abstract: The severity of the health and economic devastation resulting from outbreaks of viruses such as Zika, Ebola, SARS-CoV-1 and, most recently, SARS-CoV-2 underscores the need for tools which aim to delineate critical disease dynamical features underlying observed patterns of infectious disease spread. The growing emphasis placed on genome sequencing to support pathogen outbreak response highlights the need to adapt traditional epidemiological metrics to leverage this increasingly rich data stream. Further, the rapidity with which pathogen molecular sequence data is now generated, coupled with advent of sophisticated, Bayesian statistical techniques for pathogen molecular sequence analysis, creates an unprecedented opportunity to disrupt and innovate public health surveillance using 21st century tools. Bayesian phylogeography is a modeling framework which assumes discrete traits -- such as age, location of sampling, or species -- evolve according to a continuous-time Markov chain process along a phylogenetic tree topology which is inferred from molecular sequence data. While myriad studies exist which reconstruct patterns of discrete trait evolution along an inferred phylogeny, attempts to translate the results of phyloegographic analyses into actionable metrics that can be used by public health agencies to direct the development of interventions aimed at reducing pathogen spread are conspicuously absent from the literature. In this dissertation, I focus on developing an intuitive metric, the phylogenetic risk ratio (PRR), which I use to translate the results of Bayesian phylogeographic modeling studies into a form actionable by public health agencies. I apply the PRR to two case studies: i) age-associated diffusion of influenza A/H3N2 during the 2016-17 US epidemic and ii) host associated diffusion of West Nile virus in the US. I discuss the limitations of this (and Bayesian phylogeographic) approaches when studying non-geographic traits for which limited metadata is available in public molecular sequence databases and statistically principled solutions to the missing metadata problem in the phylogenetic context. Then, I perform a simulation study to evaluate the statistical performance of the missing metadata solution. Finally, I provide a solution for researchers whom are interested in using the PRR and phylogenetic UTMs in their own genomic epidemiological studies yet are deterred by the idiosyncratic, error-prone processes required to implement these methods using popular Bayesian phylogenetic inference software packages. My solution, Build-A-BEAST, is a publicly available, object-oriented system written in python which aims to reduce the complexity and idiosyncrasy of creating XML files necessary to perform the aforementioned analyses. This dissertation extends the conceptual framework of Bayesian phylogeographic methods, develops a method to translates the output of phylogenetic models into an actionable form, evaluates the use of priors for missing metadata, and, finally, provides a solution which eases the implementation of these methods. In doing so, I lay the foundation for future work in disseminating and implementing Bayesian phylogeographic methods for routine public health surveillance. / Dissertation/Thesis / Doctoral Dissertation Biomedical Informatics 2020

Orientador: Lilian Madi-Ravazzi / Resumo: As mudanças climáticas ocorridas no Pleistoceno afetaram a distribuição e os padrões de diversificação populacionais e são conhecidas como um dos potenciais impulsionadores da alta diversidade encontrada na região Neotropical. Drosophila sturtevanti pertence ao subgrupo sturtevanti do grupo saltans de Drosophila e é uma das espécies com distribuição geográfica mais ampla dentro do grupo, ocorrendo em áreas florestais de diferentes biomas. Além disso, essa espécie apresenta altos níveis de variabilidade genética para diversos marcadores, constituindo um excelente modelo para estudos de estrutura populacional, diversificação e adaptação em diferentes cenários. O objetivo desse estudo foi analisar a diferenciação genética, usando os genes Citocromo Oxidase subunidades I e II em 163 indivíduos provenientes de 21 populações de D. sturtevanti coletados em fragmentos florestais da América Central ao sul do Brasil, com ênfase na Mata Atlântica. Nossos resultados moleculares mostram que as populações de D. sturtevanti estão estruturadas na América do Sul e sua distribuição mostra uma correlação significativa com variáveis geográficas e climáticas, principalmente temperatura e umidade. Além disso, os eventos de divergência entre os grupos geográficos sugerem associação significante com as oscilações paleoclimáticas ocorridas desde o Pleistoceno tardio e, esses eventos, provavelmente moldaram a distribuição geográfica dos haplogrupos de acordo com variáveis ambientais, principalmente te... (Resumo completo, clicar acesso eletrônico abaixo) / Doutor

Molecular tools, such as sequencing of the mitochondrial DNA Control Region (CR) and genotyping of highly variable nuclear microsatellites were applied to survey the genetic diversity, population structure and phylogeography of three shark species: the whale shark, Rhincodon typus; the bull shark, Carcharhinus leucas; and the nurse shark, Ginglymostoma cirratum. The highly migratory and pelagic whale shark exhibited the largest length variation yet reported for an elasmobranch CR (1143–1332 bp), and high haplotype (h = 0.974 ± 0.008) and nucleotide diversities(π = 0.011 ± 0.006). No geographical clustering of lineages was observed and the most common haplotype was distributed globally. The haplotype frequency, however, differed between the Atlantic and Indo-Pacific populations(AMOVA, ΦST = 0.107, P < 0.001). For the bull shark, both mtDNA CR and five microsatellite loci were surveyed for animals from the Gulf of Mexico, the East coast of Florida and the Brazilian coast. Strong genetic structure was observed between theBrazilian and all northern populations for the CR (ΦST > 0.8, P < 0.001), but not for the nuclear microsatellite. The results here presented are congruent with restricted maternal gene flow between populations as a consequence of female nursery site fidelity. The philopatric tendencies as well as the relatively low levels of genetic diversity raises concerns about the conservation of this species. Finally, for the western Atlantic nurse sharks the genetic diversity estimated in a 1,166 bp fragment of the mtDNA comprising partial cytochrome b, tRNAPro, tRNAThr, and partial CR was the second smallest ever recorded for sharks (h = 0.45 ± 0.04; π = 0.0004 ± 0.0004). The data indicated moderate but significant genetic structure with the mtDNA marker (ΦST = 0.22, P<0.05) and no substantial structure in eight microsatellite loci analyzed. A population bottleneck as recent as the lower Pleistocene might have eroded the nurse shark genetic diversity and also contributed to its relatively lower population structure. The data also indicated that dispersal rather than vicariance better explains the Atlantic distribution of nurse shark, and that the Pacific nurse shark might be a cryptic sister species to Ginglymostoma cirratum.

This thesis focuses on the genetical and morphological diversity of plaited door snail (Cochlodina laminata). While small distribution ranges are typical for most species belonging to genus Cochlodina, the distribution range of C. laminata covers most of the European continent, except for its coolest and warmest parts. It has been previously suggested that this species might in fact be a complex of several species and large genetical as well as morphological diversity has been mentioned - however, yet undescribed - in previous studies. Sequences of two mitochondrial genes were used (16S rDNA, COI) and thirteen morphological characteritics have been assessed to investigate this diversity. I discovered that the current concept of C. laminata as a species is not in accordance with the discovered genetical nor morphological variability. The original species C. laminata/C. dubiosa form a common species complex and also interpretation of C. fimbriata will need to be assessed in more detail in the future. Other Central European species are valid species.

The Arabidopsis arenosa species complex is closely related to the model species Arabidopsis thaliana. Distribution range of the diploid lineage covers most parts of Central and South-eastern Europe with a remarkable diversity of ecological niches from sea level to alpine peaks. There is still little known about genetic relationships among the diploid populations of A. arenosa. The evolutionary history of the diploid cytotype across its entire range was explored by using 14 nuclear microsatellite loci. Five lineages occupying biogeographically distinct regions were identified in Arabidopsis arenosa complex. These lineages were labelled as Western Carpathians, Eastern Carpathians, Pannonian Lowland, Dinaric Alps and Baltic Shore (according to geographical regions where these lineages occur). Powered by TCPDF (www.tcpdf.org)

The genus Pelasgus (Cyprinidae) is endemic to the southern part of the Balkan Peninsula and includes seven species. In this work, a multilocus approach has been applied to study phylogenetic relationships between the species and their populations and to revise their distribution areas. 180 specimens from 47 localities from 30 river drainages were analyzed, comprehensively covering the distribution range of the genus. Moreover, samples from type localities of all species were included in the analyses. Mitochondrial (cytochrome b) and nuclear markers (the first intron of ribosomal protein S7, recombination activating gene RAG1 and rhodopsin) were used. Existence of seven well supported lineages was revealed based on cytochrome b, which is the most variable marker. These lineages correspond to P. laconicus, P. marathonicus, P. minutus, P. stymphalicus, P. thesproticus, P. prespensis and Pelasgus sp. The most variable nuclear marker was first intron of S7, which provides almost the same results as cytochrome b, revealing six well supported lineages, whereas RAG1 and rhodopsin appear to be less informative, revealing only four well supported clades. These markers did not separate several species (P. marathonicus, P. stymphalicus, P. thesproticus, and Pelasgus sp.) due to low variability of the markers...

Earth-boring dung beetles of the genus Lethrus Scopoli, 1777 belong to the family Geotrupidae, classified into three subfamilies (Geotrupinae, Lethrinae a Taurocerastinae). The description of about 120 species, divided into nine subgenera, is based on morphology and geographic distribution. Shape of mandibles, ventral mandible processes, pronotum and structure of external male genitalia are used as diagnostic morphological characters for taxa. The richest species diversity is known from Central Asia. The distribution area reaches, in the east, up to Mongolia and China, and in the west, up to Southeast Europe. All species are robust, relatively large flightless beetles with low dispersial ability. They feed on parts of fresh plants instead of feces like other dung beetles. Master thesis is focused on the species distributed in the Eastern Mediterranean and Central Europe. This area is inhabited only by nominotypical subgenus Lethrus. The main goal of thesis is to clear up phylogenetic relationships between species of subgenus and speciation events using molecular genetic methods. We have examined 91 samples of the genus Lethrus using two mitochondrial genes - cytochrome b (382 bp, 80 sequences), cytochrome oxidase I (815 bp, 87 sequences) and nuclear gene 28S rDNA (D2-D5) (1100 bp, 11 sequences)....

Orientador: Clarisse Palma da Silva / Resumo: A filogeografia surgiu como uma ponte entre várias disciplinas evolutivas, como a genética populacional, filogenia e biogeografia, estabelecendo ligações entre os estudos micro e macro evolutivos. A filogeografia tem sido cada vez mais utilizada para estudar a evolução de regiões com altos índices de diversidade, como a região Neotrópical. Os Neotrópicos apresentam uma grande variedade de biomas, incluindo a Floresta Atlântica, a segunda maior floresta tropical da América do Sul, contendo mais de 60% de todas as espécies terrestres do planeta. Um número crescente de estudos filogeográficos com espécies da Floresta Atlântica nos ajudado a entender os processos evolutivos que gradualmente formaram essa grande biodiversidade. Realizamos análises filogeográficas, avaliando padrões de estrutura e diversidade genética, tempo de divergência das linhagens e a demografia histórica do complexo de espécies Pitcairnia flammea (Bromeliaceae), grupo adaptado a inselbergs neotropicais naturalmente fragmentados, baseados em conjuntos de dados de microssatélites nucleares e sequências plastidiais. Nossos resultados mostraram baixa a moderada diversidade genética nuclear dentro de populações de P. flammea, e alta estrutura genética populacional, com poucos haplótipos de DNA plastidial compartilhados entre populações, indicando fluxo gênico limitado e baixa conectividade entre afloramentos rochosos. Não encontramos nenhuma estrutura filogeográfica clara, além de duas linhagens evolutivas que di... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Phylogeography has emerged as a bridge between several evolutionary disciplines, such as population genetics, phylogeny and biogeography, establishing the link between micro and macroevolutionary studies. Phylogeography has been increasingly used to study the evolution of regions with high diversity indexes, such as the Neotropic region. The Neotropics presents a wide variety of biomes, including the Atlantic Rainforest, the second largest tropical rainforest in South America containing more than 60% of all terrestrial species on the planet. An increasing number of phylogeographic studies in Atlantic Rainforest species have helped us to understand the evolutionary process that gradually formed such great biodiversity. We performed phylogeographic analyses, assessing genetic structure patterns, timing of lineage divergence and historical demography of Pitcairnia flammea species complex (Bromeliaceae), which are adapted to naturally fragmented Neotropical inselbergs, based on nuclear microsatellites and plastid sequence data sets. Our results showed low to moderate nuclear genetic diversity within P. flammea populations, and high population genetic structure, with few plastid DNA haplotype shared among populations, indicating limited gene flow and low connectivity among rock outcrops. We found no clear phylogeographic structure, besides two evolutionary lineage which diverged approximately 2 Mya., suggesting an important role of early Pleistocene climatic changes in the diversi... (Complete abstract click electronic access below) / Mestre

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