Uidates mtDNA fülogeneesi radadel; essee väikeste kõrvalepõigetega sellest, mida see meile inimese migratsioonidest kõnelda võib

Väitekirja elektrooniline versioon ei sisalda publikatsiooneMeie genoomidesse on kirjutatud kogu informatsioon, mida rakuline masinavärk inimolendi kokkupanekuks vajab. Ja mitte ainult. Kasutades ad hoc raamistikku on võimalik kaasaegsete inimeste genoomide alusel mineviku inimese migratsioone rekonstrueerida. Pikka aega on sellealaste uuringute musternäidiseks olnud mitokondriaalne DNA (mtDNA) ja Y-kromosoom, eelkõige seetõttu, et need on haploidsed ja mitterekombineeruvad - nende fülogeneesi on autosoomidega võrreldes lihtsam rekonstrueerida. Fülogeneesis kajastub paljude evolutsioonitegurite, sealhulgas migratsioonide mõju, seega – teoreetiliselt on võimalik fülogeneesi uurides inimese rännetega seotud küsimustele vastuseid leida. Üks tee antud küsimustele vastamiseks on uurida meid huvitavate populatsioonide üldist varieeruvust ja paigutada see laiemasse perspektiivi. Näiteks selgub meie tööst, et Euraasiale ja Aafrikale iseloomulike liinide üldine osakaal on Etioopia ja Jeemeni mtDNA geenitiigis peaaegu identne, suurem lahutusaste toob aga esile nende märkimisväärseid erinevusi. Prantsusmaa puhul ilmneb, et kui üldisel tasemel ei erineta lähedastest naabermaadest, siis geograafilist fookust kintsendades kerkivad esile Püreneedest põhjas või lõunas elavate baskide vahelised erinevused. Samuti tuleb esile, Bretagne´i administratiivüksuste seas on Finistère`l teistest tugevamad seosed Suurbritannia ja Skandinaaviaga. Kaugel ida pool, Kesk-Aasias Hindukuši Afganistaani-osa paljusid erinevaid etnilisi populatsioone uurides saime tuge seisukohale, et Kesk-Aasia on olnud paljude migratsioonilainete risteel ja nende mõjud on kaasaegsetesse populatsioonidesse jätnud märgatava jälje. Teise võimaluse küsimustele vastuseid leida andis fookuse suunamine üksikutele spetsiifilistele haplogruppidele. Haplogruppide M1 ja U6 fülogeneesi uurimine lükkas ümber varasema hüpoteesi nende samaaegsest levikust. Me ei leidnud ka kindlaid tõendeid seoste kohta nende haplogruppide ja afroaasia keelte leviku vahel.Inscribed in our genomes, there is all the necessary information for the cellular machinery to build a human being. And then some. Using an ad hoc framework, it is possible to attempt to infer past human migrations by looking at the current variation present in these genomes. Mitochondrial DNA (mtDNA) and the Y chromosome have long been the poster child for doing it, chiefly thanks to their haploid and non-recombining nature, allowing to reconstruct their phylogeny in a more straightforward way than for the autosomes. These phylogenies have been shaped by evolutionary forces, amongst them migrations. Hence, by studying the former, it is theoretically possible to tackle questions germane to the latter. One way to address our questions is to study the general composition of a specific population or several, and to place it into a broader perspective. For instance, we showed that, whilst the overall proportion of Eurasian and African specific lineages is almost identical in Ethiopian and Yemeni mtDNA gene pool, a finer level of resolution revealed marked differences in them. In the case of France, it is globally not dissimilar from its close neighbours, yet narrowing down the geographical focus exposes dissimilarities between the Basques living north of the Pyrénées from those south of them. And amongst the administrative departments of Brittany, Finistère displays tighter connections with Britain and Scandinavia. Much further east, in Central Asia, exploring various ethnic populations of the Afghan Hindu Kush gave support to the notion that Central Asia has been a long-standing cross-road of multiple waves of migrations, each leaving perceptible traces in the extant populations. As for another way of answering questions, we shifted our focus to some specific haplogroups, with a new examination of M1 and U6 phylogenies that confuted the previously purported concomitance of their spread. We also did not find strong evidence of connections between their spread and that of the Afro-Asiatic languages.https://www.ester.ee/record=b5257709~S

Mutation Rate Switch inside Eurasian Mitochondrial Haplogroups: Impact of Selection and Consequences for Dating Settlement in Europe

R-lineage mitochondrial DNA represents over 90% of the European population and is significantly present all around the planet (North Africa, Asia, Oceania, and America). This lineage played a major role in migration “out of Africa” and colonization in Europe. In order to determine an accurate dating of the R lineage and its sublineages, we analyzed 1173 individuals and complete mtDNA sequences from Mitomap. This analysis revealed a new coalescence age for R at 54.500 years, as well as several limitations of standard dating methods, likely to lead to false interpretations. These findings highlight the association of a striking under-accumulation of synonymous mutations, an over-accumulation of non-synonymous mutations, and the phenotypic effect on haplogroup J. Consequently, haplogroup J is apparently not a Neolithic group but an older haplogroup (Paleolithic) that was subjected to an underestimated selective force. These findings also indicated an under-accumulation of synonymous and non-synonymous mutations localized on coding and non-coding (HVS1) sequences for haplogroup R0, which contains the major haplogroups H and V. These new dates are likely to impact the present colonization model for Europe and confirm the late glacial resettlement scenario

Origin and spread of human mitochondrial DNA haplogroup U7

Human mitochondrial DNA haplogroup U is among the initial maternal founders in Southwest Asia and Europe and one that best indicates matrilineal genetic continuity between late Pleistocene hunter-gatherer groups and present-day populations of Europe. While most haplogroup U subclades are older than 30 thousand years, the comparatively recent coalescence time of the extant variation of haplogroup U7 (~16–19 thousand years ago) suggests that its current distribution is the consequence of more recent dispersal events, despite its wide geographical range across Europe, the Near East and South Asia. Here we report 267 new U7 mitogenomes that – analysed alongside 100 published ones – enable us to discern at least two distinct temporal phases of dispersal, both of which most likely emanated from the Near East. The earlier one began prior to the Holocene (~11.5 thousand years ago) towards South Asia, while the later dispersal took place more recently towards Mediterranean Europe during the Neolithic (~8 thousand years ago). These findings imply that the carriers of haplogroup U7 spread to South Asia and Europe before the suggested Bronze Age expansion of Indo-European languages from the Pontic-Caspian Steppe region

Straightforward synthesis of poly(lauryl acrylate)-b-poly(stearyl acrylate) diblock copolymers by ATRP

International audienc

Ethiopian Mitochondrial DNA Heritage: Tracking Gene Flow Across and Around the Gate of Tears

Approximately 10 miles separate the Horn of Africa from the Arabian Peninsula at Bab-el-Mandeb (the Gate of Tears). Both historic and archaeological evidence indicate tight cultural connections, over millennia, between these two regions. High-resolution phylogenetic analysis of 270 Ethiopian and 115 Yemeni mitochondrial DNAs was performed in a worldwide context, to explore gene flow across the Red and Arabian Seas. Nine distinct subclades, including three newly defined ones, were found to characterize entirely the variation of Ethiopian and Yemeni L3 lineages. Both Ethiopians and Yemenis contain an almost-equal proportion of Eurasian-specific M and N and African-specific lineages and therefore cluster together in a multidimensional scaling plot between Near Eastern and sub-Saharan African populations. Phylogeographic identification of potential founder haplotypes revealed that approximately one-half of haplogroup L0–L5 lineages in Yemenis have close or matching counterparts in southeastern Africans, compared with a minor share in Ethiopians. Newly defined clade L6, the most frequent haplogroup in Yemenis, showed no close matches among 3,000 African samples. These results highlight the complexity of Ethiopian and Yemeni genetic heritage and are consistent with the introduction of maternal lineages into the South Arabian gene pool from different source populations of East Africa. A high proportion of Ethiopian lineages, significantly more abundant in the northeast of that country, trace their western Eurasian origin in haplogroup N through assorted gene flow at different times and involving different source populations

Divorcing the Late Upper Palaeolithic demographic histories of mtDNA haplogroups M1 and U6 in Africa

<p>Abstract</p> <p>Background</p> <p>A Southwest Asian origin and dispersal to North Africa in the Early Upper Palaeolithic era has been inferred in previous studies for mtDNA haplogroups M1 and U6. Both haplogroups have been proposed to show similar geographic patterns and shared demographic histories.</p> <p>Results</p> <p>We report here 24 M1 and 33 U6 new complete mtDNA sequences that allow us to refine the existing phylogeny of these haplogroups. The resulting phylogenetic information was used to genotype a further 131 M1 and 91 U6 samples to determine the geographic spread of their sub-clades. No southwest Asian specific clades for M1 or U6 were discovered. U6 and M1 frequencies in North Africa, the Middle East and Europe do not follow similar patterns, and their sub-clade divisions do not appear to be compatible with their shared history reaching back to the Early Upper Palaeolithic. The Bayesian Skyline Plots testify to non-overlapping phases of expansion, and the haplogroups’ phylogenies suggest that there are U6 sub-clades that expanded earlier than those in M1. Some M1 and U6 sub-clades could be linked with certain events. For example, U6a1 and M1b, with their coalescent ages of ~20,000–22,000 years ago and earliest inferred expansion in northwest Africa, could coincide with the flourishing of the Iberomaurusian industry, whilst U6b and M1b1 appeared at the time of the Capsian culture.</p> <p>Conclusions</p> <p>Our high-resolution phylogenetic dissection of both haplogroups and coalescent time assessments suggest that the extant main branching pattern of both haplogroups arose and diversified in the mid-later Upper Palaeolithic, with some sub-clades concomitantly with the expansion of the Iberomaurusian industry. Carriers of these maternal lineages have been later absorbed into and diversified further during the spread of Afro-Asiatic languages in North and East Africa.</p

Divorcing the Late Upper Palaeolithic demographic histories of mtDNA haplogroups M1 and U6 in Africa.

BACKGROUND: A Southwest Asian origin and dispersal to North Africa in the Early Upper Palaeolithic era has been inferred in previous studies for mtDNA haplogroups M1 and U6. Both haplogroups have been proposed to show similar geographic patterns and shared demographic histories. RESULTS: We report here 24 M1 and 33 U6 new complete mtDNA sequences that allow us to refine the existing phylogeny of these haplogroups. The resulting phylogenetic information was used to genotype a further 131 M1 and 91 U6 samples to determine the geographic spread of their sub-clades. No southwest Asian specific clades for M1 or U6 were discovered. U6 and M1 frequencies in North Africa, the Middle East and Europe do not follow similar patterns, and their sub-clade divisions do not appear to be compatible with their shared history reaching back to the Early Upper Palaeolithic. The Bayesian Skyline Plots testify to non-overlapping phases of expansion, and the haplogroups' phylogenies suggest that there are U6 sub-clades that expanded earlier than those in M1. Some M1 and U6 sub-clades could be linked with certain events. For example, U6a1 and M1b, with their coalescent ages of ~20,000-22,000 years ago and earliest inferred expansion in northwest Africa, could coincide with the flourishing of the Iberomaurusian industry, whilst U6b and M1b1 appeared at the time of the Capsian culture. CONCLUSIONS: Our high-resolution phylogenetic dissection of both haplogroups and coalescent time assessments suggest that the extant main branching pattern of both haplogroups arose and diversified in the mid-later Upper Palaeolithic, with some sub-clades concomitantly with the expansion of the Iberomaurusian industry. Carriers of these maternal lineages have been later absorbed into and diversified further during the spread of Afro-Asiatic languages in North and East Africa

Mutation Rate Switch inside Eurasian Mitochondrial Haplogroups: Impact of Selection and Consequences for Dating Settlement in Europe

R-lineage mitochondrial DNA represents over 90% of the European population and is significantly present all around the planet (North Africa, Asia, Oceania, and America). This lineage played a major role in migration “out of Africa” and colonization in Europe. In order to determine an accurate dating of the R lineage and its sublineages, we analyzed 1173 individuals and complete mtDNA sequences from Mitomap. This analysis revealed a new coalescence age for R at 54.500 years, as well as several limitations of standard dating methods, likely to lead to false interpretations. These findings highlight the association of a striking under-accumulation of synonymous mutations, an over-accumulation of non-synonymous mutations, and the phenotypic effect on haplogroup J. Consequently, haplogroup J is apparently not a Neolithic group but an older haplogroup (Paleolithic) that was subjected to an underestimated selective force. These findings also indicated an under-accumulation of synonymous and non-synonymous mutations localized on coding and non-coding (HVS1) sequences for haplogroup R0, which contains the major haplogroups H and V. These new dates are likely to impact the present colonization model for Europe and confirm the late glacial resettlement scenario

Comprehensive analysis of a large genomic sequence at the putative B-cell chronic lymphocytic leukaemia (B-CLL) tumour suppresser gene locus

In many haematological diseases, and more particularly in B-cell chronic lymphocytic leukaemia (B-CLL), the existence of a tumour suppressor gene located within the frequently deleted region 13q14.3, has been put forward. A wide candidate region spanning from marker D13S273 to D13S25 has been proposed and an extensive physical map has been constructed by several teams. In this study, we sequenced a minimal core deleted region that we have previously defined and annotated it with flanking available public sequences. Our analysis shows that this region is gene-poor. Furthermore, our work allowed us to identify new alternative transcripts, spanning core regions, of the previously defined candidate genes DLEU1 and DLEU2. Since their putative involvement in B-CLL was controversial, our present study provide support for reconsidering the DLEU1 and DLEU2 genes as B-CLL candidate genes, with a new definition of their organisation and context. © 2001 Elsevier Science B.V. All rights reserved