Thesis (Ph. D.)--University of Rhode Island, 2005. / Typescript. Includes bibliographical references (leaves 252-262).

Thesis (M.S.)--Oregon State University, 2010. / Printout. Includes bibliographical references (leaves 61-67). Also available on the World Wide Web.

Thesis (M.Sc.)--Memorial University of Newfoundland, 2002. / Bibliography: leaves 193-200.

L’hybridation est un phénomène observé tant chez les plantes que chez les animaux, mais qui n’avait toutefois jamais été détecté chez le zooplancton marin. Cette thèse vise à caractériser l’hybridation entre Calanus glacialis et C. finmarchicus afin d’évaluer son impact sur la dynamique des populations dans l’ouest de l’Atlantique. De plus, les méthodes d’identification morphologique et génétique sont comparées et combinées afin de tester leur capacité à discriminer les espèces parentales et les hybrides. Dans le deuxième chapitre, une grande variabilité spatio-temporelle du chevauchement de la longueur de prosome entre les espèces C. glacialis et C. finmarchicus est montrée pour les copépodites de stade V. Ce chevauchement de taille entraine une identification erronée et donc, une sous-estimation considérable de l’abondance de C. glacialis dans l’estuaire du Saint-Laurent et sur la côte du Labrador. Au troisième chapitre, la présence d’hybrides est d’abord établie. Il existe une grande variabilité spatiale dans la fréquence des hybrides dans la zone hybride, soit de l’archipel canadien arctique au golfe du Maine, chez le stade copépodite V. De plus, la longueur de prosome des hybrides varie en fonction des génotypes dans l’aire d’étude. Dans le quatrième chapitre, il est mis en évidence que la phénologie reproductive des femelles adultes hybrides est intermédiaire à celles des espèces parentales dans l’estuaire du Saint-Laurent. En revanche, le succès reproducteur et le phénotype des femelles adultes hybrides sont similaires à ceux de leur ancêtre maternel. Les hybrides représentent une faible proportion de la production totale d’œufs de mars à juillet. Ainsi, malgré la présence de flux génique entre C. glacialis et C. finmarchicus, les espèces parentales conservent leur intégrité et sont isolées temporellement dans la zone hybride. Les effets sur la dynamique des populations des espèces parentales semblent minimes. Les recherches à vernir devraient tenter de révéler l’hybridation entre ces espèces dans d’autres zones et d’investiguer l’effet des variations de phénologie reproductive et d’advection sur l’abondance d’hybrides. L’hybridation entre d’autres espèces de zooplancton marin semble également plausible. / Hybridization is a phenomenon observed in plants and animals which to date has never been detected in marine zooplankton. This thesis aims to characterise hybridization between Calanus glacialis and C. finmarchicus in order to evaluate the impact on species population dynamics in the West Atlantic. In addition, morphological and genetic identification were compared and combined to test their potential for discrimination of parental species and hybrids. In the second chapter, a great spatio-temporal variability in overlap in prosome length between C. glacialis and C. finmarchicus is shown for stage V copepodites. This overlap in prosome length has the consequence of misidentifying and thus, considerably underestimating C. glacialis’ abundance in the St. Lawrence Estuary and on the Labrador Coast. In the third chapter, it is shown that hybrids exist, and that there is substantial spatial variability in their frequency in the hybrid zone, from the Canadian Arctic Archipelago to the Gulf of Maine, for the copepodite stage V. Moreover, hybrid size varied as a function of genotypic composition. In the fourth chapter is shown that hybrid adult females have an intermediate reproductive phenology to that of their parental species in the St. Lawrence Estuary. Contrastingly, fitness and phenotypes of hybrid adult females are similar to those of their maternal ancestor. Hybrids represent a small proportion of total egg production from March to July. Thus, although gene flow occurs between these species, parental species are maintained and mainly isolated temporally within the hybrid zone. The effects of hybridization on species population dynamics are probably minor. Future studies should aim to study hybridization between these species in other zones and the effects of variation in their reproductive phenology and advection on hybrid abundance. Hybridization between other marine zooplankton species is also likely.

Zooplankton are the major primary consumers in pelagic ecosystems, providing the principal pathway for energy transfer from primary production to higher trophic levels. The marine copepod Calanus finmarchicus is an important component of the pelagic food web in the North Atlantic and peripheral ecosystems, and forms an essential dietary component of a number of commercially important fish. As part of its life cycle, many C. finmarchicus overwinter in a diapause phase (a dormant overwintering phase where development is suppressed in adaptation to the seasonal food supply) at depths of 500 to 2000 m, but little is known about the triggers that initiate and terminate diapause, or the internal processes associated with these triggers. Understanding these processes is important, given that subtle changes in the environmental conditions which may affect diapause could have consequences for the entire Calanus-based ecosystem. In this study I took advantage of relatively easy access to a deep (> 100 m), isolated population of C. finmarchicus in Loch Etive (a sea loch on the west coast of Scotland) to sample Calanus finmarchicus monthly between April 2006 and June 2007 and measure lipid dynamics and gene expression associated with diapause. Chapter 1 of this thesis provides a general introduction to diapause and Calanus finmarchicus, Chapter 2 reports on the population of C. finmarchicus in Loch Etive, Chapter 3 reports changes in the lipid class and fatty acid composition of individual copepods, Chapter 4 reports on differential gene expression between diapausing and active C. finmarchicus and Chapter 5 provides a general discussion and puts this research into context. This study provides some initial insight into possible gene expression patterns, but further work is needed to attribute specific gene expression patterns with initiation and termination of diapause.

‘Critical Habitat’ is the habitat required to close the life history of an endangered species and is a fundamental requirement for species recovery for two reasons; the role of habitat in population limitation and viability must be determined, and the habitat must be protected. The North Atlantic right whale is an endangered species that annually migrates to the Grand Manan Basin and Roseway Basin Critical Habitats to feed on diapausing calanoid copepods that are typically aggregated at depths of 100 to 150 m. In this thesis I quantify spatial and temporal variation in the copepod prey field and occupancy of right whales in Roseway Basin, and use this information to identify the location and extent of right whale Critical Habitat. To accomplish this, I measured copepod abundance and energy density (kJ m-3) using optical, acoustic and net collection methods during 2007 to 2009. Oceanographic processes that affect variation in the copepod prey field include slope water intrusions, water mass density, gyre-like circulation and frontal features. Aggregations of diapausing copepods are maintained on the southern slope of Roseway Basin by cross-isobath tidal advection, and are advected along-isobath by the residual flow. Tidal advection at a front, coupled with along-isobath advection and shear in the horizontal currents serve to accumulate copepods along the slope where aggregations are maintained for at least 7 days. The abundance, stage-structure, species composition and aggregation locations of copepods, as well as the hydrography and circulation, were variable among the three years of the study. A 20 year time series of right whales, copepods and hydrography revealed that interannual whale occupancy in the Critical Habitats is variable and can be explained by prey field variation only in Roseway Basin. Factors other than the local prey field affect the number of whales that occupy Grand Manan Basin. Variation in the right whale prey field could not be explained by temperature and phytoplankton-dependent growth in the Scotia - Fundy -Gulf of Maine region. The results of this thesis assisted in establishing the Roseway Basin right whale Critical Habitat in 2008, and the cross-disciplinary nature of the study also provides new insights into the relationships between biology and physics in Scotian Shelf - Gulf of Maine basins.

Thesis: Ph. D., Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Department of Biology; and the Woods Hole Oceanographic Institution), 2015. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Zooplankton, such as copepods, are highly abundant environmental reservoirs of many bacterial pathogens. Although copepods are known to support diverse and productive bacterial communities, little is understood about whether copepods are affected by bacterial attachment and whether they can regulate these associations through mechanisms such as the innate immune response. This thesis investigates the potential role that copepod physiology may play in regulating Vibrio association and the community structure of its microbiome. To this end, the intrinsic ability of oceanic copepod hosts to transcriptionally respond to mild stressors was first investigated. Specifically, the transcriptional regulation of several heat shock proteins (Hsps), a highly conserved superfamily of molecular chaperones, in the copepod Calanusfinmarchicus was examined and demonstrated that Hsps are a conserved element of the copepod's transcriptional response to stressful conditions and diapause regulation. To then investigate whether copepod hosts respond to and regulate their microbiota, the transcriptomic response of an estuarine copepod Eurytemora affinis to two distinct Vibric species, a free-living strain (V. ordalii 12B09) and a zooplankton specialist (V. sp. F10 9ZB36), was examined with RNA-Seq. Our findings provide evidence that the copepod E. affinis does distinctly recognize and respond to colonizing vibrios via transcriptional regulation of innate immune response elements and transcripts involved in maintaining cuticle integrity. Our work also suggests that association with E. affinis can significantly impact the physiology of Vibrio colonists. Finally, the inter-individual variability of the C.finmarchicus microbiome was examined to identify how specifically and predictably bacterial communities assemble on copepods and whether host physiology influences the bacterial community structure. Our findings suggest that copepods have a predictable "core microbiome" that persists throughout the host's entrance into diapause, a dormancy period characterized by dramatic physiological changes in the host. However, diapausing and active populations harbor distinct flexible microbiomes which may be driven by factors such including the copepod's feeding history, body size, and bacterial interactions. This thesis work highlights the role of copepods as dynamic reservoirs of diverse bacterial communities and implicates copepod host physiology as an important contributor to the activity, abundance, and community structure of its microbiome. / by Amalia Aruda Almada. / Ph. D.

Les copépodes sont au cœur des flux de matière et d'énergie dans les réseaux trophiques arctiques et subarctiques. La structure et les fonctions des communautés de copépodes dépendent de l'assemblage des espèces dont elles sont constituées, mais on en connait très peu sur les interactions interspécifiques qui peuvent influencer ces propriétés. Les copépodes ont la capacité d'ingérer leurs propres œufs et nauplii (cannibalisme) ainsi que ceux des autres espèces (prédation intraguilde). Il est donc possible que ce type de prédation ait le potentiel de contrôler le recrutement et la dynamique des espèces de copépodes. L'objectif principal des travaux de recherche présentés dans ce mémoire de maîtrise était donc de mieux comprendre la dynamique des interactions interspécifiques au sein des communautés de copépodes arctiques et subarctiques et plus précisément, la prédation intraguilde soupçonnée de façonner ces communautés. Des expériences en laboratoire ont permis de caractériser la prédation intraguilde de l'espèce arctique Metridia longa sur les œufs d'une autre espèce arctique Calanus hyperboreus, ainsi que la prédation intraguilde de cette dernière sur les œufs de l'espèce subarctique Calanus finmarchicus. Différentes conditions de température, concentration d'œufs et nourriture alternative ont été testées. Parmi les conditions d'incubation testées et les différences individuelles dans les traits des prédateurs (par ex. longueur du prosome, stade de développement), seulement la concentration des œufs a eu un effet significatif et positif sur l'ingestion des œufs, et ce pour les deux relations étudiées. Environ un quart des prédateurs incubés ont rempli plus de la moitié de leurs besoins métaboliques avec l'ingestion des œufs seulement. Par la suite, un modèle de distribution verticale des œufs de C. hyperboreus dans le Golfe d'Amundsen a été développé avec l'intégration de la prédation de M. longa afin de vérifier les implications écologiques de cette interaction interspécifique. Nos résultats montrent une relation asymétrique où M. longa a peu d'impact sur le recrutement de C. hyperboreus alors que les œufs interceptés par M. longa peuvent représenter une partie importante de ses besoins métaboliques durant l'hiver. Cependant, l'ingestion des nauplii n'a pas été considérée et devrait être étudiée puisque que ces larves représentent également des proies de choix, susceptibles d'être davantage visées. Ainsi l'impact de la prédation intraguilde aurait pu être sous-estimée.