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.

Amaranth (Amaranthus caudatus L.) is an important pseudocereal in the Andes. The seed has excellent nutritional value (high in protein, essential amino acids, and minerals) and ample capacity for growth in diverse, harsh Andean subsistence-production conditions such as water deficiency, salt stress, and soil mineral nutrient deficiency. The objective of this study was to characterize and quantify the genetic diversity among a series of 178 mostly Peruvian amaranth genotypes using 96 biallelic single-nucleotide polymorphism (SNP) markers. A total of 96 co-dominant, biallelic markers were developed using KASPar™ assays on a 96.96 Fluidigm EP1 array system. The 178 amaranth genotypes included white-opaque and white-translucent (vitreous) putative A. caudatus seed types, along with black-seeded A. hybridus and brown-seeded types, all isolated from among 48 accessions of the CICA-UNSAAC collection. Variation among and within samples and accessions was compared for empirically determined clusters (northern, north-central, south-central, and southern Peruvian Andes). Variation was highest within samples for all groups, but only in white-seeded amaranth was the p-value significant (17.43). The greatest variation among samples was found in the vitreous-seeded group (99.35). The highest average observed heterozygosity within-groups (Ho) was 0.19 in the brown-seeded group, and expected within-group heterozygosity (He) was highest in the vitreous-seeded group (0.359). Cluster analysis (UPGMA), PCA and PCO results partitioned the amaranth accessions into six discrete clusters. Clusters did not manifest obvious structure among accessions, which indicates that genetic diversity has been conserved across a broad region of the Peruvian Andes. The diversity characterization pointed to a center of origin and domestication of A. caudatus in the Ayacucho-Cusco region of southern Peru.

<p>Campylobacter jejuni is the main cause of bacterial diarrhoeal illness in developed countries, with ~7000 cases being reported each year in Sweden. C. jejuni has received growing attention since it’s recognition as a human pathogen in the 1970s, but its epidemiology is complex and much still remains unknown. There are several potential reservoirs for C. jejuni, including environmental sources as water and soil, wild and domesticated animals, particularly poultry, but also other livestock and pets. In this study 348 Swedish C. jejuni isolates from the year 2000 from humans (n = 164) and broilers (n = 184) were characterized with multilocus sequence typing (MLST) with the aim of comparing the population structures and diversity of C. jejuni between isolates from the two hosts. MLST is a method for characterization of bacterial isolates that indexes the variation in DNA sequence of multiple protein encoding housekeeping genes. A secondary aim in this study was to compare populations of C. jejuni from 11 subgroups of isolates based on location of the sampling. The overlap between the populations was analyzed numerically based on genotypes detected and with analysis of phylogeny, gene flow and molecular variation. It was shown that the population structure of C. jejuni isolates from broilers and humans show a high degree of similarity, supporting broilers as an important source of human infection. However, even though the population structure of human and broiler C. jejuni were almost genetically indistinguishable other sources of C. jejuni infections in humans cannot be ruled out since the same genotypes can be found in other sources as well. Analysis of the 11 subgroups suggested that there may be a difference in populations infecting humans in different Swedish regions, and between populations of C. jejuni in broilers from different slaughterhouses. But this could be a result of chance since most of the subgroups were small. Future studies to improve the understanding of C. jejuni epidemiology, for which MLST has proven itself as a valid method, is important to develop control strategies to prevent infection with this common cause of diarrhoeal illness.</p>

<p>The white-tailed eagle is a formerly threatened raptor that is commonly used as a flagship and indicator species in conservation work. This thesis uses molecular genetic methods to study sex determination of nestlings, genetic variability, population structure and phylogeography of the white-tailed eagle.</p><p>Fourteen microsatellite markers were developed and tested for the white-tailed eagle.</p><p>A method to sex white-tailed eagle nestlings in the field is presented. The method is based on just one tarsus measure, and is suitable for situations where a single person is handling the nestlings alone in a treetop.</p><p>Most European white-tailed eagle populations underwent extreme declines during the 20th century. The results presented here show that bottlenecked populations have maintained significant levels of genetic diversity. Gene flow between regions is not a main explanation for this, as indicated by both genetic and ringing data. Instead, the long generation time of white-tailed eagles has acted as an intrinsic buffer against rapid loss of genetic diversity. Additionally, local conservation led to protection of more genetic diversity than if conservation had focused on the large remnant population in Norway.</p><p>Mitochondrial DNA of white-tailed eagles is structured in two main clades with a predominantly eastern and western Eurasian distribution. The clades likely correspond to separate Ice Age refugia but do not grant classification as evolutionary significant units given their current extensive overlap across large parts of Eurasia.</p><p>Microsatellite variation was studied in populations across Eurasia. Variability was rather constant across the continent, but clearly lower on Iceland and Greenland. This is best explained by founder effects during their colonisation, but only weak bottlenecks during colonisation of and persistence on the continent. Current population differentiation between Europe and eastern Eurasia is not compatible with a zero gene flow model but requires some amount of gene flow over evolutionary time scales.</p>

The white-tailed eagle is a formerly threatened raptor that is commonly used as a flagship and indicator species in conservation work. This thesis uses molecular genetic methods to study sex determination of nestlings, genetic variability, population structure and phylogeography of the white-tailed eagle. Fourteen microsatellite markers were developed and tested for the white-tailed eagle. A method to sex white-tailed eagle nestlings in the field is presented. The method is based on just one tarsus measure, and is suitable for situations where a single person is handling the nestlings alone in a treetop. Most European white-tailed eagle populations underwent extreme declines during the 20th century. The results presented here show that bottlenecked populations have maintained significant levels of genetic diversity. Gene flow between regions is not a main explanation for this, as indicated by both genetic and ringing data. Instead, the long generation time of white-tailed eagles has acted as an intrinsic buffer against rapid loss of genetic diversity. Additionally, local conservation led to protection of more genetic diversity than if conservation had focused on the large remnant population in Norway. Mitochondrial DNA of white-tailed eagles is structured in two main clades with a predominantly eastern and western Eurasian distribution. The clades likely correspond to separate Ice Age refugia but do not grant classification as evolutionary significant units given their current extensive overlap across large parts of Eurasia. Microsatellite variation was studied in populations across Eurasia. Variability was rather constant across the continent, but clearly lower on Iceland and Greenland. This is best explained by founder effects during their colonisation, but only weak bottlenecks during colonisation of and persistence on the continent. Current population differentiation between Europe and eastern Eurasia is not compatible with a zero gene flow model but requires some amount of gene flow over evolutionary time scales.

North Atlantic and South Atlantic swordfish (Xiphias gladius L.) are currently managed as two stocks separated at 5°N. While previous studies of genetic population structure using both mitochondrial and nuclear DNA confirm two genetically distinct stocks, sampling coverage has not been uniform or representative of all areas and estimates of admixture in areas of contact have not been provided. In this study, we examined: 1) the applicability of high-resolution melting analysis (HRMA) in population genetic studies of non-model organisms, 2) the use of nuclear markers in Atlantic swordfish and the methodology whereby nuclear gene variation can be quickly screened, identified, and genotyped using short-amplicon (SA) HRMA and unlabeled probe (UP) HRMA, and 3) the use of HRMA to characterize nuclear markers to study the genetic population structure of Atlantic swordfish using representative samples of the entire basin to provide an estimation of population admixture by means of Bayesian individual assignment. High resolution melting analysis (HRMA) is shown to be a highly sensitive, rapid, closed-tube genotyping method amenable to high throughput and, though until recently primarily confined to clinical studies, suitable for population studies in non-model species. Ten nuclear markers were genotyped primarily by SA- and UP-HRMA in North Atlantic (n=419), South Atlantic (n=296), and Mediterranean (n=59) swordfish. Comparisons of pairwise FST, AMOVA, PCoA, and Bayesian individual assignments were congruent with previous finding of three discrete populations with comparatively low levels of estimated gene flow for a marine organism (FST = 0.039-0.126). Population admixture was identified and estimated in the Northeast Atlantic and appeared to be asymmetrical, with swordfish from the South Atlantic found among North Atlantic localities but no North Atlantic migrants identified in the South Atlantic. The Mediterranean boundary currently at the Strait of Gibraltar is found to extend west into Atlantic waters to approximately 8°W. Similarly, the boundary between North and South Atlantic swordfish should be revised to a line that extends north from 0°N 45°W to 25°N 45°W and from that position, as a nearly horizontal line, eastwards to the African coast. Finally, I show that Bayesian individual assignment using the developed marker set can be used for mixed stock allocation in the Northeast Atlantic.

<p>Uncovering the DNA regulatory logic in complex organisms has been one of the important goals of modern biology in the post-genomic era. The sequencing of multiple genomes in combination with the advent of DNA microarrays and, more recently, of massively parallel high-throughput sequencing technologies has made possible the adoption of a global perspective to the inference of the regulatory rules governing the context-specific interpretation of the genetic code that complements the more focused classical experimental approaches. Extracting useful information and managing the complexity resulting from the sheer volume and the high-dimensionality of the data produced by these genomic assays has emerged as a major challenge which we attempt to address in this work by developing computational methods and tools, specifically designed for the study of the gene regulatory processes in this new global genomic context. </p><p>First, we focus on the genome-wide discovery of physical interactions between regulatory sequence regions and their cognate proteins at both the DNA and RNA level. We present a motif analysis framework that leverages the genome-wide</p><p>evidence for sequence-specific interactions between trans-acting factors and their preferred cis-acting regulatory regions. The utility of the proposed framework is demonstarted on DNA and RNA cross-linking high-throughput data.</p><p>A second goal of this thesis is the development of scalable approaches to dimension reduction based on spectral decomposition and their application to the study of population structure in massive high-dimensional genetic data sets. We have developed computational tools and have performed theoretical and empirical analyses of their statistical properties with particular emphasis on the analysis of the individual genetic variation measured by Single Nucleotide Polymorphism (SNP) microrarrays.</p> / Dissertation

The vigorous economic growth in Japan after World War II triggered the demographic change of low fertility, low mortality and increasing life expectancy. Japan¡¦s ¡§Dankainosedai¡¨ (Baby boomer) getting old led to a rapid aging society in the past twenty years. Currently, the percentage of older people in Japan significantly exceeds global average and even reaches a level so called super-aging society. Such phenomenon of baby bust and population aging not only deteriorates the economic growth but also reduces government¡¦s budget for public construction, leads to rural-urban divide, and causes major social issues such as family support, retirement and healthcares. Recent literature focusing on influence of demographic transition on economic growth was primarily based on cross-sectional data or panel data. Few articles presented analysis using the prefecture -by- prefecture or regional data as a base. Therefore, we try to clarify the interaction between demographic change and economic growth by using 47 prefectures¡¦ statistic data of Japan, which is very well collected and ideal for conducting documental regression analysis. The objective of this paper is to provide some conclusions from Japan which might be useful for the government of Taiwan when making population and economic policy. Following Bloom and Williamson¡]1998¡^, this paper seek to examine the links between several variables, such as demographic change , and economic growth, by running regressions on panel data covering 47 prefectures of Japan during 1975-2008. We found that population growth, age structure, physical capital and industrial structure did have significant impact on growth rates of Japan. Population growth as a whole and the young and elderly dependants had a strong negative impact on economic growth, while growth of the working-age population and physical capital had strong positive impact. The result shown that the economic growth of Japan was impeded for a few years since the age structure of population was shifted to constrictive type which is caused by baby bust and aging. We also tried different frameworks to examine the influence of various variables, such as selecting some prefectures with unique feature, segmenting seven major economic regions, or dividing years in two periods ¡]before and after the year with bubble economy 1989¡^. We can make a conclusion that comparing with the period 1975 -1989, the economic growth rate during 1990-2008 slumped due to the changes of age structure, physical capital and industrial structure.

This study presents evidence from mitochondrial and nuclear loci that there is genetic divergence among and within geographic populations of Lagenorhynchus obscurus. The effect of seasonal variation on the genetic structure within New Zealand was examined with mitochondrial DNA control region sequences from 4 localities. Analysis of nested haplotype clades indicated genetic fragmentation and at least 1 historical population expansion within New Zealand. AMOVA and Fst values from nuclear and mitochondrial DNA sequences suggested significant divergence between New Zealand, South Africa, Argentina, and Peru. Dispersal via the west-wind drift was not supported by patterns of population structure among regions. Alternatively, these data support reciprocal exchange among all four regions with 100% posterior probability for a root of origin in the Indian/Atlantic Oceans. The degree of divergence between Peru and other regions indicates the isolation of Peruvian stock is temporally correlated with the constriction of Drake’s passage in the Plio-Pleistocene. There is evidence that the Plio-Pliestocene paleoceanography of the Indian and Southern Atlantic Oceans influenced phylogeography with shifts of temperate sea surface temperatures northward ~5º of latitude, disrupting the dispersal corridor between New Zealand and Atlantic populations. A preference for temperate waters along continental shelves is proposed as an explanation for lack of contemporary genetic exchange among regions. This study supports the polyphyly of the genus Lagenorhynchus. North Atlantic species form a monophyletic Lagenorhynchus. In the Southern Hemisphere, L. australis/L. cruciger and L. obliquidens/L. obscurus do not form a monophyletic group. I discuss the taxonomic implications and propose taxonomic revision of the genus based on these results. Measures of character interaction indicate that combined evidence from nuclear and mitochondrial genes provide better phylogenetic resolution among delphinid lineages than any data partition independently, despite some indications of conflict among mitochondrial and nuclear data.

The Canary Island pine, Pinus canariensis, is an endemic tree that forms one of the main forest ecosystems within the archipelago, and whose distribution has been reduced in the last five centuries by clear cutting for the extraction of timber and tar. It was in the XXth century that exploitation declined and reforestation programs were brought forward for the restoration of an ecosystem that harbours a number of endangered endemic species of plants and animals. In addition to reforestation efforts, an understanding of population genetic processes is also necessary for the successful conservation management of the Canarian pine forest, particularly in light of gathering evidence for local adaptation.<br /><br />In this thesis historical and contemporary gene flow within P. canariensis was studied with nuclear and chloroplast microsatellite markers. High immigration rates (0.68–0.75) were estimated as expected for an outcrossing windpollinated tree. Nevertheless, significant population differentiation (theta = 0.019, RST = 0.044) was detectable for sites separated by only a few kilometres. Within the context of reforestation programs the high levels of gene flow detected would appear to have a positive effect on reforested stands by facilitating the immigration of local alleles from natural stands into potentially genetically depauperate first generation gene pools of reforested stands.<br /><br />Historical population growth was revealed with chloroplast microsatellites for most populations of P. canariensis. Population expansions for the pine parasite weevil Brachyderes rugatus were also detected, broadly coinciding with the population expansions within the Canary Island pine forests. Given the estimated times of expansion, these population demographic increases would seem likely related to the process of colonisation of newly emerged islands or local patches after volcanic disturbance. Detection and dating of these expansions from chloroplast microsatellites was, to some degree, negatively affected by homoplasy (i.e. parallel and back mutations).<br /><br />Coalescent simulations of the evolution of chloroplast microsatellites were applied to study the effects of homoplasy in the statistical analysis of population structuring. Measures of genetic diversity based on number of haplotypes and genetic distances were differently affected. Genetic distances were underestimated but were proportional to the actual value. These effects help to explain the lower performance of statistical analyses for the detection and dating of population expansions. Further research on the effects of homoplasy in the analysis of population differentiation using chloroplast microsatellites is essential.