Les mammifères marins sont des espèces clés des écosystèmes. Ils subissent un nombre important de modifications de leur milieu qui nécessitent la mise en place de stratégie de conservation. Pour cela la connaissance de la structure des populations est primordiale. Une étude de génétique des populations a été menée sur deux espèces emblématiques de la mer d'Iroise. Pour le marsouin commun, espèce connaissant un retour le long des côtes françaises, nos travaux montrent, de manière inattendue, que ce retour est le résultat de deux déplacements différents et qu'il y a une hybridation entre les individus issus de la population de la péninsule Ibérique et ceux du Nord de l'Europe. Ces déplacements sont certainement liés à des modifications de la disponibilité des proies suite à des changements du milieu. Pour le phoque gris, nos résultats montrent une grande richesse génétique, avec une structure ancestrale pour la région de contrôle mitochondriale et une panmixie pour les loci microsatellites, indiquant la présence d'une population à l'échelle du plateau celtique. Une différenciation est observée entre les années d'échouages paires et impaires ainsi qu'une signature génétique potentielle d'individu issus d'une autre population. Enfin nous avons mené une étude pilote pour un observatoire de la biodiversité génétique des mammifères marins par la technique de code barres ADN. Cette étude montre que cet observatoire serait une manière innovante et pertinente pour suivre la biologie des mammifères marins. L'ensemble de nos résultats permettent de mieux comprendre les modifications de l'écosystème et sont un support à la mise en place de stratégie de conservation. / Marine mammals are key species of ecosystems. They undergo numerous environment modifications which require conservation plans. For that, the knowledge about population structure is primary. Studies of population genetic were led about two flagship species of the Iroise Sea. For the harbour porpoise, a specie who know a return along french coasts, our works unexpectedly show this return is the result of two movements and an hybridization between individuals of the Iberia population and those of North Europe population. These movements are, probably, linked to modifications of prey's availability caused by environment changes. For the grey seal, our works show a great genetic richness, with an ancestral structure for the mitochondrial control region and a panmixia for the microsatellites loci, which are signs of a population at the scale of Celtic Shelf. A differentiation was observed between the stranding years even and odd and a possible genetic signal of individuals from another population. Finally we led a pilot study for marine mammal genetic biodiversity observatory with the DNA barcoding technique. This study shows this observatory may be a relevant and innovative means to follow the marine mammal biology. All our results bring new information about ecosystem variations and are a help for the establishment of conservation strategy.

Thesis (Ph.D.) - University of St Andrews, April 2009.

The aim of this report was to establish what category the harbour porpoise is listed as on the Swedish national redlist as well as analyze what potential sub-criteria the species fulfills besides criteria already established. The aim was also to evaluate the willingness to pay for conservation of the harbour porpoise for the first time and make a comparison of the willingness to pay between geographic places where the harbour porpoise is currently existing and where it is not. The subpopulation of the harbour porpoise in Skagerrak-Kattegat is listed as vulnerable (VU) on the national redlist and the subpopulation in the Baltic sea is listed as critically endangered (CR). Actions and precautions which have been made for conservation and protection of the harbour porpoises in Swedish waters are new Swedish laws and law proposals as well as formations of organizations such as ASCOBANS and further research. The results from the survey showed that the mean of the single time payment sum those questioned were prepared to pay to retain the porpoises at a stable population level was 273 SEK. Geographically the study showed no significant difference in geographic position and where the harbour porpoise exists but showed that the inhabitants of the south-east coast were willing to pay about half the sum, 165 SEK, of the mean sum that the north-east coast were willing to pay, 335 SEK. The results regarding the populations’ conjecture of historical threats and threats nowadays showed a significant difference from reality. Overfishing of prey had the highest amount of answers as a threat both historically and nowadays. Bycatch, which is accepted as todays biggest threat by researchers and organizations, came third place in the results from the survey study with a percentage of 14.5 %.

Incidental catch, or bycatch, of harbour porpoise (Phocoena phocoena) in fishing operations is an international conservation issue. The main objective of this thesis was to develop methods for determining the impact of bycatch on the state and dynamics of porpoise populations and for calculating bycatch limits that will achieve conservation objectives in the future. I applied these methods to the North Sea as a case study. First, I analysed sighting rates of harbour porpoise on seabird surveys in the North Sea during 1980-2003 to determine whether these data could provide informative time-series of relative abundance. Some general patterns and trends in sighting rates were consistent with previous studies. However, the standardised indices of abundance were relatively imprecise and thus have limited value for a monitoring framework that relies on statistical detection of trends. Second, I used a population model to integrate available data on harbour porpoise in the North Sea and to assess the dynamics of the population during 1987-2005. There was a high probability that bycatch resulted in a decrease in abundance. The estimated life history parameters suggested a limited scope for population growth even in the absence of bycatch. The model and data were not informative about maximum population growth rate or carrying capacity. The model suggested that dispersal was the most plausible explanation for observed changes in distribution within the North Sea. Third, I considered management procedures for calculating bycatch limits. I performed simulations to compare the behaviour of the procedures, to tune the procedures to specific conservation objectives and to test the robustness of the procedures to a range of uncertainties regarding population dynamics and structure, the environment, observation and implementation. Preliminary annual bycatch limits for harbour porpoise in the North Sea ranged from 187-1685 depending on the procedure, tuning and management areas used.

The main purpose of this study was to produce and test the reliability of predictive models of cetacean distributions off the west coast of Scotland. Passive acoustic and visual surveys were carried out from platforms of opportunity between 2003 and 2005. Acoustic identifications were made primarily of harbour porpoises (Phocoena phocoena), delphinids, and sperm whales (Physeter macrocephalus). Generalised Additive Models (GAMs) were used to relate species’ distributions to a range of environmental variables over a range of temporal and spatial scales. Predictive models of delphinid distributions showed both inter-annual and inter-month variations. Combining all data for all months and years resulted in a model that combined the environmental influences from each monthly and yearly model. Overall, delphinids were found to associate with the deep (> 400m) warm water (10.5°C-12.5°C), and in areas of deep thermocline. Relationships between sperm whales and environmental variables were consistent over changes in grain size (9 km or 18 km), but not between areas. Although sperm whales were distributed in deep water characterised by weak thermoclines and strong haloclines in the most northerly area (Faroe-Shetland Channel), they were found in deep productive areas with cold surface temperature in the more southerly waters (Rockall Trough). Within the southern Inner Hebrides, high use areas for harbour porpoises were consistently predicted over time (in years) and with differing survey techniques (acoustic versus visual), but not over space (southern Inner Hebrides versus whole of the Inner Hebrides). Harbour porpoises were mainly distributed in areas with low tidal currents and with higher detection rates during spring tides. The use of prey as a predictor variable within models of delphinid distribution shows some promise: there were correlations between delphinid and herring (Clupea harengus) in shelf-waters in 2005 but not in 2004. These models can be used in mitigating acoustic threats to cetaceans in predicted high use areas off the west coast of Scotland.

Um total de 142 crânios do boto-de-Burmeister, Phocoena spinipinnis depositados em museus e coleções cientificas da Argentina, Brasil, Chile, Peru e Uruguai foram utilizados para explorar a variação geográfica em relação ao tamanho e forma do crânio de P. spinipinnis. Ademais, foi realizada uma caracterização oceanográfica da área de distribuição do boto-de- Burmeister através de dados históricos de temperatura, salinidade e oxigênio a 0 e 50m de profundidade na costa Atlântica e Pacifica. As idades dos animais foram obtidas pelas leituras das GLGs na dentina. A idade mais alta atingida por ambos os sexos foi de 10 anos. Medições na dentina mostraram dimorfismo sexual na primeira GLG e diferenças geográficas entre botos do Peru e Atlântico. Três tipos de anomalias foram registrados nos dentes, e a linha marcadora parece estar associada ao “El Niño”. Vinte e oito caracteres métricos foram utilizados para explorar o dimorfismo sexual e crescimento. A maturidade física do crânio foi estabelecida quando o comprimento côndilo-basal atingiu 95% do comprimento total (≥266mm nos machos e ≥277mm nas fêmeas). Diferenças no tamanho e forma do crânio foram analisadas através de morfometria tradicional e geométrica. Os resultados revelaram dimorfismo sexual, sendo as fêmeas maiores do que os machos. As diferenças em tamanho e forma concentraram-se principalmente na região rostral e neurocrânio. Foi observada variação geográfica entre os botos do Atlântico, Chile e Peru. P. spinipinnis do Peru são de menor tamanho em relação a os botos do Chile e Atlântico. Botos do Chile apresentam um tamanho e forma intermediária, e os botos do Atlântico são maiores (especialmente na região orbital, altura do crânio e região rostral). A distância de Mahalanobis mostrou maior separação entre os botos do Peru e do Atlântico, e menor distância entre os exemplares do Chile e Atlântico. A morfometria geométrica explica com maior clareza as diferenças entre botos do Chile e Atlântico, especialmente nas vista ventral e lateral. A correlação entre variáveis ambientais e morfométricas através da análise de correlações canônicas e dos quadrados mínimos parciais de dois blocos sugere que as diferenças observadas no tamanho e na forma dos crânios têm uma importante influência espacial, associada à variabilidade sazonal das condições oceanográficas presentes nos dois oceanos e diretamente relacionada às três áreas oceanográfica propostas neste estudo: (1) de Paita, Peru (05°01’S, 81ºW) até o sul do Golfo de Arauco, Chile (∼39°S); (2) do sul do Golfo de Arauco até o sul do Rio da Prata (∼38°S); e (3) do Rio da Prata até Santa Catarina, Brasil (28º48’S; 49°12W). Adicionalmente, propõe-se que P. spinipinnis apresenta uma distribuição contínua desde Paita, Peru ate a bacia do Rio da Prata, Argentina, podendo alcançar águas uruguaias e brasileiras em determinadas condições oceanográficas (entrada de águas mais frias e menos salinas com direção ao norte, associadas à Convergência Subtropical) / A total of 142 skulls from Burmeister’s porpoises, Phocoena spinipinnis from museums and scientific collections from Argentina, Brazil, Chile, Peru and Uruguay were analyzed to explore the geographical variation in relation to size and shape on skulls of P. spinipinnis. In addition, an oceanographic characterization of the area of distribution of Burmeister’s porpoise by historical data of temperature, salinity and oxygen the 0 and 50m of depth on the Pacific and Atlantic coast was carried out. The age of the animals was obtained by reading the Growth Layer Group in dentine. The oldest male and female were 10 years of age. Measurements in dentine showed sexual dimorphism in the first GLG and geographic differences between porpoises from Peru and Atlantic. Three types of anomalies were recorded in teeth, and the marker lines seem to be associated to “El Niño”. Twenty-eight characters were used to explore sexual dimorphism and growth. Physical maturity of the skull was established when 95% of condylobasal length was attained (≥266mm in the males and ≥277mm in the females). Differences in size and shape of skull were analyzed by traditional and geometric morphometrics. The results revealed sexual dimorphism, being the females larger than male, and the differences in size and shape are concentrated mainly in the rostral region and neurocranium. Geographic variation between porpoises from Atlantic, Chile, and Peru was observed. P. spinipinnis from Peru are smaller compared to porpoises from Chile and Atlantic. Porpoises from Chile have an intermediate shape, and porpoises from Atlantic are larger (mainly related to orbital region, skull height and rostral region). The distance of Mahalanobis showed more separation between porpoises from Peru and Atlantic, and less distance between specimens from Chile and Atlantic. Geometric morphometrics was more useful for show differences between specimens from Chile and Atlantic, especially in the ventral and lateral views. The correlation between environmental and morphometric variables by canonical analysis and two-block partial least squares suggests that the differences observed in the size and shape of skulls would have an important spatial influence, associated to the seasonal variability of the oceanographic conditions present in the two oceans, and directly related to the three oceanographic areas proposed in this study: (1) from Paita, Peru (05°01’S, 81ºW) to south of Arauco Gulf, Chile (∼39°S); (2) from south of Arauco Gulf to south of La Plata River, Argentina (∼38°S); and (3) from La Plata River to Santa Catarina, Brazil (28º48’S; 49°12W). In addition, it is proposed that P. spinipinnis presents a continuous distribution from Paita, Peru to La Plata River basin, Argentina, being able to reach Uruguayan and Brazilian waters under certain oceanographic conditions (intrusion of colder and less saline waters toward the north associated with the Subtropical Convergence).

Um total de 142 crânios do boto-de-Burmeister, Phocoena spinipinnis depositados em museus e coleções cientificas da Argentina, Brasil, Chile, Peru e Uruguai foram utilizados para explorar a variação geográfica em relação ao tamanho e forma do crânio de P. spinipinnis. Ademais, foi realizada uma caracterização oceanográfica da área de distribuição do boto-de- Burmeister através de dados históricos de temperatura, salinidade e oxigênio a 0 e 50m de profundidade na costa Atlântica e Pacifica. As idades dos animais foram obtidas pelas leituras das GLGs na dentina. A idade mais alta atingida por ambos os sexos foi de 10 anos. Medições na dentina mostraram dimorfismo sexual na primeira GLG e diferenças geográficas entre botos do Peru e Atlântico. Três tipos de anomalias foram registrados nos dentes, e a linha marcadora parece estar associada ao “El Niño”. Vinte e oito caracteres métricos foram utilizados para explorar o dimorfismo sexual e crescimento. A maturidade física do crânio foi estabelecida quando o comprimento côndilo-basal atingiu 95% do comprimento total (≥266mm nos machos e ≥277mm nas fêmeas). Diferenças no tamanho e forma do crânio foram analisadas através de morfometria tradicional e geométrica. Os resultados revelaram dimorfismo sexual, sendo as fêmeas maiores do que os machos. As diferenças em tamanho e forma concentraram-se principalmente na região rostral e neurocrânio. Foi observada variação geográfica entre os botos do Atlântico, Chile e Peru. P. spinipinnis do Peru são de menor tamanho em relação a os botos do Chile e Atlântico. Botos do Chile apresentam um tamanho e forma intermediária, e os botos do Atlântico são maiores (especialmente na região orbital, altura do crânio e região rostral). A distância de Mahalanobis mostrou maior separação entre os botos do Peru e do Atlântico, e menor distância entre os exemplares do Chile e Atlântico. A morfometria geométrica explica com maior clareza as diferenças entre botos do Chile e Atlântico, especialmente nas vista ventral e lateral. A correlação entre variáveis ambientais e morfométricas através da análise de correlações canônicas e dos quadrados mínimos parciais de dois blocos sugere que as diferenças observadas no tamanho e na forma dos crânios têm uma importante influência espacial, associada à variabilidade sazonal das condições oceanográficas presentes nos dois oceanos e diretamente relacionada às três áreas oceanográfica propostas neste estudo: (1) de Paita, Peru (05°01’S, 81ºW) até o sul do Golfo de Arauco, Chile (∼39°S); (2) do sul do Golfo de Arauco até o sul do Rio da Prata (∼38°S); e (3) do Rio da Prata até Santa Catarina, Brasil (28º48’S; 49°12W). Adicionalmente, propõe-se que P. spinipinnis apresenta uma distribuição contínua desde Paita, Peru ate a bacia do Rio da Prata, Argentina, podendo alcançar águas uruguaias e brasileiras em determinadas condições oceanográficas (entrada de águas mais frias e menos salinas com direção ao norte, associadas à Convergência Subtropical) / A total of 142 skulls from Burmeister’s porpoises, Phocoena spinipinnis from museums and scientific collections from Argentina, Brazil, Chile, Peru and Uruguay were analyzed to explore the geographical variation in relation to size and shape on skulls of P. spinipinnis. In addition, an oceanographic characterization of the area of distribution of Burmeister’s porpoise by historical data of temperature, salinity and oxygen the 0 and 50m of depth on the Pacific and Atlantic coast was carried out. The age of the animals was obtained by reading the Growth Layer Group in dentine. The oldest male and female were 10 years of age. Measurements in dentine showed sexual dimorphism in the first GLG and geographic differences between porpoises from Peru and Atlantic. Three types of anomalies were recorded in teeth, and the marker lines seem to be associated to “El Niño”. Twenty-eight characters were used to explore sexual dimorphism and growth. Physical maturity of the skull was established when 95% of condylobasal length was attained (≥266mm in the males and ≥277mm in the females). Differences in size and shape of skull were analyzed by traditional and geometric morphometrics. The results revealed sexual dimorphism, being the females larger than male, and the differences in size and shape are concentrated mainly in the rostral region and neurocranium. Geographic variation between porpoises from Atlantic, Chile, and Peru was observed. P. spinipinnis from Peru are smaller compared to porpoises from Chile and Atlantic. Porpoises from Chile have an intermediate shape, and porpoises from Atlantic are larger (mainly related to orbital region, skull height and rostral region). The distance of Mahalanobis showed more separation between porpoises from Peru and Atlantic, and less distance between specimens from Chile and Atlantic. Geometric morphometrics was more useful for show differences between specimens from Chile and Atlantic, especially in the ventral and lateral views. The correlation between environmental and morphometric variables by canonical analysis and two-block partial least squares suggests that the differences observed in the size and shape of skulls would have an important spatial influence, associated to the seasonal variability of the oceanographic conditions present in the two oceans, and directly related to the three oceanographic areas proposed in this study: (1) from Paita, Peru (05°01’S, 81ºW) to south of Arauco Gulf, Chile (∼39°S); (2) from south of Arauco Gulf to south of La Plata River, Argentina (∼38°S); and (3) from La Plata River to Santa Catarina, Brazil (28º48’S; 49°12W). In addition, it is proposed that P. spinipinnis presents a continuous distribution from Paita, Peru to La Plata River basin, Argentina, being able to reach Uruguayan and Brazilian waters under certain oceanographic conditions (intrusion of colder and less saline waters toward the north associated with the Subtropical Convergence).

Um total de 142 crânios do boto-de-Burmeister, Phocoena spinipinnis depositados em museus e coleções cientificas da Argentina, Brasil, Chile, Peru e Uruguai foram utilizados para explorar a variação geográfica em relação ao tamanho e forma do crânio de P. spinipinnis. Ademais, foi realizada uma caracterização oceanográfica da área de distribuição do boto-de- Burmeister através de dados históricos de temperatura, salinidade e oxigênio a 0 e 50m de profundidade na costa Atlântica e Pacifica. As idades dos animais foram obtidas pelas leituras das GLGs na dentina. A idade mais alta atingida por ambos os sexos foi de 10 anos. Medições na dentina mostraram dimorfismo sexual na primeira GLG e diferenças geográficas entre botos do Peru e Atlântico. Três tipos de anomalias foram registrados nos dentes, e a linha marcadora parece estar associada ao “El Niño”. Vinte e oito caracteres métricos foram utilizados para explorar o dimorfismo sexual e crescimento. A maturidade física do crânio foi estabelecida quando o comprimento côndilo-basal atingiu 95% do comprimento total (≥266mm nos machos e ≥277mm nas fêmeas). Diferenças no tamanho e forma do crânio foram analisadas através de morfometria tradicional e geométrica. Os resultados revelaram dimorfismo sexual, sendo as fêmeas maiores do que os machos. As diferenças em tamanho e forma concentraram-se principalmente na região rostral e neurocrânio. Foi observada variação geográfica entre os botos do Atlântico, Chile e Peru. P. spinipinnis do Peru são de menor tamanho em relação a os botos do Chile e Atlântico. Botos do Chile apresentam um tamanho e forma intermediária, e os botos do Atlântico são maiores (especialmente na região orbital, altura do crânio e região rostral). A distância de Mahalanobis mostrou maior separação entre os botos do Peru e do Atlântico, e menor distância entre os exemplares do Chile e Atlântico. A morfometria geométrica explica com maior clareza as diferenças entre botos do Chile e Atlântico, especialmente nas vista ventral e lateral. A correlação entre variáveis ambientais e morfométricas através da análise de correlações canônicas e dos quadrados mínimos parciais de dois blocos sugere que as diferenças observadas no tamanho e na forma dos crânios têm uma importante influência espacial, associada à variabilidade sazonal das condições oceanográficas presentes nos dois oceanos e diretamente relacionada às três áreas oceanográfica propostas neste estudo: (1) de Paita, Peru (05°01’S, 81ºW) até o sul do Golfo de Arauco, Chile (∼39°S); (2) do sul do Golfo de Arauco até o sul do Rio da Prata (∼38°S); e (3) do Rio da Prata até Santa Catarina, Brasil (28º48’S; 49°12W). Adicionalmente, propõe-se que P. spinipinnis apresenta uma distribuição contínua desde Paita, Peru ate a bacia do Rio da Prata, Argentina, podendo alcançar águas uruguaias e brasileiras em determinadas condições oceanográficas (entrada de águas mais frias e menos salinas com direção ao norte, associadas à Convergência Subtropical) / A total of 142 skulls from Burmeister’s porpoises, Phocoena spinipinnis from museums and scientific collections from Argentina, Brazil, Chile, Peru and Uruguay were analyzed to explore the geographical variation in relation to size and shape on skulls of P. spinipinnis. In addition, an oceanographic characterization of the area of distribution of Burmeister’s porpoise by historical data of temperature, salinity and oxygen the 0 and 50m of depth on the Pacific and Atlantic coast was carried out. The age of the animals was obtained by reading the Growth Layer Group in dentine. The oldest male and female were 10 years of age. Measurements in dentine showed sexual dimorphism in the first GLG and geographic differences between porpoises from Peru and Atlantic. Three types of anomalies were recorded in teeth, and the marker lines seem to be associated to “El Niño”. Twenty-eight characters were used to explore sexual dimorphism and growth. Physical maturity of the skull was established when 95% of condylobasal length was attained (≥266mm in the males and ≥277mm in the females). Differences in size and shape of skull were analyzed by traditional and geometric morphometrics. The results revealed sexual dimorphism, being the females larger than male, and the differences in size and shape are concentrated mainly in the rostral region and neurocranium. Geographic variation between porpoises from Atlantic, Chile, and Peru was observed. P. spinipinnis from Peru are smaller compared to porpoises from Chile and Atlantic. Porpoises from Chile have an intermediate shape, and porpoises from Atlantic are larger (mainly related to orbital region, skull height and rostral region). The distance of Mahalanobis showed more separation between porpoises from Peru and Atlantic, and less distance between specimens from Chile and Atlantic. Geometric morphometrics was more useful for show differences between specimens from Chile and Atlantic, especially in the ventral and lateral views. The correlation between environmental and morphometric variables by canonical analysis and two-block partial least squares suggests that the differences observed in the size and shape of skulls would have an important spatial influence, associated to the seasonal variability of the oceanographic conditions present in the two oceans, and directly related to the three oceanographic areas proposed in this study: (1) from Paita, Peru (05°01’S, 81ºW) to south of Arauco Gulf, Chile (∼39°S); (2) from south of Arauco Gulf to south of La Plata River, Argentina (∼38°S); and (3) from La Plata River to Santa Catarina, Brazil (28º48’S; 49°12W). In addition, it is proposed that P. spinipinnis presents a continuous distribution from Paita, Peru to La Plata River basin, Argentina, being able to reach Uruguayan and Brazilian waters under certain oceanographic conditions (intrusion of colder and less saline waters toward the north associated with the Subtropical Convergence).