Ancient genetic landscape of archaeological human remains from Panama, South America and Oceania described through STR genotype frequencies and mitochondrial DNA sequences

The settlements of the Americas and Oceania are particularly fascinating topics. On the one side is the settlements of Australia and New Guinea (30,000 – 50,000 years ago) were the scenarios of one of the earliest migration events carried out by modern humans after left Africa, while Polynesia around 3,000 years ago was the stage of the last major colonization event. Regarding America, despite broad agreement that the Americas were initially populated via Bering, during the Upper Pleistocene 14,600 years ago, it is still a topic controversial, mysterious, shifting, and continuously conflictive as the Ice Age archaeology of the Americas, since, the dates and routes of the peopling of the Americas remain unresolved. Thus, ancient DNA studies on archaeological human remains from Oceania and America are useful to explore the genetic history of these human groups. Given that Near Oceania colonization was the endpoint of one of the earliest Out-of-Africa migrations about 50,000 years ago, and the islands of East Polynesia were the last region of the world to be colonized by humans approximately 1,000 years ago. Whilst, in America, one of the most contentious issues is whether the settlement occurred by means of a single migration or migration streams of migrations from Siberia. Because the gene flow is an important mechanism that contributes to genetic diversity among populations, the presence or absence of certain haplogroups changes the distribution of genetic diversity within populations. Thus, to understand the population dynamics of Oceanians and American peoples before European contact, it was necessary to describe the grade of nuclear and mitochondrial DNA genetic variation. One hundred twenty-five paleo-anthropological remains were analysed via genotyping of six short tandem repeats (STR) markers (nuclear DNA). Moreover, the genetic variation, inferences of demographic histories and clustering trends of these samples were evaluated through the hypervariable segment I (HVSI) of mitochondrial DNA (mtDNA). 35% of the archaeological remains analysed were genotyped successfully. Mitochondrial genetic diversity observed in Oceanian, South American and Panamanian samples reflected the genetic drift effects on these individuals through the founder effect, which happened during Upper Pleistocene when the modern humans reached these regions for the first time. The inferences of historical demographic patterns suggest that ancient individuals from Oceania went through population expansion about 37,972 years ago, which is consistent with the initial colonization of Melanesia. Whilst, ancient individuals from South America and Panama went through population expansions about 14,150 and 9,468 years ago, respectively, correspond to the initial settlement of America during the Upper Pleistocene. The clustering patterns showed that ancient individuals from Bismark Archipelago and Papua New Guinea, and the ancient individuals from New Zealand and Samoa exhibited greater affinity with each other. The cluster branch of America exhibited genetic affinities between ancient Panamanian and South American samples, probably resulted from a migratory event, along the Pacific North Coast, from North America to South America that took place between the Middle and the Upper Holocene.2021-12-2

東南アジアおよび南太平洋におけるGallus gallusの進化史 : その系統地理および個体群動態への遺伝的洞察

広島大学(Hiroshima University)博士(農学)Doctor of Philosophy in Agriculturedoctora

Papuan mitochondrial genomes and the settlement of Sahul

New Guineans represent one of the oldest locally continuous populations outside Africa, harboring among the greatest linguistic and genetic diversity on the planet. Archeological and genetic evidence suggest that their ancestors reached Sahul (present day New Guinea and Australia) by at least 55,000 years ago (kya). However, little is known about this early settlement phase or subsequent dispersal and population structuring over the subsequent period of time. Here we report 379 complete Papuan mitochondrial genomes from across Papua New Guinea, which allow us to reconstruct the phylogenetic and phylogeographic history of northern Sahul. Our results support the arrival of two groups of settlers in Sahul within the same broad time window (50–65 kya), each carrying a different set of maternal lineages and settling Northern and Southern Sahul separately. Strong geographic structure in northern Sahul remains visible today, indicating limited dispersal over time despite major climatic, cultural, and historical changes. However, following a period of isolation lasting nearly 20 ky after initial settlement, environmental changes postdating the Last Glacial Maximum stimulated diversification of mtDNA lineages and greater interactions within and beyond Northern Sahul, to Southern Sahul, Wallacea and beyond. Later, in the Holocene, populations from New Guinea, in contrast to those of Australia, participated in early interactions with incoming Asian populations from Island Southeast Asia and continuing into Oceania

Decreased Rate of Evolution in Y Chromosome STR Loci of Increased Size of the Repeat Unit

Polymorphic Y chromosome short tandem repeats (STRs) have been widely used in population genetic and evolutionary studies. Compared to di-, tri-, and tetranucleotide repeats, STRs with longer repeat units occur more rarely and are far less commonly used.In order to study the evolutionary dynamics of STRs according to repeat unit size, we analysed variation at 24 Y chromosome repeat loci: 1 tri-, 14 tetra-, 7 penta-, and 2 hexanucleotide loci. According to our results, penta- and hexanucleotide repeats have approximately two times lower repeat variance and diversity than tri- and tetranucleotide repeats, indicating that their mutation rate is about half of that of tri- and tetranucleotide repeats. Thus, STR markers with longer repeat units are more robust in distinguishing Y chromosome haplogroups and, in some cases, phylogenetic splits within established haplogroups.Our findings suggest that Y chromosome STRs of increased repeat unit size have a lower rate of evolution, which has significant relevance in population genetic and evolutionary studies

The light skin allele of SLC24A5 in South Asians and Europeans shares identity by descent

Skin pigmentation is one of the most variable phenotypic traits in humans. A non-synonymous substitution (rs1426654) in the third exon of SLC24A5 accounts for lighter skin in Europeans but not in East Asians. A previous genome-wide association study carried out in a heterogeneous sample of UK immigrants of South Asian descent suggested that this gene also contributes significantly to skin pigmentation variation among South Asians. In the present study, we have quantitatively assessed skin pigmentation for a largely homogeneous cohort of 1228 individuals from the Southern region of the Indian subcontinent. Our data confirm significant association of rs1426654 SNP with skin pigmentation, explaining about 27% of total phenotypic variation in the cohort studied. Our extensive survey of the polymorphism in 1573 individuals from 54 ethnic populations across the Indian subcontinent reveals wide presence of the derived-A allele, although the frequencies vary substantially among populations. We also show that the geospatial pattern of this allele is complex, but most importantly, reflects strong influence of language, geography and demographic history of the populations. Sequencing 11.74 kb of SLC24A5 in 95 individuals worldwide reveals that the rs1426654-A alleles in South Asian and West Eurasian populations are monophyletic and occur on the background of a common haplotype that is characterized by low genetic diversity. We date the coalescence of the light skin associated allele at 22–28 KYA. Both our sequence and genome-wide genotype data confirm that this gene has been a target for positive selection among Europeans. However, the latter also shows additional evidence of selection in populations of the Middle East, Central Asia, Pakistan and North India but not in South India

Vaade inimese Y kromosoomile – fülogenees, populatsiooni dünaamika ja asutajasündmused

Väitekirja elektrooniline versioon ei sisalda publikatsiooneRahvastikusündmused on jätnud oma jälje iga inimese genoomi. Täna suudame neid ’lugeda’ nii praegu elavate kui juba ammu surnud inimeste geneetilisest materjalist. Y-kromosoom on eriline genoomi osa, mis pärandub edasi vaid mööda isaliini, kõikide maailma isaliinide omavahlelist sugulust näitab nende ‘sugupuu’. Täna saame ka Y-kromosoomilt ohtralt DNA-lugemeid, mis võimaldavad võrratult täpsemalt hinnata inimese isaliinide mitmekesisust ning harude lahknemisaegu isaliinide puul. Doktoritöös uuriti mineviku rahvastikusündmusi peamiselt inimese Y-kromosoomi andmeid analüüsides. Töö tulemused näitasid, et inimese kõikide teadaolevate isaliinide viimane ühine eellane elas Aafrikas umbes 250 tuhat aastat tagasi, paljude liinide arvukuse kasv toimus aga viimase 15 tuhande aasta sees. Üllatuslikult leidsime ka, et 4–8 tuhat aastat tagasi kahanes järsult järglasi saavate meeste suhteline arv, samas kui naistel see arv ei muutunud. Kuna sigivate meeste arvukus vähenes samal ajal, kui muutusid inimeste eluviisid – mindi üle küttimiselt ja koriluselt põlluharimisele, võisid need kultuurilised muutused mõjutada meeste reproduktiivkäitumist. Lisaks näitasime, et Lõuna-Siberist pärit Baikali-äärse 24 000 aasta vanuse ülempaleoliitilise Malta kultuuri esindaja ema- ja isaliin ei ole tüüpilised tänased seal piirkonnas levinud Ida-Euraasia liinid, näidates geneetilise pärandi olulist muutumist läbi aja. Asutajasündmused, mil uus rahvakild tekib mingi algse grupi väikesest alamhulgast, jätavad uue grupi geneetilisse pärandisse iseloomuliku jälje. Neid analüüsisime Euroopa romi ja aškenaasi leviidi meeste seas. Lõuna-Aasia päritolu H1a1-M82 tüüpi isaliin on levinud ka Euroopa romide seas, viidates nende algkodule. Romide liinidele kõige sarnasemad on Loode- ja Põhja-India meeste seas levinud variandid, viidates võimalikule Romide päritolupiirkonnale. Tüüpiline aškenaasi leviitide isaliin R1a-Y2619 on kõige tõenäolisemalt pärit Lähis-Idast. Näitasime, et see kuulus aškenaasi leviitide asutajaliinide hulka, kuid selle levik oli seotud pigem aškenaasi juutide populatsiooni üldise laienemisega.Demographic processes have left their traces into every human genome. Today we can ‘read’ them from the genetic material of people living now and those passed away long ago. Mitochondrial DNA and Y chromosome (chrY) are parts of the genome that pass on through maternal and paternal lines. The relationships of all these lineages in the world are captured in a global ‘family tree’ of maternal or paternal lineages. Just recently it became possible to attain high numbers of sequencing reads also from chrY. This enables to assess the variation of human paternal lineages and date their splits on the tree with unmatched precision. This thesis investigates the past demographic events mainly by analysing the sequencing datasets of human chrY. We showed that the most common ancestor of all known paternal lineages lived in Africa about 250 thousand years ago (kya) and many of the now widespread lineages started to expand 15 kya. Then, 4–8 kya the relative number of males who had offspring (Nm) decreased drastically, while in females it did not change. Since the decrease of Nm coincided with the changes of lifestyle from hunting and gathering to farming, the decrease in the number of breeding males could have been caused by cultural forces that influence the reproductive behaviour of men. The maternal and paternal lineages of a southern Siberian 24,000 years-old Upper Palaeolithic individual from near Lake Baikal are not typical East Eurasian lineages found in the area today. This testifies for population changes affecting the genetic make-up of the people living in that region. Founder events during which a new population forms as a small subset of an initial group, leave distinct traces into the genomic legacy of the newly formed group. We analysed these traces in the paternal gene pool of European Roma and Ashkenazi Levites. H1a1a-M82 is a paternal lineage carried by 12% of South Asian men. The same lineage is spread among European Roma whose variants have closest relations to men from north western and northern India, pointing to their potential place of origin. The main lineage among Ashkenazi Levites, R1a-Y2619, originates in the Near East and it was probably carried by the first founders of the Ashkenazi Levites. The increase in numbers of carriers of this lineage was not an event specific to Levites, but part of the general Ashkenazi Jewish expansion