Population structure, genetic diversity and social system were investigated in four species of dolphins, thought to present contrasting habitat preferences and social organisation: spinner dolphins, rough-toothed dolphins, long-finned and short-finned pilot whales. To overcome methodological limitations, I combined molecular markers (mitochondrial DNA, -or mtDNA-, and microsatellite loci) and observational data (photo-identification and mass strandings) where possible. Genetic samples were obtained from skin biopsies of free-ranging (n = 243) and stranded (n = 375) dolphins. As with many species of delphinids, spinner dolphins (Stenella longirostris) form communities in which social and reproductive boundaries are poorly understood. In French Polynesia, capture-recapture analyses based on photographs of distinctly marked individuals (DMIs) and microsatellite genotypes (12 loci) indicated a community of about 150 dolphins around Moorea that is relatively closed on a generational time scale. Distinct communities, likely to follow a similar demographic pattern, were observed around neighbouring islands (Tahiti, Raiatea, Huahine and Bora Bora), as indicated by photo-identification data and restricted gene flow (FST = 0.143, n = 154). Surprisingly high levels of insular mtDNA genetic diversity (average pi = 1.44%, suggesting Nef ~ 100,000) contrasted with demographic characteristics of these communities. There was no evidence for a recent bottleneck effect, suggesting that this pattern is the result of metapopulation structure, based on numerous insular communities connected through male and female gene flow. Investigation of the worldwide mtDNA diversity and phylogeography of long-finned and short-finned pilot whale species revealed a complex evolutionary history (Globicephala melas, n = 434; and G. macrorhynchus, n = 134, including published and unpublished sequences). Strong genetic differentiation between long-finned pilot whales from the North Atlantic (G. m. melas) and Southern Hemisphere (G. m. edwardii) indicated severely restricted gene flow, although shared haplotypes suggested some recent contact between the two subspecies. Low genetic distances among haplotypes and a star-like phylogeny suggested a recent worldwide expansion for this species. Higher levels of diversity (although low compared to other cetaceans) were found in short-finned pilot whales, in particular among samples from around Japan. Phylogeographic studies suggested that Japanese samples originate from three distinct populations, one of which could be the ancestral population of the species. Overall, my results confirmed that worldwide mtDNA diversity is low in the two species, probably due to a recent worldwide population expansion and, potentially, to a matrilineal social structure. The molecular ecology of the mass strandings of long-finned pilot whales around New Zealand was investigated to test the hypothesis that individuals stranding together are part of an extended matrilineal group. Analyses of mtDNA sequences indicate that more than one haplotype was found in five of the seven mass strandings investigated (n = 275), demonstrating that groups are sometimes composed of unrelated maternal lineages. This was further supported by analyses of relatedness within and between strandings based on microsatellites (14 loci). These analyses discount kinship as the only factor causing large mass strandings in long-finned pilot whales. Parentage analyses confirmed some aspects of previous studies in the North Atlantic, suggesting a social system with at least some level of male and female philopatry to the maternal group, and infrequent paternities within the group. In a detailed study of a large mass stranding (Stewart Island 2003, n = 122), there was no correlation between position of the whales on the beach and genetic relatedness (based on 20 microsatellite loci), discounting the assumption that kinship bonds are maintained during these traumatic events. This was further supported by the striking separation of stranded mothers and dependant calves. This disruption of kinship bonds could help explain the behavioural distress of stranded individuals and the tendency of many whales to re-strand even after being re-floated. Finally, a study of rough-toothed dolphins (Steno bredanensis) in the Society Archipelago, French Polynesia, provided new insights in the ecology of this poorly-known species. Although traditionally viewed as a pelagic dolphin, analyses supported a pattern of local communities, in some ways similar to spinner dolphins, with fine-scale population genetic structure (FST = 0.60, p < 0.001 based on mtDNA, n = 65) and local fidelity. These communities also showed a low level of mtDNA haplotype diversity (four unique haplotypes at Moorea compared to 18 for spinner dolphins), suggesting the potential influence of a matrilineal social structure similar to long-finned pilot whales.

Population structure, genetic diversity and social system were investigated in four species of dolphins, thought to present contrasting habitat preferences and social organisation: spinner dolphins, rough-toothed dolphins, long-finned and short-finned pilot whales. To overcome methodological limitations, I combined molecular markers (mitochondrial DNA, -or mtDNA-, and microsatellite loci) and observational data (photo-identification and mass strandings) where possible. Genetic samples were obtained from skin biopsies of free-ranging (n = 243) and stranded (n = 375) dolphins. As with many species of delphinids, spinner dolphins (Stenella longirostris) form communities in which social and reproductive boundaries are poorly understood. In French Polynesia, capture-recapture analyses based on photographs of distinctly marked individuals (DMIs) and microsatellite genotypes (12 loci) indicated a community of about 150 dolphins around Moorea that is relatively closed on a generational time scale. Distinct communities, likely to follow a similar demographic pattern, were observed around neighbouring islands (Tahiti, Raiatea, Huahine and Bora Bora), as indicated by photo-identification data and restricted gene flow (FST = 0.143, n = 154). Surprisingly high levels of insular mtDNA genetic diversity (average pi = 1.44%, suggesting Nef ~ 100,000) contrasted with demographic characteristics of these communities. There was no evidence for a recent bottleneck effect, suggesting that this pattern is the result of metapopulation structure, based on numerous insular communities connected through male and female gene flow. Investigation of the worldwide mtDNA diversity and phylogeography of long-finned and short-finned pilot whale species revealed a complex evolutionary history (Globicephala melas, n = 434; and G. macrorhynchus, n = 134, including published and unpublished sequences). Strong genetic differentiation between long-finned pilot whales from the North Atlantic (G. m. melas) and Southern Hemisphere (G. m. edwardii) indicated severely restricted gene flow, although shared haplotypes suggested some recent contact between the two subspecies. Low genetic distances among haplotypes and a star-like phylogeny suggested a recent worldwide expansion for this species. Higher levels of diversity (although low compared to other cetaceans) were found in short-finned pilot whales, in particular among samples from around Japan. Phylogeographic studies suggested that Japanese samples originate from three distinct populations, one of which could be the ancestral population of the species. Overall, my results confirmed that worldwide mtDNA diversity is low in the two species, probably due to a recent worldwide population expansion and, potentially, to a matrilineal social structure. The molecular ecology of the mass strandings of long-finned pilot whales around New Zealand was investigated to test the hypothesis that individuals stranding together are part of an extended matrilineal group. Analyses of mtDNA sequences indicate that more than one haplotype was found in five of the seven mass strandings investigated (n = 275), demonstrating that groups are sometimes composed of unrelated maternal lineages. This was further supported by analyses of relatedness within and between strandings based on microsatellites (14 loci). These analyses discount kinship as the only factor causing large mass strandings in long-finned pilot whales. Parentage analyses confirmed some aspects of previous studies in the North Atlantic, suggesting a social system with at least some level of male and female philopatry to the maternal group, and infrequent paternities within the group. In a detailed study of a large mass stranding (Stewart Island 2003, n = 122), there was no correlation between position of the whales on the beach and genetic relatedness (based on 20 microsatellite loci), discounting the assumption that kinship bonds are maintained during these traumatic events. This was further supported by the striking separation of stranded mothers and dependant calves. This disruption of kinship bonds could help explain the behavioural distress of stranded individuals and the tendency of many whales to re-strand even after being re-floated. Finally, a study of rough-toothed dolphins (Steno bredanensis) in the Society Archipelago, French Polynesia, provided new insights in the ecology of this poorly-known species. Although traditionally viewed as a pelagic dolphin, analyses supported a pattern of local communities, in some ways similar to spinner dolphins, with fine-scale population genetic structure (FST = 0.60, p < 0.001 based on mtDNA, n = 65) and local fidelity. These communities also showed a low level of mtDNA haplotype diversity (four unique haplotypes at Moorea compared to 18 for spinner dolphins), suggesting the potential influence of a matrilineal social structure similar to long-finned pilot whales.

Dissertation (Ph.D.)--Auburn University, 2006. / Abstract. Vita. Includes bibliographic references.

Made available in DSpace on 2014-06-11T19:35:42Z (GMT). No. of bitstreams: 0 Previous issue date: 2010-11-08Bitstream added on 2014-06-13T19:05:54Z : No. of bitstreams: 1 ronesteves_ej_dr_botib.pdf: 4620761 bytes, checksum: 37f231a286b69188af941b49e1c48977 (MD5) / Morphometric, meristic, morphological and phylogenetic analysis from the seahorse Hippocampus reidi (Ginsburg 1933) (Teleostei: Syngnathidae) from the northeastern coast of Venezuela was performed, through the application of techniques using conventional and molecular taxonomy from the sequenced fragments of genes Cytochrome Oxidase I and Cytochrome B as genetic markers. The results indicate that it is not possible to identify the different taxa of Venezuelan Caribbean region, based only on a single type of characters, so it is necessary to use information meristic, morphological and morphometric together to identify them, achieving identify the variables snout length (SnL), body width in the thoracic region (TW9), head length (HL), height of the coronet (CH), number of supra oculars spines (ES) and prominent position of the rings in dorsal view, as diagnostic features at specific level. The application of molecular techniques was very useful in the correct identification and separation of individuals of both species, highlighting the importance and usefulness of the genes Cytochrome Oxidase I and Cytochrome B as molecular markers. Additionally, we carried out a population genetic analysis under the phylogeographic approach, with the species Hippocampus reidi, that was the most abundant in the sampling regions, in order to compare the genetic diversity based on information obtained from the Cytochrome B gene mitochondrial DNA sequences to determine the geographical structure and propose a phylogeographic hypotheses in order to establish the relationship between and within populations of the Caribbean Sea (Laguna de la Restinga, Laguna de las Marites, Cariaco Gulf and Gulf of Venezuela) and the locality of Natal, Brazil, located in the Western Atlantic Ocean. The results of nucleotide diversity and haplotype diversity, together with the presence of several unique haplotypes in each... (Complete abstract click electronic access below) / Fue realizado el análisis morfométrico, merístico, morfológico y filogenético del caballo de mar Hippocampus reidi (Ginsburg 1933) (Teleostei: Syngnathidae) de la costa nororiental de Venezuela, mediante la aplicación de técnicas de taxonomía convencional y molecular utilizando fragmentos secuenciados de los genes Citocromo Oxidasa I y Citocromo B como marcadores genéticos. Los resultados indican que no es posible identificar las diferentes entidades taxonómicas de la región caribeña venezolana con base solamente en un solo tipo de caracteres, por lo que es necesario utilizar información merística, morfológica y morfométrica de forma conjunta para la identificación de las mismas, lográndose identificar las variables longitud del rostro (SnL), ancho del cuerpo en la región torácica (TW9), longitud de la cabeza (HL), altura de la coroneta (CH), número de espinas supra oculares (ES) y posición de los anillos prominentes en vista dorsal, como caracteres diagnósticos a nivel específico. La aplicación de las técnicas moleculares fue de suma utilidad en la correcta identificación y separación de los individuos de las dos especies, resaltando la importancia e utilidad de los genes Citocromo Oxidasa I y Citocromo B como marcadores moleculares para estas especies. Adicionalmente, fue realizado un análisis genético poblacional bajo el enfoque filogeográfico, con la especie Hippocampus reidi que resultó ser la más abundante en las regiones de muestreo, con la finalidad de comparar la diversidad genética, con base en la información obtenida de secuencias del gen Citocromo B del ADN mitocondrial, para determinar la estructura geográfica y proponer una hipótesis filogeográfica que establezca las relaciones entre y dentro de las poblaciones del Mar Caribe (Laguna de la Restinga, Laguna de las Marites, Golfo de Cariaco y Golfo de Venezuela) y la localidad de Natal... (Resumen completo clicar acceso eletrônico abajo)

Orientador: Claudio de Oliveira / Banca: Ricardo Benine / Banca: Alexandre Wagner / Banca: Daniela Calcanotto / Banca: Anderson Luis Alves / Resumen: Fue realizado el análisis morfométrico, merístico, morfológico y filogenético del caballo de mar Hippocampus reidi (Ginsburg 1933) (Teleostei: Syngnathidae) de la costa nororiental de Venezuela, mediante la aplicación de técnicas de taxonomía convencional y molecular utilizando fragmentos secuenciados de los genes Citocromo Oxidasa I y Citocromo B como marcadores genéticos. Los resultados indican que no es posible identificar las diferentes entidades taxonómicas de la región caribeña venezolana con base solamente en un solo tipo de caracteres, por lo que es necesario utilizar información merística, morfológica y morfométrica de forma conjunta para la identificación de las mismas, lográndose identificar las variables longitud del rostro (SnL), ancho del cuerpo en la región torácica (TW9), longitud de la cabeza (HL), altura de la coroneta (CH), número de espinas supra oculares (ES) y posición de los anillos prominentes en vista dorsal, como caracteres diagnósticos a nivel específico. La aplicación de las técnicas moleculares fue de suma utilidad en la correcta identificación y separación de los individuos de las dos especies, resaltando la importancia e utilidad de los genes Citocromo Oxidasa I y Citocromo B como marcadores moleculares para estas especies. Adicionalmente, fue realizado un análisis genético poblacional bajo el enfoque filogeográfico, con la especie Hippocampus reidi que resultó ser la más abundante en las regiones de muestreo, con la finalidad de comparar la diversidad genética, con base en la información obtenida de secuencias del gen Citocromo B del ADN mitocondrial, para determinar la estructura geográfica y proponer una hipótesis filogeográfica que establezca las relaciones entre y dentro de las poblaciones del Mar Caribe (Laguna de la Restinga, Laguna de las Marites, Golfo de Cariaco y Golfo de Venezuela) y la localidad de Natal... (Resumen completo clicar acceso eletrônico abajo) / Abstract: Morphometric, meristic, morphological and phylogenetic analysis from the seahorse Hippocampus reidi (Ginsburg 1933) (Teleostei: Syngnathidae) from the northeastern coast of Venezuela was performed, through the application of techniques using conventional and molecular taxonomy from the sequenced fragments of genes Cytochrome Oxidase I and Cytochrome B as genetic markers. The results indicate that it is not possible to identify the different taxa of Venezuelan Caribbean region, based only on a single type of characters, so it is necessary to use information meristic, morphological and morphometric together to identify them, achieving identify the variables snout length (SnL), body width in the thoracic region (TW9), head length (HL), height of the coronet (CH), number of supra oculars spines (ES) and prominent position of the rings in dorsal view, as diagnostic features at specific level. The application of molecular techniques was very useful in the correct identification and separation of individuals of both species, highlighting the importance and usefulness of the genes Cytochrome Oxidase I and Cytochrome B as molecular markers. Additionally, we carried out a population genetic analysis under the phylogeographic approach, with the species Hippocampus reidi, that was the most abundant in the sampling regions, in order to compare the genetic diversity based on information obtained from the Cytochrome B gene mitochondrial DNA sequences to determine the geographical structure and propose a phylogeographic hypotheses in order to establish the relationship between and within populations of the Caribbean Sea (Laguna de la Restinga, Laguna de las Marites, Cariaco Gulf and Gulf of Venezuela) and the locality of Natal, Brazil, located in the Western Atlantic Ocean. The results of nucleotide diversity and haplotype diversity, together with the presence of several unique haplotypes in each... (Complete abstract click electronic access below) / Doutor

Orientador: Edson Seizo Mori / Coorientador: Danillo Pinhal / Banca: Guaracy Tadeu Rocha / Banca: Adriane Pinto Wasko / Resumo: Schizolobium parahyba é uma árvore nativa da Floresta Atlântica e é classificada como invasora da Floresta Estacional Semidecidual. A invasão biológica é considerada uma das maiores causas de perda de biodiversidade. As populações invasoras possuem diferentes padrões genéticos de estabelecimento, como as invasões repetitivas, crípticas, por introgressões e hibridizações. Neste contexto complexo, as misturas populacionais podem ser uma peça central no sucesso do estabelecimento de populações invasoras por favorecer a adaptabilidade local e diminuir a depressão endogâmica. Por meio do uso de uma nova técnica desenvolvida no presente trabalho de pesquisa baseada em Next-Generation Sequencing, a Restriction-Site Associated DNA-Sequencing com quatro restrições enzimáticas simultâneas, foram detectados parâmetros genéticos como relações de parentesco, subestrutura populacional e medidas variabilidade e diferenciação genética de populações invasoras e naturalizadas desta espécie. Com quase 5.000 locos polimórficos foi possível detectar processos de mistura populacional e das dinâmicas particulares de cada área estudada. Houveram casos de troca de material genético entre populações invasoras e naturalizadas e indícios de que a ação antrópica intensifica o processo de mistura populacional. As análises de subestrutura populacional sugeriram que a ação antrópica favoreceu a formação de subpopulações nas áreas estudadas. A utilização de marcadores moleculares com alta informatividade mostrou ser uma poderosa ferramenta para monitoramento de populações invasoras. / Abstract: Schizolobium parahyba is a native tree of Atlantic Rain Forest and is classified as Seasonally Semideciduous Forest invader. Biological invasion is considered major ones cause of biodiversity loss. Invasive populations have different genetic patterns of establishment, as repetitive invasions , cryptic invasoin, introgression and hybridization. In this complex context, population mixtures can be a centerpiece in the successful establishment of invasive populations by favoring local adaptability and reducing inbreeding depression. Through the use of a new technique developed in this research based on Next- Generation Sequencing, Restriction - site Associated DNA Sequencing with four simultaneous enzymatic restriction , genetic parameters were detected, as relatedness, population substructure and variability and genetic differentiation measures of invasive and naturalized populations of this species . With nearly 5,000 polymorphic loci was possible to detect processes of population mixture and the particular dynamics of each studied area. There have been cases of exchange of genetic material between invasive and naturalized populations and evidence that human action intensifies the process of population mixture. Analyses of population substructure suggested that human action favored the formation of subpopulations in the study areas. The use of molecular markers with high informativeness proved to be a powerful tool for monitoring of invasive populations / Mestre

Made available in DSpace on 2014-06-11T19:30:21Z (GMT). No. of bitstreams: 0 Previous issue date: 2013-12-02Bitstream added on 2014-06-13T18:40:23Z : No. of bitstreams: 1 000758823.pdf: 1966579 bytes, checksum: ad584d90fa1ba8a15edf2765b91f1744 (MD5) / Schizolobium parahyba é uma árvore nativa da Floresta Atlântica e é classificada como invasora da Floresta Estacional Semidecidual. A invasão biológica é considerada uma das maiores causas de perda de biodiversidade. As populações invasoras possuem diferentes padrões genéticos de estabelecimento, como as invasões repetitivas, crípticas, por introgressões e hibridizações. Neste contexto complexo, as misturas populacionais podem ser uma peça central no sucesso do estabelecimento de populações invasoras por favorecer a adaptabilidade local e diminuir a depressão endogâmica. Por meio do uso de uma nova técnica desenvolvida no presente trabalho de pesquisa baseada em Next-Generation Sequencing, a Restriction-Site Associated DNA-Sequencing com quatro restrições enzimáticas simultâneas, foram detectados parâmetros genéticos como relações de parentesco, subestrutura populacional e medidas variabilidade e diferenciação genética de populações invasoras e naturalizadas desta espécie. Com quase 5.000 locos polimórficos foi possível detectar processos de mistura populacional e das dinâmicas particulares de cada área estudada. Houveram casos de troca de material genético entre populações invasoras e naturalizadas e indícios de que a ação antrópica intensifica o processo de mistura populacional. As análises de subestrutura populacional sugeriram que a ação antrópica favoreceu a formação de subpopulações nas áreas estudadas. A utilização de marcadores moleculares com alta informatividade mostrou ser uma poderosa ferramenta para monitoramento de populações invasoras. / Schizolobium parahyba is a native tree of Atlantic Rain Forest and is classified as Seasonally Semideciduous Forest invader. Biological invasion is considered major ones cause of biodiversity loss. Invasive populations have different genetic patterns of establishment, as repetitive invasions , cryptic invasoin, introgression and hybridization. In this complex context, population mixtures can be a centerpiece in the successful establishment of invasive populations by favoring local adaptability and reducing inbreeding depression. Through the use of a new technique developed in this research based on Next- Generation Sequencing, Restriction - site Associated DNA Sequencing with four simultaneous enzymatic restriction , genetic parameters were detected, as relatedness, population substructure and variability and genetic differentiation measures of invasive and naturalized populations of this species . With nearly 5,000 polymorphic loci was possible to detect processes of population mixture and the particular dynamics of each studied area. There have been cases of exchange of genetic material between invasive and naturalized populations and evidence that human action intensifies the process of population mixture. Analyses of population substructure suggested that human action favored the formation of subpopulations in the study areas. The use of molecular markers with high informativeness proved to be a powerful tool for monitoring of invasive populations

京都大学 / 新制・課程博士 / 博士(農学) / 甲第23236号 / 農博第2443号 / 新制||農||1083(附属図書館) / 学位論文||R3||N5326(農学部図書室) / 京都大学大学院農学研究科応用生物科学専攻 / (主査)教授 吉田 天士, 教授 澤山 茂樹, 准教授 神川 龍馬 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DFAM

Yes / Mycobacterium africanum (Maf) causes a substantial proportion of human tuberculosis in some countries of West Africa, but little is known on this pathogen. We compared the genomes of 253 Maf clinical isolates from Ghana, including N = 175 Lineage 5 (L5) and N = 78 Lineage 6 (L6). We found that the genomic diversity of L6 was higher than in L5 despite the smaller sample size. Regulatory proteins appeared to evolve neutrally in L5 but under purifying selection in L6. Even though over 90% of the human T cell epitopes were conserved in both lineages, L6 showed a higher ratio of non-synonymous to synonymous single nucleotide variation in these epitopes overall compared to L5. Of the 10% human T cell epitopes that were variable, most carried mutations that were lineage-specific. Our findings indicate that Maf L5 and L6 differ in some of their population genomic characteristics, possibly reflecting different selection pressures linked to distinct ecological niches. / Supported by the Wellcome Trust Intermediate Fellowship awarded to DYM (Grant Number 097134/Z/11/Z) and by the Swiss National Science Foundation (grants 310030_166687, IZRJZ3_164171 and IZLSZ3_170834), the European Research Council (309540-EVODRTB) and SystemsX.ch.

The newly recognized ammonia-oxidizing archaea (AOA) makes re-evaluation of the contribution to ammonia oxidization by both AOA and ammonia-oxidizing bacteria (AOB) necessary and meaningful. The growing population and increasing anthropogenic activities around coastlines have affected wetland and coastal marine ecosystems through discharging polluted water containing large amounts of reactive inorganic nitrogen. The objectives of this study were to detect the phylogenetic diversity and abundance of ammonia oxidizers including AOA and AOB on different scales and to elucidate the distribution patterns along an anthropogenic pollution gradient from the coastal wetland of the Mai Po Nature Reserve in Hong Kong to the South China Sea (SCS). Generally, besides lineages shared by similar environments, various endemic lineages were also observed in the polluted mangrove sediments of Hong Kong, and in the coastal, and deep-sea surface and subsurface sediments from the SCS indicating their geographical distance should be responsible for these phylogenetic distinctions. The community structures of AOA and AOB observed were proposed to be associated with environmental parameters including metals and total phosphorus (TP) separately in the sediments while their abundance was correlated with the pH value and temperature. On the other hand, along a profile of surface sediments with stable salinity from the coastal margin to the slope in the SCS, a clear community structure transition was detected for both AOA and AOB, showing major differences in each of their responses. Although the abundance of AOA was lower than that of AOB in the subsurface sediment samples from the SCS, the statistical support for relationships between AOA and nitrite concentration shed new light on the active contributor to the subsurface nitrogen cycle in the oxygen minimum zone from the deep-sea sediments. On a large scale, along the anthropogenic pollution gradient from the Pearl River Delta to the coastal margin and then the SCS, the dominant genus transition from Nitrosomonas to Nitrosospira was detected in response to the salinity and anthropogenic influences. Among a wide spectrum of environmental conditions in the western Pacific, a suite of statistical analyses clearly delineated the shallow and deep-sea sediments clusters suggesting that the depth and other contributing environmental factors involved shape the current distribution pattern of AOA. On a global scale, our understanding about the systematics and evolution of AOA was advanced through phylogenetic analyses. Salinity, lifestyle and temperature were proposed to be responsible for the global distribution patterns of AOA. On the basis of studies in the anthropogenic influence areas, the methods to detect specific responses of ammonia oxidizers to known anthropogenic pollution were concluded. Highlights of this study advance not only our understandings about phylogenetic diversity of ammonia oxidizers and the driving forces shaping their community structure and distribution patterns, but also a revised comprehensive view about them on the larger scale. / published_or_final_version / Biological Sciences / Doctoral / Doctor of Philosophy