This PhD thesis studies the evolution of the peculiar mitochondrial DNA (mtDNA) in the mollusc Melarhaphe neritoides. We measured mtDNA diversity and elucidated the evolutionary forces that shape the evolution of the organelle.The mtDNA in M. neritoides harbours a remarkable amount of polymorphism at selectively neutral nucleotide sites (π_syn = 6.8 %), called hyperdiversity when above the threshold of 5 %. We revealed that an elevated mutation rate (µ = 5.8 × 10-5 per site per year at the COI locus), which is 1000 fold higher than in other metazoans, is likely the primary force generating mtDNA hyperdiversity. Such mtDNA hyperdiversity may be more common across other phyla and more frequently linked to high µ values, than currently appreciated.Natural selection is a second force, which shapes mtDNA hyperdiversity. Positive selection influences the overall mtDNA polymorphism in the 16S, COI and Cytb genes, including synonymous sites at which mtDNA hyperdiversity is calculated. Therefore, synonymous sites in M. neritoides are not neutral but possibly positively selected. Strong purifying selection maintains a low non-synonymous polymorphism in the 13 protein-coding genes of the mitogenome, so that a very few changes in nucleotide sequence induce changes in amino acid sequence. The effective population size of this planktonic-dispersing species is surprisingly small in the North East Atlantic (Ne = 1303), likely biased by selection, and for this reason, Ne is a poor indicator of mtDNA hyperdiversity.Migration is a third force, which homogenises the gene pool of the species through high rates of gene flow, predominantly eastward, and results in high connectivity and panmixia over the entire North East Atlantic.Genetic drift, the fourth force, is not sufficient in M. neritoides to lower mtDNA diversity, and populations show no differentiation.This thesis also highlights an important pitfall. The use of hyperdiverse markers may easily lead to erroneous interpretations of differentiation statistics and connectivity pattern, due to the lack of shared haplotypes in datasets induced by a high µ. First, D_EST may reach a maximal value of 1 but is not indicative of differentiation in terms of fixation (D_EST = 1 ≠ φ_ST = 1), and only reflects differentiation in terms of lack of shared haplotypes. Second, the signal of gene flow is concealed in haplotype network bush-like pattern.Rapid evolution of mtDNA results in significant selection pressure for co-adaptation of the nuclear genome encoding mitochondrial proteins. The elevated µ underlying mtDNA hyperdiversity provides an interesting framework for better understanding how mutational dynamics and selection that drive mitonuclear coevolution contribute to speciation. / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

Please read the abstract in the section 00front of this document. / Thesis (PhD)--University of Pretoria, 2010. / Zoology and Entomology / unrestricted

O Brasil é o país mais rico do mundo em espécies de psitacídeos (cerca de 74), sendo 17 delas ameaçadas de extinção. Entre elas está a arara-azul (Anodorhynchus hyacinthinus) que é considerada vulnerável e pode se tornar ameaçada num futuro próximo, em conseqüência do intenso tráfico ilegal e perda do seu habitat. No presente estudo estimamos os níveis de variabilidade e caracterizamos a estrutura genética de populações naturais de A. hyacinthinus. Analisamos 10 locos de microssatélites de 98 indivíduos e seqüências concatenadas de genes mitocondriais (ND5, citocromo-b e ND2; 2123 pb total) de 80 indivíduos. O índice de diversidade genética foi considerado baixo em relação a outras espécies de psitacídeos. Além disso, os índices RST e a análise bayesiana dos dados de microssatélites indicaram moderada estruturação genética entre indivíduos de quatro regiões geográficas (Pantanal norte, Pantanal sul, norte e nordeste), mas os índices de FST indicaram diferenciação somente entre três regiões (norte e nordeste sem diferenciação). A estruturação entre essas três regiões foi congruente com a forte estruturação genética apontada pelos índices de FST e pela rede de haplótipos das seqüências mitocondriais. Baseado nos dados mitocondriais o tempo de divergência entre os grupos genéticos de A. hyacinthinus foi estimado em 16 a 42 mil anos atrás, o que corresponde ao final do Pleistoceno. Ainda, os resultados apontaram para uma população demograficamente estável ao longo do tempo, o que pode indicar que a baixa variabilidade pode ser uma característica da espécie. Entretanto, a rede de haplótipos apresenta forma em estrela com alguns haplótipos de baixa freqüência, o que pode indicar expansão recente, principalmente para região nordeste. Baseado nos dados de estruturação genética populacional, foi possivel indicar a possível origem de indivíduos apreendidos e sem procedência conhecida, o que é importante para realizar ações preventivas de repressão e fiscalização. Adicionalmente, foram analisados sete locos de microssatélites de filhotes amostrados no mesmo ninho (mesma estação reprodutiva, estações reprodutivas consecutivas e estações alternadas) em duas regiões do Pantanal. Os resultados sugerem que a espécie é predominantemente monogâmica estrita, mas há pelo menos 12,5% de paternidade extra-par e 6,5% de parasitismo de ninho. Além disso, foram confirmados dados obtidos em campo de que muitos casais utilizam o mesmo ninho em anos consecutivos e alternados. Finalmente, padronizamos a sexagem molecular de amostras de penas de muda. Concluindo, os resultados genéticos obtidos nesse trabalho trazem informações sobre os processos envolvidos na história evolutiva dessa espécie, além de contribuir com informações sobre o comportamento reprodutivo das araras-azuis proporcionando mais subsídios para elaboração de programas de conservação. / Brazil has the highest number of parrot species in the world (about 74), 17 of them endangered. Among them is the hyacinth macaw (Anodorhynchus hyacinthinus), which is considered vulnerable and could become endangered in the near future, due to the intense illegal traffic and loss of habitat. In this study we estimated levels of variability and characterized the genetic structure of natural populations of hyacinth macaws. We analyzed 10 microsatellite loci from 98 individuals and concatenated sequences of mitochondrial genes (ND5, cytochrome b and ND2, 2,123 bp total) from 80 individuals. The genetic diversity index was low compared to those from other species of parrots. In addition, RST indeces and Bayesian analysis of microsatellite data showed moderate genetic structure among individuals of four regions in Brazil (north Pantanal, south Pantanal, north and northeast), but FST indeces indicate differentiation only between three regions (north and northeast without differentiation). This is in accordance with the strong genetic structure indicated by FST indeces and haplotype network based on mitochondrial sequences. Based on the mitochondrial data, the time of divergence of the genetic groups of hyacinth macaws was estimated to have occurred 16 to 42 thousand years ago, which corresponds to the late Pleistocene. Still, the results suggest that the population has been demographically stable over time, which may indicate that the low variability levels may be a characteristic of the species. However, the haplotype network presents a star shape, which indicate recent expansion, specially in the northeast. Additionally, given the population genetic structure data, it was possible to identify the most probable region of origin of apprehended individuals, this information is important to plan preventive and repressive control. Additionally, we analyzed seven microsatellite loci of chicks sampled in the same nest (same breeding season, alternate breeding seasons and consecutive seasons) in two regions of the Pantanal. The results suggest that the species is predominantly monogamous, but there is at least 12.5% of extra-pair paternity and 6.5% of brood parasitism. Furthermore, the genetic data is congruent with field observations that suggest that many couples return to the same nest in consecutive and alternative breeding seasons. Finally, we standardized for a molecular sexing protocol for molten feathers. In conclusion, the genetic results obtained in this study provide information about the processes involved in the evolutionary history and the reproductive behavior of hyacinth macaws that may help plan conservation actions.

The effects of landscape structure on wildlife populations have drawn more attention from ecologists and wildlife managers as landscapes have rapidly changed worldwide. The objectives of this study were to (1) conduct a statewide habitat suitability assessment for wild turkeys (Meleagris gallopavo) in Mississippi using machine learning methods; (2) determine landscape-abundance relationships of wild turkeys at 2 spatial scales; and (3) measure genetic distinction of wild turkey populations in Mississippi. I found that habitat suitability for wild turkeys was positively related to amount of forest cover. Wild turkey relative abundance peaked at an optimal hardwood forest proportion of 0.29 and increased with enhanced landscape configuration at the annual dispersal scale, supporting the landscape composition hypothesis. Using microsatellite analysis of 224 birds, I found 3 distinct genetic clusters in Mississippi; however, population genetic differentiation neither fit to the isolation by distance or isolation by resistance models but may have behavioral cues.

京都大学 / 新制・課程博士 / 博士(理学) / 甲第24310号 / 理博第4880号 / 新制||理||1698(附属図書館) / 京都大学大学院理学研究科生物科学専攻 / (主査)教授 曽田 貞滋, 准教授 渡辺 勝敏, 教授 中務 真人 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DFAM

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Population structure is influenced by extrinsic factors, such as landscape architecture and dispersal barriers. Lotic network architecture is known to constrain ecological, demographic and evolutionary processes, including population genetic structure. I assessed the population structure of a widespread aquatic salamander, Necturus maculosus, across three river basins in central and eastern Kentucky. I examined the role of network architecture, anthropogenic barriers, and spatial scale on patterns of population structure. I also provided a review of N. maculosus capture methods and offer an improved trap design. I identified significant structuring between the combined Licking/Kinniconick basin and the Kentucky River basin, with further structure within each basin. I found evidence for both hierarchically organized populations structure (e.g. Stream Hierarchy Model), as well as population structure unaffected by network hierarchy (e.g. Death Valley Model). These results highlight the importance of scale when examining population structure. Whereas one model may suffice to explain population structure at a local scale, a second model may be necessary to accurately describe the population structure across larger spatial scales. These results suggest that local factors affect population structure uniquely across a species’ range, and support a multi-model approach for assessing population structure.

Queixadas (Tayassu pecari) são mamíferos ungulados sociais que vivem em bandos que facilmente ultrapassam 100 indivíduos. Os objetivos do presente estudo foram: 1) avaliar se há relação entre o parentesco e a estrutura social das queixadas e 2) re-analisar se há diferenciação genética entre queixadas de duas localidades do Pantanal do Mato Grosso do Sul, utilizando maior amostragem de indivíduos e de marcadores microssatélites. Foram genotipadas 184 amostras de queixadas (53 da Fazendo Rio Negro, RN e 131 da Fazenda Santa Emília, SE) para 15 microssatélites. O número de alelos encontrados variou de 2 a 12, com média de 4,60 em RN e 5,07 em SE. Embora o número de alelos médio foi significativamente maior em SE do que em RN (p < 0,05), a riqueza alélica média (4,59 na RN e 4,69 na SE) e as heterozigosidades médias observada e esperada (0,50 e 0,53 na RN e 0,55 e 0,55 na SE, respectivamente) foram similares em ambas as localidades, (p > 0,05). A mediana do coeficiente de parentesco em ambas as localidades foi significativamente maior entre os indivíduos de mesmo grupo de coleta do que entre os indivíduos de grupos de coleta diferentes, tanto para a análise incluindo todos os indivíduos como para a análise sem os indivíduos jovens. Isso sugere que tal resultado não é influenciado por possível captura de um jovem com seu progenitor. De forma similar, a mediana do coeficiente de parentesco considerando o sexo dos indivíduos (macho/macho, macho/fêmea e fêmea/fêmea) dentro e entre os grupos de coleta foi significativamente maior entre as categorias dentro dos grupos de coleta do que entre os grupos de coleta, tanto com os indivíduos jovens como sem os indivíduos jovens. Tais resultados sugerem que o parentesco possui influência na formação dos grupos sociais. O valor de FST encontrado entre as localidades foi de 0,017 e significativamente diferente de zero e o valor de DEST foi de 0,015. A análise Bayesiana, assumindo o modelo de mistura entre as populações e frequências alélicas correlacionadas, apontou o valor de K=1 como sendo o mais provável. Quando a localidade de coleta foi informada, o valor de K mais provável foi de 2 e os agrupamentos corresponderam exatamente às localidades amostradas. Esses resultados indicam que as queixadas das duas localidades estudadas compõem duas populações com alto fluxo gênico entre elas / White-lipped peccaries (Tayassu pecari) are social ungulates that live in herds of usually more than 100 individuals. The aims of the present study were: 1) to evaluate whether there is any correlation between relatedness and social structure of white-lipped peccaries and 2) to re-examine whether there is significant genetic differentiation in white-lipped peccaries from two adjacent locations of the Brazilian Pantanal, based on a larger sample of individuals and of microsatellite markers. In total, 184 peccaries (53 from Fazenda Rio Negro, RN and 131 from Fazenda Santa Emilia, SE) were genotyped for 15 microsatellites. The number of alleles observed per microsatellite varied from 2 to 12, with a mean of 4.60 in RN and 5.07 in SE. Although the mean number of alleles was significantly higher in SE than in RN (p < 0.05), the mean allelic richness (4.59 in RN and 4.69 in SE) and mean observed and expected heterozygosities (0.50 and 0.53 in RN and 0.55 and 0.55 in SE, respectively) were similar in both locations (p > 0,05). The median of the coefficient of relatedness in both locations was significantly higher between individuals captured together than between individuals from different capture groups, both for the analyses including all individuals as for the analyses without the youngsters. This suggests that this result is not influenced by the possible capture of a young with its parent. Similarly, the median of the coefficient of relatedness according to gender (male vs. male, male vs. female, and female vs. female) was significantly higher within than among capture groups, including or excluding young individuals. Those results suggest that relatedness has some importance in the social structure of white-lipped peccaries. The FST between the locations was 0.017 and significantly different from zero and the DEST was 0.015. The Bayesian analysis, assuming the model of population mixture and correlated allele frequencies, showed that the most likely K was 1. When the collection site was included in the analysis, the most likely value of K was 2 and the clusters corresponded exactly to the locations of origin of the samples. Those results suggest that the white-lipped peccaries of the two sites studied comprise two populations with high levels of gene flow between them

L’objectif de ce projet est de réaliser l’étude d’écologie moléculaire, non pas d’une espèce isolée, mais d’un groupe fonctionnel. Dans l’écosystème forestier africain, certaines espèces sont caractéristiques de la forêt, d’autres de la savane, et ont connu des phases d’expansion et de régression au cours des changements climatiques du quaternaire. Leur génome a-t-il enregistré un signal commun de l’histoire démographique qui en a résulté ? J’ai travaillé sur 9 espèces du genre Zaprionus (Drosophilidae). J’ai obtenu pour six d’entre elles un jeu de données complet comprenant deux échantillonnages populationnels N=20 (15 dans un cas) pour 10 gènes nucléaires et un gène mitochondrial. J’ai cherché la trace d’expansions démographiques en utilisant le DT de Tajima, le FS de Fu, la distribution mismatch. Avec les horloges moléculaires disponibles, l’histoire démographique de chaque espèce a été explorée par des méthodes bayésiennes sous BEAST (ADN mitochondrial) ou dans un modèle avec recombinaison utilisant FastSimCoal (ADN nucléaire). Cinq espèces d’affinités forestières présentent la signature d’une expansion de population. C’est le cas de Z. aff. proximus, Z. davidi, Z. sepsoides, Z. taronus et Z. vittiger. Une sixième espèce, Z. indianus, semble avoir une histoire démographique plus complexe ce qui serait compatible avec son écologie savanicole. Les délais imposés par la lourdeur des outils numériques disponibles ont limité à ce stade l’exploitation complète de ces données. En conclusion, le génome de toutes les espèces, de savane ou de forêt, porte la signature des changements climatiques passés. Ceci valide les prémisses de notre approche d’une "génomique des écosystèmes". / The aim of this project was to carry out a molecular ecology study, not only on a single species, but on a whole functional group. In the africain forest ecosystem, some species are typical of the forest while others are typical of the savanna, and have undergone stages of expansion and regression during Quaternary climate changes. Do their genomes share a common signature of the ensuing demographic history? I worked on nine species from the Zaprionus genus (Drosophilidae). For six species, I was able to gather a complete dataset including two population samples of N=20 (15 in one case) for 10 nuclear genes and one mitochondrial gene. I investigated the signature of population expansion by using Tajima’s DT, Fu’s FS, and the mismatch distribution. The demographic history of each species was investigated using Bayesian methods including BEAST (for mtDNA) and a recombination model using FastSimCoal (for nuclear DNA), with available molecular clocks. Five forest-dwelling species show the signature of a population expansion: Z. aff. proximus, Z. davidi, Z. sepsoides, Z. taronus et Z. vittiger. A sixth species, Z. indianus, shows a more complex history in agreement with its dependence on savanna. The completion of the analysis of the whole dataset was precluded by the time-consuming numerical procedures involved. To conclude, the genome of all of these species – either form savanna of from the forest – shows the signature of past climatic changes, thus validating an "ecosystem genomics" approach.