THE ANALYSIS OF ANCIENT DNA: FROM MITOCHONDRIA TO PATHOGENS

Ancient DNA (aDNA) is arguably one of the most difficult science fields to work in due to the constant battle against contamination and degradation; however, it is also one of the most rewarding. aDNA researchers have consistently garnered interest the world over with their findings and sparking the curiosity of many who wish to know more about who we are as Homo sapiens. Mitochondrial DNA (mtDNA) and pathogen DNA were used in this dissertation to understand more about where populations came from, how they moved, and what their environment was like through the identification of their maternally inherited mtDNA and pathogens. This is a synthesis of my work and collaboration with other researchers both in lab and at the computer to add more data to the story of humankind

concepts - methods - visualization

While Darwin’s grand view of evolution has undergone many changes and shown up in many facets, there remains one outstanding common feature in its 150-year history: since the very beginning, branching trees have been the dominant scheme for representing evolutionary processes. Only recently, network models have gained ground reflecting contact-induced mixing or hybridization in evolutionary scenarios. In biology, research on prokaryote evolution indicates that lateral gene transfer is a major feature in the evolution of bacteria. In the field of linguistics, the mutual lexical and morphosyntactic borrowing between languages seems to be much more central for language evolution than the family tree model is likely to concede. In the humanities, networks are employed as an alternative to established phylogenetic models, to express the hybridization of cultural phenomena, concepts or the social structure of science. However, an interdisciplinary display of network analyses for evolutionary processes remains lacking. Therefore, this volume includes approaches studying the evolutionary dynamics of science, languages and genomes, all of which were based on methods incorporating network approaches

Induse jõe oru inimeste, parside, India juutide ja Tharu hõimu geneetilise põlvnemise piiritlemine

Väitekirja elektrooniline versioon ei sisalda publikatsiooneKäesolev on viies Tartu Ülikoolis valminud väitekiri Lõuna-Aasia rahvaste geneetilisest ajaloost. Asustatud kaasaegse inimese poolt märksa enne viimase jääaja maksimumi, elab tänapäeval selles regioonis üle 1.8 miljardi inimese – pea veerand inimkonnast. Seega ei ole võimalik süvitsi mõista kaasaegse inimese geneetise varieeruvuse kujunemist, sh eriti väljapool Sahara-alust Aafrikat, omamata detailsemat teadmist Lõuna-Aasia rahvaste geneetikast Väitekiri põhineb neljal ilmunud artiklil. Neist esimeses uurisime Kirde-Indiat asustavaid rahvaid seoses võimaliku pärinevusega Induse oru kultuurist ja järgnenud vedade ajastust. Teine ja kolmas artikkel on pühendatud migratsioonidele, mis tõid Indiasse religioosses mõttes uusi rahvagruppe: parsid Iraanist alates 7. sajandi lõpupoolelt ja juudid, kelle saabumine Indiasse on toimunud mitme lainena. Neljandas artiklis on vaatluse all Nepaalis, kuid ka India põhjapoolsetes osariikides elutsev rahvarohke tharu hõim. Esimes artikli huvitavamaks leiuks on usutavasti juba vedade ajastust tuntud Rori populatsiooni genoomis väljenduv suurem geneetiline afiinsus põhjapoolse stepivööndi rahvastega, samuti ka lääne-eurooplastega, mis räägib põhja-lõunasuunalistest migratsiooni(de)st eelajaloolisel ajal. Parside saabumist Lõuna-Aasiasse seostatakse Iraani islamiseerumisega 7. sajandil. Võrreldes parside genoome nende ajaloolises kontekstis leidsime ulatusliku segunemise Lõuna-Aasia rahvastega, sealjuures asümeetriliselt isa ja emaliinides. Sama saab väita ka Indias judaistliku traditsiooni elemente säilitanud erinevate kogukondade kohta, kelle genoomis on siiski selgelt säilunud Lähis- ja Kesk-Ida pärandit. Puudutavalt aga geneetiliselt ulatuslikult varieeruvat tharu hõimu, kelle hulgas on selgesti eristatav ka Ida-Aasia komponent, segunenuna Lõuna-Aasia pärandiga, paistab õigustatud olevat neid vaadelda esmajoones mitte sedavõrd deemilise, kuivõrd just kultuurilise konstruktsioonina.Presented hereby is the 5th in a series of PhD theses prepared in Tartu University, addressing genetics of population history of the South Asian peoples. Inhabited considerably before the Last Glacial Maximum, the region harbors by now about 1.8 billion humans – almost a quarter of the global population. Therefore, understanding of present-day variation of the latter, in particular outside sub-Saharan Africa, is not possible without deeper knowledge about genetics of South Asian populations. This thesis is based on four published papers. The first one is focused on selected populations inhabiting northeastern Indus Valley, bearing, in particular, in mind ancient Indus Valley civilization and following it Vedic period. The second and the third paper address historically somewhat better known migrations, bringing to India religiously distinct Parsi and Jewish peoples. The fourth paper analyses the genetic variation of a populous Tharu tribe, living predominantly in Nepal, but also in northern provinces of India. Perhaps the most interesting finding of the first paper is that the presumably identified already in Vedic texts, Ror population exhibits significant genetic affinity with northern Steppe and West European peoples, testifying about prehistoric north to south migration(s). The arrival of Parsis to South Asia in 7th century was a consequence of the Islamization of Iran. Comparing Parsi genomes in their historic contexts, we observed their extensive admixture with South Asians, in particular, asymmetrically in paternal and maternal lineages. Nearly the same can be said about different Indian communities that preserved Judaist traditions: their genomes show affinities to peoples living in the Near and Middle East. As far as the genetically highly diverse Tharu tribe is concerned, a clearly distinct East Asian contribution can be seen, admixed with South Asian genetic heritage. It seems justified to identify the Tharu as cultural, rather than demic phenomenon.https://www.ester.ee/record=b542949

Advances in the study of ancient biomolecules in archaeological dental calculus

Studies of ancient microbiomes can shed light on several aspects of human history and microbial evolution, as well as aid in understanding modern day diseases. During recent years, studies of archaeological dental calculus have gained much interest, as this calcified microbial biofilm preserves biomolecules over long periods of time, and can hold information about health, disease, diet, the human host, and occasionally even the living environment and occupational activities of an individual. However, continued advances in the research of dental calculus are essential, in order to make sure that this finite archaeological material is utilized in the best way possible. This thesis presents several such developments, beginning with a thorough review of formation and occurrence of archaeological dental calculus, as well as its past and current study, in order to set a basis for understanding the research into this topic. Thereafter, state-of-the-art archaeogenetic and palaeoproteomic methods are employed to advance the study of archaeological dental calculus at different stages in the research process, from project design and laboratory processing, to analysis and result interpretation. Taken together, the four manuscripts presented in the thesis push forward the development of the field of biomolecular research of archaeological dental calculus. They provide researchers with valuable information for study design and result interpretation, as well as introduce new types of analyses into the field

Reticulate Evolution: Symbiogenesis, Lateral Gene Transfer, Hybridization and Infectious heredity

info:eu-repo/semantics/publishedVersio

Washington University Senior Undergraduate Research Digest (WUURD), Spring 2018

From the Washington University Office of Undergraduate Research Digest (WUURD), Vol. 13, 05-01-2018. Published by the Office of Undergraduate Research. Joy Zalis Kiefer, Director of Undergraduate Research and Associate Dean in the College of Arts & Scien

Using MapReduce Streaming for Distributed Life Simulation on the Cloud

Distributed software simulations are indispensable in the study of large-scale life models but often require the use of technically complex lower-level distributed computing frameworks, such as MPI. We propose to overcome the complexity challenge by applying the emerging MapReduce (MR) model to distributed life simulations and by running such simulations on the cloud. Technically, we design optimized MR streaming algorithms for discrete and continuous versions of Conway’s life according to a general MR streaming pattern. We chose life because it is simple enough as a testbed for MR’s applicability to a-life simulations and general enough to make our results applicable to various lattice-based a-life models. We implement and empirically evaluate our algorithms’ performance on Amazon’s Elastic MR cloud. Our experiments demonstrate that a single MR optimization technique called strip partitioning can reduce the execution time of continuous life simulations by 64%. To the best of our knowledge, we are the first to propose and evaluate MR streaming algorithms for lattice-based simulations. Our algorithms can serve as prototypes in the development of novel MR simulation algorithms for large-scale lattice-based a-life models.https://digitalcommons.chapman.edu/scs_books/1014/thumbnail.jp

Macroevolution: Explanation, Interpretation and Evidence

info:eu-repo/semantics/publishedVersio