in both putative populations, at seven Mexican and two Central American nesting beaches, and in six out of nine inferred clusters, including three out of four Mexican clusters. Bottleneck events may have played some role in cluster differentiation. Migration was significant from Mexico to Central America at multiple levels, but did not necessarily agree with potential migrants elucidated by ordination. Migration was generally lower between ordination-inferred clusters than between nesting sites or Bayesian-inferred clusters. Phylogenetic trees generally supported structuring by ordination, rather than by Bayesian inference. Structuring in ordination not tied to bottleneck events could be due to mating behaviors or patterns of nesting beach colonization dictated by environmental features. In this study, ordination provided a more practical and nuanced framework for defining MUs and DIPs in ETP ORs than did STRUCTURE. This may be due to hierarchical structuring within ETP ORs that may be present in other sea turtle populations and species. In the case of ETP ORs, hierarchical structure may be an artefact of recent population bottlenecks and subsequent recolonization of nesting beaches, or due to mating at foraging grounds or along migratory routes. Bayesian inference may not be the best method for population inference in highly migratory species such as sea turtles, which have a high potential for broad scale genetic connectivity, and therefore may display hierarchical population structuring not easily related to nesting sites. Future studies, and perhaps published studies, should incorporate Bayesian inference and ordination, as well as other measures of population divergence and descriptive statistics, when searching for population structure in highly migratory species such as sea turtles.</div>

We examine the eastern Pacific Ocean Intertropical Convergence Zone (ITCZ) both in its mean state and transient phases using a combined diagnostic, theoretical and numerical modeling approach. We note that the ITCZ is perpetually in a transient state with strong variability occurring on 4-8 day time scales. Transients, about half the amplitude of the mean ITCZ, propagate northwards from the near-equatorial southern hemisphere eventually increasing the convection in the vicinity of the mean ITCZ convection. It is argued that the mean ITCZ is continually inertially unstable with incursions of anticyclonic vorticity advected across the equator resulting in the creation of a divergence-convergence doublet. The low-level convergence generates convection and vortex tube stretching which generates cyclonic vorticity counteracting the northward advection of anticyclonic vorticity. During a cycle, the heating in the mid-troposphere near 10°N oscillated between 6 and 12 K/day at the inertial frequency of the latitude of the mean convection. The shallow meridional circulation, noted in the mean field in other studies, appears to be a result of the transient nature of the ITCZ. It is hypothesized that westward propagating equatorial waves result from the inertial oscillation of the ITCZ. To test that the waves are formed in situ in the eastern Pacific and not remnants of waves propagating from the Atlantic or promoted by the Central and South American orography, several numerical experiments are undertaken using a high-resolution regional model spanning the western Atlantic Ocean and the eastern Pacific. In the control case, the model is initialized at all boundaries with full high-frequency observations. In two additional experiments, these transients are filtered out, and a third experiment is run with the topography over a large part of Central and South America removed. In all experiments, westward propagating waves are formed in the region of high CEPG suggesting that the hypothesis of in situ development may be correct.

The remarkable salinity difference between the upper Pacific and Atlantic Oceans is often explained through net export of water vapour across Central America. To investigate this mechanism a study of salinity signals in the Equatorial Pacific Ocean current system was made looking at responses to fresh water input from two sources (local versus remote - Atlantic Ocean) as well as a combination of the two. Statistical analyses (Empirical Orthogonal Functions, Single Value Decomposition and Wavelet analysis) were used to split the main sources of the atmospheric freshwater input into local and remote contributions and to quantify both contributions. The remote source was assumed to have been transported over Central America from the Atlantic Ocean as an atmospheric freshwater flux, whereas the local source originated in the Pacific Ocean itself. The analysis suggests that 74% of the total variance in precipitation over the tropical eastern Pacific is due to water vapour transport from the Atlantic. It also demonstrates strong influence of ENSO events, with maximum correlation at a two months time lag. During La Ni�a periods the precipitation variance is more closely related to water vapour transport across Central America (the remote source), while during El Ni�o periods it is more closely related to the water vapour transport by Southerly winds along the west coast of South America (the local source). The current and temperature fields provided by the Modular Ocean Model (version 2) were used to study the changes in the salinity field when freshwater was added to or removed from the model. ECMWF ERA-40 data taken from the ECMWF data server was used to determine the atmospheric flux of freshwater at the ocean surface, in the form of evaporation minus precipitation (E-P). The Mixed Layer Depth (MLD) computed from temperature and salinity fields determines to what depth the salinity's dilution/concentration takes place for every grid point. Each MLD was calculated from the results of the previous time step, and the water column was considered well mixed from the surface to this depth. The statistical relationships were used to reconstruct the precipitation over the tropical eastern Pacific. A numerical ocean model, which uses currents and temperature from a global ocean model and is forced by precipitation, was used to study the ocean's response to either the remote or the local source acting in isolation. Through time lag correlation analysis of the sea surface salinity anomalies produced by the variation in the reconstructed precipitation fields, it is found that the anomaly signals of salinity propagate westward along the Equator at a rate of approximately 0.25 m.s-1 (6.1 degrees per month).

Coral mortality caused by El Niño–Southern Oscillation (ENSO) activity and its related disturbances has been researched throughout the Eastern Pacific. In the past three decades, disturbances related to the El Niño–Southern Oscillation (ENSO) have been shown to influence coral growth in the Eastern Pacific. In the Galápagos Islands, Ecuador, more than 97% of corals experienced mortality after the severe 1982-1983 ENSO episode. However, two of the most dominant coral species found in a coral community adjacent to Devil’s Crown; Psammocora stellata and Diaseris distorta survived this severe ENSO event. By reconstructing sediment cores of the coral community, this study assessed how the coral assemblage has changed over the past 7,700 years of the Holocene epoch. The historical reconstructions were then related to existing records of Holocene ENSO variability in order to determine if changes in the relative abundance of coral species were related to ENSO activity and disturbances. We observed high variability in the relative abundances of P. stellata and D. distorta in the cores, including an increase in the abundance of D. distorta at approximately 2,200 yBP. Between the two species, opposite abundance trends were observed and supported by Detrended Correspondence Analysis (DCA) and Non-metric Multidimensional Scaling (NMDS) ordination analysis. Overall, the high variance in coral composition at the site throughout the Holocene documents repeated disturbance events in this region.

Porites lobata is an important reef building coral in the tropical eastern Pacific and the dominant Porites species in the Galápagos archipelago. Following the 1982-83 El Niño-Southern Oscillation the Galápagos Islands experienced 97-99% coral mortality, leaving many areas throughout the archipelago denuded of corals. Because very few long term assessments have been conducted on the growth and resilience of P. lobata to natural disturbances in the Galápagos Islands (Glynn et al., 2001; Glynn et al., 2009), benthic surveys were performed on a uniquely dense aggregation of P. lobata colonies at Devil’s Crown, Floreana Island between 1993 and 2011. Annual changes in live tissue area were calculated for the majority of the population (n=17) using Coral Point Count with Excel extensions (CPCe 3.6) software to determine growth and recovery trends for this aggregation. Total live tissue area (n=10) increased from 1993 to 2011, however due to high interannual variability this increase was not significant. Within this overall pattern, a general trend of decline was observed in live tissue cover from 1993 to 2000, with increases in tissue area observed from 2000 to 2011. Severe bleaching (85-100%) was observed during the 1998 survey, followed by 42% tissue loss (n=10), coinciding with sea water warming associated with the very strong 1997-1998 El Niño-Southern Oscillation event. Subsequent regrowth of coral tissue was observed during the 2001 survey with continued recovery through 2009. Multiple comparison testing revealed a significant difference between the impacted state (1999) and the recovered state (2009), (p = 0.002, Dunn’s method, n=17), suggesting this aggregation required a period of ten years to recover from this disturbance. During this recovery period the moderately strong 2007-2008 La Niña, with accompanying stressful low temperatures, occurred but did not interrupt tissue regrowth. Warmer than average sea surface temperatures occurred during the warm months from 2008 to 2011, during which time a cool period occurred from 2010 to 2011. While the magnitude and duration of temperature anomalies during warming were not as great as those observed during the 1997-98 ENSO, low temperatures observed during the cool period were similar to those experienced throughout the 2007-08 La Niña. During this time total live tissue cover was reduced by 19% (n=10); however it is unknown whether this was due to warming or the following cool period. Based on results from the 1997-98 El Niño and 2007-08 La Niña, this reduction in live tissue was most likely caused by elevated sea surface temperatures. Data on the growth and resilience of P. lobata populations at Devil’s Crown will be used for conservation and management of this important resource.