PhD offer - deadline Oct 15th 2022
Increasing our understanding of climate change impacts on a keystone species in the Arctic: the hooded seal
Project description: Over recent decades, the Arctic has experienced a warming three times faster than the global average, resulting in major changes in ice and oceanographic conditions. These structural changes impact organisms at every level of the Arctic food web from phytoplankton to top predators. Ice seals are considered bio-indicators of the Artic ecosystem health, yet little is known about how ice seals have responded both horizontally and vertically to seasonal and annual changes in the Arctic ecosystem in the past. As the Arctic continues to lose ice, this study will examine future consequences of these ecosystem changes on ice seals.
Successful candidates will combine biologging-derived behavioural and movement data, environmental data and simulation modelling to 1) characterize the foraging behaviours of hooded seals using tri-dimensional movement data, their relation to foraging efficiency, and to their habitat characteristics; 2) assess changes in foraging efficiencies through time-series data and their links to population trajectory; 3) build models that predict the future vertical distribution of the Arctic hooded seal. This research will allow us to infer mechanistic links between the ice seals foraging ecology and their physical environment, and better understand the impacts of environmental changes on ice seal individuals and populations from forecasts of climate induced habitat shifts.
Qualifications: We seek candidates with an MSc in Marine Ecology, Biology or Ocean Sciences. Rigorous candidate with creative and collaborative spirit that will help foster a collegial culture that is grounded in equity, diversity and inclusiveness. She/He must be highly autonomous and able to adapt quickly to different lab/team/country settings as this PhD is co-supervised between French and Canadian institutions. Proficiency in English is mandatory. The candidate is expected to complete his PhD in 36mo (France requirements).
* Programming (proficient in R and/or matlab)
* Advanced statistical modelling
* Biologging data analysis
* Oceanographic data analysis
* Scientific writing and communication
Location: The candidate will be registered at La Rochelle University in France but will be co-supervised between Dr Tiphaine Jeanniard du Dot from Centre d’Etudes Biologiques de Chize at La Rochelle University and Dr Ruth Joy from School of Environmental Science at Simon Fraser University in Canada. The candidate will be expected to start their degree in France but to spend time in both institutions/countries in the course of their degree.
Start date: March 2023
To apply: Please send CV with references, Statement of Research Interest (1 page) and unofficial copy of transcripts to Dr Tiphaine Jeanniard du Dot Tiphaine.email@example.com and Dr Ruth Joy firstname.lastname@example.org
Application deadline: Oct 15th 2022.
POST-DOCS & STUDENTS
Current post-docs & students
Jade Vacquie-Garcia, Post-doc ECOMM
LIVELY-HOODS: Foraging strategies of ice-associated seals facing the drastic changes occurring in the Arctic in the last 30 years: the case study of the two hooded seal stocks, Cystophora cristata.
Atmosphere and oceans are warming worldwide but the Arctic’s surface temperatures are warming 3 times faster than the global average along with a decline of sea ice and a deepening of the thermocline. These rapid changes are impacting the horizontal and vertical distribution of organisms, which are susceptible to affect the structure of Arctic food webs and the entire ecosystem dynamic and/or functioning. However, our current capacity to predict impacts of climate changes on marine species and ecosystems is limited because time series of sufficient length to assess these changes are often lacking. In the “Lively-Hoods” project, we propose to investigate the effect of these changes on the Arctic ecosystem by combining all available datasets in the last 30 years on a top marine predator species, the hooded seal. Hooded seal is an Arctic pagophilic species heavily dependent on sea ice for its life cycle and, as a top predator, is an ecological indicator of the Arctic ecosystem. In addition, the two recognized hooded seals stocks show contrasted population trajectories in their respective geographical range, which provides an additional opportunity to better understand how the rapid changes occuring in their environments affect marine species. In that context, the objectives of the project are (i) to investigate how environmental changes have impacted spatial strategies and diets of the two stocks of hooded seals within the last 30 years, (ii) to compare the responses of the two stocks and link these changes to differences in their population trajectories and (iii) to predict their evolution in the future given forecasted environmental changes continuum.
Lola Gilbert, PhD candidate
Role of marine mammals in nutrient fluxes and carbon storage
The research carried out as part of my PhD aims to study the biofeedback mechanisms that marine mammals can have on the ecosystem, particularly through their role in providing the photic zone with nutrients and micronutrients via their faeces. The idea is to quantify the role of marine mammals no longer just as consumers of upper levels of trophic networks but also on the development of primary levels by stimulating the growth of phytoplankton, and thus indirectly the storage of carbon within trophic networks. Based on bioenergetic models linking the absorption of nutrients through the consumption of prey and the excretion of residues, the approach developed as part of my work will include different spatial and temporal scales, different ecosystems and different communities of marine mammals. The data mobilised will include population estimates from aerial census campaigns, telemetry data, analyses of prey and faeces nutrient content and stranding data. Thanks to models predicting the impacts of changes in the abundance of these predators on the dynamics of nutrients in surface waters at the different spatiotemporal scales studied, the aim of this work is to provide scientific arguments to guide public conservation policies.
Mathilde Chevallay, PhD candidate
Inferring myctophid habitat from the fine scale foraging behaviours of their predators in the Southern Ocean
Myctophids represent a large part of the oceans fish biomass in the Southern Ocean and play a major role in the transfer of energy from zooplankton to higher trophic levels including seabirds and marine mammals. Yet, little is known about their distribution and their habitat characteristics despite their ecological importance. To understand the ecology of these key species in the Southern Ocean, my research investigate the very fine scale feeding behaviour of 4 of their main predators (king penguins (Aptenodytes patagonicus), macaroni penguins (Eudyptes chrysolophus), Antarctic fur seals (Arctocephalus gazella), and elephant seals (Mirounga leonina) in relation to the characteristics of their habitat as a way to infer prey habitat and distribution in their environment. To do so, I use latest stet of the art biologging devices such as underwater micro-sonar tags to determine the inter- and intraspecific differences in small-scale deep-sea foraging behaviors among these 4 predators and in the specific targeted mesopelagic prey, as well as the influence of in-situ oceanographic parameters on the distribution of these species. Ultimately, my work will help filling a knowledge gap in the links between oceanographic parameters, distribution and habitat characteristics of major prey species in the marine environment and their link to their predators' behaviours and foraging success, which is essential to untangle ecosystem functioning.
Baglan Aitu, MSc
Deep learning applied to active acoustic biologging data
However, consequences of environmental changes on ecosystem functioning often remain poorly assessed. It is therefore essential to better assess the horizontal and vertical distributions of marine organisms in relation to habitat characteristics, as well as the impact these have on the distribution and foraging behaviours of top marine predators. To do so, a state-of-the-art custom-made active micro-sonar tag has been recently developed that record echograms of organisms at sea. Twenty southern elephant seals – 14 from Kerguelen islands, and 6 from Argentina – were equipped with these new micro-sonars, together with a GPS, a pressure sensor and a tri-axial accelerometer that provide behavioural data for the seals. The volume of recovered high-resolution acoustic data prohibits manual analysis in their entirety and consequently requires the development of accurate and relevant data processing methods. Consequently, the objective of this study is to develop a methodology based on machine learning approaches to first extract the part of the dataset where relevant signals of prey encounters are present within the echograms. A second step will consist in classifying these extracted signals into isolated versus schooling prey, active versus passive prey, as well as categories of size and intensity of the acoustic signals.
Maria Isabel Barros, MSc
Categorization of marine organisms detected by seal-borne micro-sonar tags using machine learning methods.
To understand the consequences of environmental changes on ecosystem functioning and particularly on intermediate trophic levels (i.e. nekton: zooplankton, gelatinous, fish and squid ...), a new, innovative, state-of-the-art biological recorder was developed that allows active echosounding of water masses, and therefore record the vertical distribution and density of zooplankton and mesopelagic fish in the water column. This new recorder (i.e. micro-sonar) was deployed on twelve southern elephant seals (Mirounga leonina) and recorded on average for 30 days and at a ping frequency of 25Hz. Consequently, the volume of high-resolution acoustic data recovered, as well as other types of data recorded (high-resolution acceleration, depth, salinity, temperature etc...) is large (250GB per deployment) and growing rapidly, which consequently prohibit prohibit manual analysis in their entirety. To get the full benefit of the information recorded by such tags, our objectives were to develop a micro-sonar image processing methodology based on machine learning to regularly extract relevant information from the obtained echograms. The goal was to i) determine the overall density, frequency and size of organisms in water bodies (whether or not they are targeted by predators), ii) isolate the portion of the dataset where relevant predator-targeted prey encounter signals are present in the echograms, and classify these extracted signals into isolated vs. schooling prey, active vs. passive prey, as well as acoustic signal size and intensity categories, and iii) identify vibrissae deployment events in the echograms.
Jade Chevassu, MSc
Relationships between oceanographic parameters, marine organism assemblage and foraging efficiency of Southern elephant seals through cutting-edge biologging data
Marine ecosystems are currently subject to drastic and rapid changes from the physico-chemical level to biological levels with consequences on trophic web structures and dynamics, on top predators foraging behaviours and success. However, consequences of environmental changes on ecosystem functioning often remain poorly assessed. It is therefore essential to better assess the horizontal and vertical distribution of marine organisms, including the zooplankton and fish populations, in relation to environmental parameters, as well as the impact these have on the distribution and foraging behaviours of top marine predators, such as southern elephant seals (Mirounga leonina). The objective of my study is to better understand how southern elephant seals successfully use their environment to forage during their months-long trips at sea by 1 - classifying density and size classes of organisms in 3D in the water column on the path of elephants – including temporal variations due to nyctemeral migrations – using functional data analyses (FDA) on active acoustic profiles, 2 - assessing the relationships between these density and size classes of organisms and the characteristics of water masses (temperature, salinity) and bioluminescence events on one hand, and with elephant seals prey capture attempts and changes in body conditions on the other hand. The results will provide a greater understanding on the relationship between physico-chemical properties of the elephant seal habitats, the plankton and nekton assemblage of the food web they feed into, and the foraging efficiency related to these different ecosystemic assemblage.
Swann Heliot, MSc
Impacts of oceanographic environment on Hooded seal movement and foraging performances
Arctic ecosystems face one of the fastest environmental change on Earth, but the ecological consequences of these changes remain poorly understood due to the difficulties to collect in situ oceanographic and ecological data. As top marine predators, hooded seals integrate the cascade of events occurring from the bottom to the top of the food chain and are considered early warning indicators of environmental changes. Their life cycle depends on pack ice for access to foraging ground, and for a haul-out substrate for breeding and moulting. They are also deep divers, range throughout the Atlantic side of the high Arctic, and feed on a wide range of prey from krill to fish and squids. As such, they are the perfect platform to widely sample fast changing northern and polar ecosystems. Consequently, the goal of this study is to understand how local variations in oceanographic conditions – especially sea ice coverage, temperature, salinity, light, currents, winds and/or primary productivity – as well as prey availability affect and drive the movement patterns, foraging success and body conditions of seals. This will help us assess the physical and biological environment of “sentinel” seals and evaluate ecological consequences to environmental changes in terms of foraging strategies, efficiency and distribution.
Mathilde Chevallay, MSc
Fine scale adaptation of foraging behaviours in relation to prey capture success in fur seals
The main objective of this research is to investigate decision process of northern and Antarctic fur seals during foraging according to their foraging success. Optimal Foraging Theory predicts that predators which adopt hunting strategies that maximise their energy intake per unit of time would have more energy to allocate to reproduction and survival over a lifetime, and thus should show a greater overall fitness. Within this framework, predators must maximise acquisition and assimilation of prey and minimise the costs linked to the search, pursuit and capture of prey. As predators are foraging in a prey patch, prey abundance will decrease with the time spent in the patch, the optimal time when a predator should leave a patch to search for a more profitable one, is hypothesized to be when the local capture rate decreases below the average capture rate of the environment. As predators do not have a perfect knowledge of the spatial distribution and the quality of prey patches in their environment, they likely use their past prey capture experiences to estimate when it is optimal to leave a patch.Thanks to recent improvements in biologging, we can obtain information on both the fine-scale foraging behaviour of cryptic marine animals and indices of prey availability, and therefore provide new insights in the study of decision-making processes in cryptic marine animals that have been difficult to study up to now. Understanding decision-making processes in predators is essential to understand how they respond to prey availability and subsequently how they may respond to environmental changes.