Broad whitefish, Coregonus nasus, is an important subsistence fish species in Arctic North America, yet virtually nothing is known regarding the genetic population structure of Nearctic populations of this species. In this thesis, microsatellite DNA variation was assayed among 1213 broad whitefish from 47 localities throughout North America, with emphasis on the Mackenzie River system, Northwest Territories. Specifically, I examined geographic variation in allele frequencies to assess how historical factors (Pleistocene glaciations) have shaped the current structuring of genetic variability and population differentiation. Microsatellite data was also used to resolve the relative contributions of broad whitefish populations to subsistence fisheries in the Mackenzie River system. Overall, broad whitefish exhibit relatively high intrapopulation microsatellite variation (average 12.29 alleles/locus, average HE = 0.58) and there were declines in these measures of genetic diversity with distance from putative refugia suggesting historical factors, namely post-glacial dispersal, have influenced current microsatellite variation. Interpopulation divergence was low (overall FST = 0.07), but the main regions assayed in this study (Russia, Alaska, Mackenzie River and Travaillant Lake systems) are genetically differentiated. Strong isolation-by-distance among samples was resolved when including only those populations occupying former Beringia, but not when assaying those at the periphery of the range in the Mackenzie River system, suggesting that broad whitefish in the Mackenzie system have not occupied the region long enough since their invasion post-glacially to have approached equilibrium between gene flow and drift. Mixture analysis indicated that most fish from the lower Mackenzie River subsistence fishery originated from the Peel River, highlighting the importance of this tributary. Additionally the mixture analysis provides evidence for a putative riverine life history form in the Mackenzie River. My results indicate that glaciation and post-glacial colonization have been important in shaping the current genetic population structure of North American broad whitefish. They also illustrate the utility of microsatellite DNA to delineate population structure and patterns of genetic diversity in recently founded populations in addition to resolving contributions to fisheries. My data also support the hypothesis that there are several designatable units of conservation among broad whitefish populations and that management strategies should be implemented accordingly. / Science, Faculty of / Zoology, Department of / Graduate

O curimbatá (Prochilodus lineatus) é uma espécie de importância comercial na pesca continental brasileira, especialmente na região da bacia do Rio Grande. Diversos estudos foram realizados com o curimbatá nesta região, incluindo os de delimitação populacional. Desde então, a região passou por alterações ambientais causadas pela construção de diversas barragens, impossibilitando migrações a montante, essenciais para a reprodução de P. lineatus. O presente estudo teve como objetivo verificar o impacto das barragens, sob o ponto de vista genético, na população de curimbatá da bacia do Rio Grande. Para tanto, foi utilizada a técnica de PCR-RFLP do fragmento entre os genes ND2 e CO1 e também da região controle, ambos do mtDNA, com 10 e 15 enzimas de restrição, respectivamente. Foram realizadas coletas em nove localidades entre barragens que não possuíam escadas para a migração de peixes. As localidades são: no Rio Grande - Cardoso, Colômbia, Conceição das Alagoas, Igarapava, Pedregulho e São João Batista do Glória; no Rio Mogi-Guaçu - Pirassununga e Espírito Santo do Pinhal; e no Rio Pardo - Jaborandi. Os resultados obtidos na análise do fragmento ND2-CO1 com três amostras, sendo uma de cada rio, não evidenciaram divergência significativa. Os índices de diversidade genética (haplotípica e nucleotídica) observados foram baixos, quando comparados com outras espécies de peixes. Estes resultados são condizentes com o esperado para seqüências conservadas, por isso, optou-se pela análise de uma região mais variável, como a região controle do mtDNA. Os resultados obtidos para a região controle (Fst, distribuição de Monte Carlo, teste exato e AMOVA) evidenciaram divergência significativa entre a amostra de Jaborandi e as demais, este fato pode ser devido a uma sub-estruturação populacional, ou a um erro de identificação da localidade de coleta. As outras amostras evidenciaram que, em geral, fazem parte de uma única população sob o ponto de vista genético. Não foi observada estruturação por distância, já que não houve correlação entre a distância genética e a distância geográfica. Os índices de diversidade (nucleotídica e haplotípica) são considerados de altos a moderados, sendo que os maiores foram obtidos para as amostras localizadas em trechos onde ainda há características naturais da bacia. A presença de poucos haplótipos amplamente distribuídos e internos na rede de haplótipos e de diversos haplótipos raros localizados perifericamente na rede, são um indício de expansão populacional recente. A expansão foi averiguada, também, com testes de neutralidade e gráficos de distribuição mismatch. O tempo de expansão foi calculado em 238 mil anos, que corresponde ao Pleistoceno Médio, época de grandes mudanças climáticas na América do Sul. Em conclusão, as alterações ambientais provocadas pelas barragens não geraram, a curto prazo, diferenças significativas entre as amostras estudadas, assim como parecem não estar diminuindo a variabilidade genética do curimbatá, quando comparada com a de populações naturais de outros rios. A divergência obtida para Jaborandi deve ser melhor estudada, mas parece refletir ausência de fluxo anterior à construção das barragens. O objetivo pretendido é o de apresentar um parâmetro de comparação para estudos futuros, especialmente aqueles que enfoquem o monitoramento da variabilidade genética do curimbatá. Estudos de longo prazo devem ser realizados no intuito de auxiliar o manejo pesqueiro do curimbatá, inclusive em programas de repovoamento. / Prochilodus lineatus has a commercial importance in the Brazilian freshwater fishing, especially in the Rio Grande basin. Several studies have been done with P. lineatus in this area, including those delimiting populations. Since then, the Rio Grande basin has been changed due to environmental impacts caused by construction of several dams. The most expressive impact for this population of P. lineatus was the impossibility of upstream migration, essential for its reproduction. The present study aimed at genetically verifying the impact of dams in the population of P. lineatus from Rio Grande basin. The PCR-RFLP method was used in mitochondrial DNA fragments ND2-CO1 and control region, with 10 and 15 restriction enzymes, respectively. Nine samples colected between dams with no fish ladders were analyzed: in Rio Grande - Cardoso, Colômbia, Conceição das Alagoas, Igarapava, Pedregulho e São João Batista do Glória; in Rio Mogi-Guaçu - Pirassununga e Espírito Santo do Pinhal; and in Rio Pardo – Jaborandi. Analysis results of the ND2-CO1 fragment with three samples, one from each river, did not show significant divergence. Values of haplotype and nucleotide diversity were low when compared to other fish species. These results are expected for conserved sequences, so analysis of a more variable region, such as the control region, was chosen. Results of the control region (Fst, Monte Carlo distribution, exact test and AMOVA) showed a significant divergence between Jaborandi sample and the others. This could be due to a population structure, or to an error in the locality identification. The other samples seem to be part of a single population. Isolation by distance was not verified since there is no correlation between genetic and geographic distances. Values of haplotype and nucleotide diversity ranged from high to moderate, with the highest values found in samples from localities where natural features of the basin still exist. Presence of few and widely distributed haplotypes internally in the haplotype net, and the occurrence of several other rare haplotypes distributed peripherically in the haplotype net, are typical of a recent population expansion. The expansion was also verified in neutrality tests and mismatch distribution. The calculated expansion time is 238 thousands of years that correspond to the Median Pleistocene, a period of great climatic changes in South America. In conclusion, the environmental changes caused by dams did not generate significant differences among the analyzed samples, in a short-term, and did not seem to be decreasing the genetic variability of P. lineatus, when compared to other natural populations. Divergence obtained for Jaborandi should be better studied, but seems to reflect the absence of gene flow prior to the construction of dams. These work intents to present a comparative parameter for future studies, especially those monitoring the genetic variability of P. lineatus. Longterm studies must be conducted to help fisheries management of P. lineatus, including restock programs.

O cluster Drosophila buzzatii é formado por sete espécies endêmicas da América do Sul e que apresentam relação ecológica obrigatória com cactos. Dentre estas espécies, Drosophila serido possui ampla distribuição geográfica, na Caatinga e ao longo da costa Atlântica, e é considerada uma espécie politípica sendo dividida em dois grupos: populações do nordeste e do litoral. Com o objetivo de compreender os processos que moldaram a distribuição atual das populações de D. serido foram realizadas análises com sequências dos genes nucleares period e kl-5, ligados aos cromossomos sexuais X e Y, respectivamente, genes nucleares autossômicos GstD1 e E5, e gene mitocondrial COI. Dentre os resultados obtidos, a homogeneidade genética entre as populações do Nordeste e a divisão norte-sul entre as populações da costa Atlântica foram observadas em todos os marcadores. Três padrões quanto à estruturação populacional na costa Atlântica foram observados para os diferentes marcadores. A hipótese de que a Chapada Diamantina seja o centro de dispersão para a espécie foi confirmada pelo presente trabalho, no entanto, o TMRCA estimado para populações de Santa Catarina sugerem que estas sejam populações ancestrais de D. serido, sendo que o Nordeste teria sido colonizado a partir delas. Eventos de expansão de área e fragmentação alopátrica foram sugeridos como inferências filogeográficas para explicar o isolamento atual de populações de D. serido em Goiás e Minas Gerais. De acordo com as estimativas do TMRCA, é possível que os eventos causais dos processos históricos inferidos estejam relacionados à influencia das flutuações climáticas do Quaternário na distribuição geográfica da vegetação/cactos, afetando indiretamente as populações de moscas cactofílicas. É possível que eventos de seleção, associado aos fatores ecológicos quanto ao uso de cactos, também possam ter contribuído para o processo de diversificação populacional, uma vez que foi encontrada evidência de seleção positiva para os genes autossômicos. / Drosophila buzzatii cluster comprises seven species endemic of South America and that present a mandatory ecological association with cacti. Among these species, Drosophila serido has a wide geographical range, in Caatinga and along Atlantic coast, and is considered as a polytypic species, divided in two groups: northeast and coast populations. The purpose of this study was understand the process that shaped the current distribution of D. serido populations through genetic analysis using sequences of nuclear genes period and kl-5, X- and Y-linked, respectively, autosomal genes GstD1 e E5, and mitochondrial gene COI. The genetic homogeneity among Northeast populations and the north-south division among coast Atlantic populations were observed for all markers. Three patterns related to population structure in coast Atlantic were seen for the different markers. Hypothesis that Diamantina Plateau was the dispersion center for the species were confirmed at this study, although, TMRCA estimated for Santa Catarina populations suggested that these ones were ancestral, and that Northeast would be colonized from them. Expansion range and allopatric fragmentation were historical events suggested as phylogeographic inferences to explain the current isolation of D. serido populations in Goiás and Minas Gerais. According to TMRCA estimations, it is possible that causal events of historical process inferred were related to the influence of climatic fluctuations during Quaternary in the geographic distribution range of vegetation/cacti, indirectly affecting the populations of cactofilic flies. Furthermore, selection events, associated with ecological factors due to cacti use, as well as contributed to diversification process in populations, once it was found evidence of positive selection at autosomal genes.

京都大学 / 0048 / 新制・課程博士 / 博士(理学) / 甲第22286号 / 理博第4600号 / 新制||理||1660(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 工藤 洋, 教授 田村 実, 准教授 高山 浩司 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DGAM

Robust monitoring combined with genetic analyses are important approaches to protect and manage large carnivore populations successfully. The aim of this master thesis is to analyse Eurasian lynx (Lynx lynx) population within whole Slovakia for the first time using 15 microsatellite loci. Noninvasive genetics is an effective tool for monitoring animal species with large home ranges and low population densities. Noninvasive samples including feces, hair, urine and buccal swabs were collected together with tissue samples from dead (mostly roadkill) individuals. 187 samples were collected between 2017-2019, resulting in 59 successful genotypes. Two samples were incorrectly determined in the field and excluded from further analyses since they were wildcat samples. For population genetics analyses and demography, the dataset from the "Veľké šelmy 2" project was extended with 98 genotypes in collaboration with the Institute of Vertebrate Biology CAS. Overall, 68 lynx individuals were detected in the dataset of 155 genotypes. Relatedness analysis resulted in 67 significant relationships of the first degree and 9 significant relationships of the second degree. These results suggest a high relatedness among the whole population. According to the present thesis, Slovakian lynx population has the third lowest...

Orientador: Lilian Madi-Ravazzi / Resumo: Drosophila prosaltans e Drosophila austrosaltans, do grupo saltans de Drosophila, são espécies neotropicais com distribuição em áreas florestais da América Central e do Sul e que podem ser encontradas em simpatria. A literatura sobre o grupo saltans de Drosophila é escassa e muitos trabalhos não são tão recentes. Assim, poucas são as informações disponíveis sobre os aspectos biológicos de ambas as espécies. Para D. prosaltans, existem trabalhos de isolamento reprodutivo, estrutura e polimorfismo cromossômico que apontam uma diferenciação de suas populações, entretanto, as informações em relação à diferenciação populacional de D. austrosaltans são praticamente inexistentes. Tal fato nos motivou a investigar os padrões de diversidade genética populacional dessas espécies provenientes de diferentes fitofisionomias de Mata Atlântica utilizando os microssatélites como marcador molecular. Foram desenvolvidos oligonucleotídeos de microssatélites específicos para D. prosaltans, cuja transferibilidade testada para D. austrosaltans mostrou resultados positivos. Identificamos na análise de 12 locos para D. prosaltans, uma alta heterozigosidade média (Ho = 0.45 ± 0.03) e uma diferenciação genética populacional moderada (Fst = 0.17 ± 0.02). Foi observada a formação de dois agrupamentos genéticos distintos nas populações de D. prosaltans, que não se correlacionam com a distribuição regional ou de fitofisionomia das populações, podendo esse padrão ser decorrente de características ecológica... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Drosophila prosaltans and Drosophila austrosaltans, from the Drosophila saltans group, are neotropical species with distribution in forest areas of Central and South America and that can be sympatric. The literature on the Drosophila saltans group is scarce and many works are not so recent. Thus, little information is available on the biological aspects of both species. For D. prosaltans, there are works of reproductive isolation, structure and chromosomal polymorphism that point to a differentiation of its populations, however, the information regarding the population differentiation of D. austrosaltans is practically nonexistent. This fact motivated us to investigate the patterns of population genetic diversity of these species from different Atlantic Forest phytophysiognomies using microsatellites as a molecular marker. Microsatellite oligonucleotides specific for D. prosaltans were developed, whose transferability tested for D. austrosaltans showed positive results. In the analysis of 12 loci for D. prosaltans, we identified a high mean heterozygosity (Ho = 0.45 ± 0.03) and a moderate population genetic differentiation (Fst = 0.17 ± 0.02). The formation of two distinct genetic groups was observed in D. prosaltans populations, which do not correlate with the regional or phytophysiognomic distribution of the populations, and this pattern may be due to ecological characteristics, shared ancestral polymorphism, recurrent mutation and genetic drift (founder effect). The succes... (Complete abstract click electronic access below) / Mestre

Increasing longevity and  falling fertility have increased interest in financing retirement age and have increased the burden of old age in an ageing society. This research is based on data from 41 countries of OECD and BRICS, between 1995 and 2017. By employing the fixed-effect estimation method, this study is to test and compare the relationship between the child and old-age dependency ratios, life expectancy and savings rate of these countries. The two groups of countries represent developed (OECD) and emerging (BRICS) countries with different level of development and states of ageing. The estimation results show that the savings rate of OECD countries can be explained by the old-age and child dependency ratios and life expectancy, but life expectancy has a greater impact on the savings rate. However, although the savings rate in BRICS countries is also positively affected by life expectancy, the impact of child dependency ratio is much greater than life expectancy. But, the effect of old-age dependency ratios on savings is insignificant in BRICS countries.

The evolution of antibiotic resistance provides a well-documented, rapid, and recent example of a selection driven process that has occurred in many bacterial species. An exhaustive collection of Moraxella catarrhalis that spans a transition to chromosomally encoded penicillin resistance was used to analyze genetic changes accompanying the transition. The population was characterized by high haplotypic diversity with 148 distinct haplotypes among 372 isolates tested at three genomic regions. The power of a temporally stratified sample from a single population was highlighted by the finding of high genetic diversity throughout the transition to resistance, population numbers that remained high over time, and no evidence of departures from neutrality in the allele frequency spectra throughout the transition. The direct temporal analysis documented the persistence, antibiotic status, and haplotypic identity of strains undergoing apparent clonal expansions. Several haplotypes that were β-lactamase nonproducers in early samples converted to producers in later years. Maintenance of genetic diversity and haplotype conversions from sensitive to resistant supported the hypothesis that penicillin resistance determinants spread to a diverse array of strains via horizontal exchange. Genetic differentiation between sample years, estimated by FST, was increasing at a rate that could cause complete haplotype turnover in less than 150 years. Widespread linkage disequilibrium among sites within one locus (copB) suggested recent mutation followed by clonal expansion. Nonrandom associations between haplotypes and resistance phenotypes provided further evidence of clonal expansion for some haplotypes. Nevertheless, the population structure was far from clonal as evidenced by a relatively low frequency of disequilibria both within sites at a second locus (M46) as well as between loci. The haplotype-antibiotic resistance association that was accompanied by gradual haplotype turnover is consistent with a hypothesis of genetic drift at marker loci with directional selection at the resistance locus.

Western prairie clover [Dalea ornata (Douglas ex Hook.) Eaton & J. Wright] is a perennial legume that occurs in the northern Great Basin, Snake River Basin, and southern Columbia Plateau, whereas Searls prairie clover [Dalea searlsiae (A. Gray) Barneby], also a perennial legume, occurs in the southern Great Basin and surrounding areas. Understanding the genetic and ecotypic variation of these prairie clovers is a prerequisite for developing populations suitable for rangeland revegetation in the western USA. DNA sequences of internal transcribed spacer (ITS/5.8S) and trnK/matK were used to study the phylogeny of these species. The species were distinguished by DNA sequences from both regions and conserved haplotypes were observed between and within species. Common-garden plots of 22 collections of western prairie clover from Idaho, Oregon, and Washington and 20 collections of Searls prairie clover from Utah and Nevada were established in northern Utah for phenotypic evaluation. Significant variation was detected among the collections for all traits measured in the common gardens for both species. Flowering date was correlated with collection-site temperature and elevation in western prairie clover collections, whereas biomass-related traits were closely related with collection-site precipitation in Searls prairie clover. Population structure from amplified fragment length polymorphism (AFLP) markers resulted in two distinct, genetically differentiated groups and a third admixed group in western prairie clover, and flowering date played a significant role in discriminating those genetic-based groupings of collections. For western prairie clover, two populations are recommended for development, one from the Deschutes River watershed and another from the remaining collections. For Searls prairie clover, two genetically different groups of collections were identified from southern Utah and eastern Nevada and from northwestern Utah. Three western Nevada collections exhibited close association with eastern Nevada and southern Utah groups for AFLP-markers but with collections from northwestern Utah for phenotypic traits. Strong isolation by distance was observed for Searls prairie clover collections suggesting that genetic drift and gene flow are major factors for determining population structure in this species. As a result, two regional seed sources should be developed for Searls prairie clover, one from northwestern Utah and the other from eastern Nevada and southern Utah.

A vast range of factors shape the genetic structure of plant populations. In this thesis, I focus on two of them. The first factor, polyploidization, is a process of chromosome set multiplication through whole-genome duplication within a single species (autopolyploids) or hybridization of two different species (allopolyploids). It rapidly brings changes into genomes, allowing species to occupy distinct niches, adapt to new habitats, colonize them, or adapt to changing environment in their native range. But it comes at a certain cost - difficulties in mitosis and meiosis, changes in cellular architecture. Furthermore, after cytotype establishment, new individuals have to deal with cytotype exclusion effect, competition with parental individuals and higher nutrition requirements. In this thesis, I present the effect of polyploidization on populations of three species- Arabidopsis arenosa, Aster amellus and Festuca rubra. The second factor changing the population genetic structure presented in this thesis is the fragmentation of populations. Population fragmentation can be caused by natural or anthropogenic activities and often leads to overall reduction in population size and reduced connectivity among fragments. Restricted gene flow may threaten long-term population survival due to inbreeding...