Characterization of ancient Eurasian influences within modern human genomes
Kuupäev
2021-07-02
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Ajakirja pealkiri
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Abstrakt
Tänapäeva inimgenoomid on iidsete komponentide segu. Tänu vana DNA (aDNA) uuringute arengule saame me nende komponentide päritolu kindlaks teha ja neid uurida. Kuid aDNA ei pruugi olla kättesaadav või võib paljudel juhtudel olla madala kvaliteediga, kuna DNA struktuur laguneb aja ja erinevate keskkonnamõjude tõttu. Õnneks saame neid iidseid kihte kindlaks teha ja eraldada ka tänapäeva inimgenoomidest, kasutades lokaalse põlvnemise tuletamise meetodeid. Selle lähenemisega saame uurida segunenud populatsioone, millel on tugevalt erinevad põlvnemiskomponendid, demograafilisest ja funktsionaalsest aspektist. Käesolev doktoritöö keskendub kahele sellisele rühmale: Lõuna-Aasia populatsioonidele, mis koosnevad Lääne-Euraasia ja Lõuna-Aasia komponentidest, ja Etioopia populatsioonidele, mis koosnevad Euraasia ja Aafrika komponentidest. Doktoritöö esimeses osas käsitletakse Lõuna-Aasia mineviku demograafilisi sündmusi, ulatuslikku genoomset varieeruvust ja segunemisjärgset looduslikku valikut, genereerides tänapäeva Lõuna-Aasia genoomide kahe peamise põlvnemiskomponendi jaoks surrogaadid. Teises osas hinnatakse üht lokaalse põlvnemise tuletamise põhist meetodit segunenud genoomide põlvnemiskomponentides valiku tuvastamise parandamise osas ja meetodit rakendatakse Lõuna-Aasia genoomide puhul. Kolmandas ja viimases osas rakendatakse esimeses osas kirjeldatule sarnast lähenemist Etioopia genoomide puhul, et määrata täpselt tänapäeva etiooplaste Euraasia põlvnemiskomponendi allikas.
Modern day human genomes are mixtures of ancient components. Thanks to advancements in ancient DNA (aDNA) research, we can detect the origins of these components and study them. However, aDNA might either not be available or be of low quality in many situations due to DNA structure being subject to degradation related to time and different environmental factors. Thankfully, we can identify and extract these ancient layers also from contemporary human genomes with local ancestry inference methods. With this approach, we can study admixed populations, which have highly divergent ancestral components, in terms of demography and functional analyses. This thesis particularly focuses on two such groups: South Asian populations, which are composed of West Eurasian and South Asian ancestries, and Ethiopian populations, which are composed of Eurasian and African ancestries. In the first part of my dissertation, past demographic events, diverse genomic variation and post-admixture natural selection in South Asia are investigated by generating surrogates for the two main ancestral components of contemporary South Asian genomes. In the second part, a local ancestry inference-based method is evaluated for improving selection detection in ancestral components of admixed genomes and it is applied on South Asian genomes. In the third and the last part, a similar approach to the first part is conducted for Ethiopian genomes to pinpoint the source of Eurasian ancestry in contemporary Ethiopians
Modern day human genomes are mixtures of ancient components. Thanks to advancements in ancient DNA (aDNA) research, we can detect the origins of these components and study them. However, aDNA might either not be available or be of low quality in many situations due to DNA structure being subject to degradation related to time and different environmental factors. Thankfully, we can identify and extract these ancient layers also from contemporary human genomes with local ancestry inference methods. With this approach, we can study admixed populations, which have highly divergent ancestral components, in terms of demography and functional analyses. This thesis particularly focuses on two such groups: South Asian populations, which are composed of West Eurasian and South Asian ancestries, and Ethiopian populations, which are composed of Eurasian and African ancestries. In the first part of my dissertation, past demographic events, diverse genomic variation and post-admixture natural selection in South Asia are investigated by generating surrogates for the two main ancestral components of contemporary South Asian genomes. In the second part, a local ancestry inference-based method is evaluated for improving selection detection in ancestral components of admixed genomes and it is applied on South Asian genomes. In the third and the last part, a similar approach to the first part is conducted for Ethiopian genomes to pinpoint the source of Eurasian ancestry in contemporary Ethiopians
Kirjeldus
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Märksõnad
Eurasia, ancient DNA, DNA, genetic origin, genomes