ORCID Profile
0000-0002-6297-7808
Current Organisations
KU Leuven
,
Centro Euro-Mediterraneo sui Cambiamenti Climatici
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Publisher: Cold Spring Harbor Laboratory
Date: 13-03-2015
Abstract: It is commonly thought that human genetic ersity in non-African populations was shaped primarily by an out-of-Africa dispersal 50–100 thousand yr ago (kya). Here, we present a study of 456 geographically erse high-coverage Y chromosome sequences, including 299 newly reported s les. Applying ancient DNA calibration, we date the Y-chromosomal most recent common ancestor (MRCA) in Africa at 254 (95% CI 192–307) kya and detect a cluster of major non-African founder haplogroups in a narrow time interval at 47–52 kya, consistent with a rapid initial colonization model of Eurasia and Oceania after the out-of-Africa bottleneck. In contrast to demographic reconstructions based on mtDNA, we infer a second strong bottleneck in Y-chromosome lineages dating to the last 10 ky. We hypothesize that this bottleneck is caused by cultural changes affecting variance of reproductive success among males.
Publisher: Springer Science and Business Media LLC
Date: 07-04-2017
DOI: 10.1038/SREP46044
Abstract: 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.
Publisher: Oxford University Press (OUP)
Date: 11-08-2011
Abstract: Milk consumption and lactose digestion after weaning are exclusively human traits made possible by the continued production of the enzyme lactase in adulthood. Multiple independent mutations in a 100-bp region--part of an enhancer--approximately 14-kb upstream of the LCT gene are associated with this trait in Europeans and pastoralists from Saudi Arabia and Africa. However, a single mutation of purported western Eurasian origin accounts for much of observed lactase persistence outside Africa. Given the high levels of present-day milk consumption in India, together with archaeological and genetic evidence for the independent domestication of cattle in the Indus valley roughly 7,000 years ago, we sought to determine whether lactase persistence has evolved independently in the subcontinent. Here, we present the results of the first comprehensive survey of the LCT enhancer region in south Asia. Having genotyped 2,284 DNA s les from across the Indian subcontinent, we find that the previously described west Eurasian -13910 C>T mutation accounts for nearly all the genetic variation we observed in the 400- to 700-bp LCT regulatory region that we sequenced. Geography is a significant predictor of -13910*T allele frequency, and consistent with other genomic loci, its distribution in India follows a general northwest to southeast declining pattern, although frequencies among certain neighboring populations vary substantially. We confirm that the mutation is identical by descent to the European allele and is associated with the same>1 Mb extended haplotype in both populations.
Publisher: American Association for the Advancement of Science (AAAS)
Date: 21-08-2015
Abstract: Several theories have been put forth as to the origin and timing of when Native American ancestors entered the Americas. To clarify this controversy, Raghavan et al. examined the genomic variation among ancient and modern in iduals from Asia and the Americas. There is no evidence for multiple waves of entry or recurrent gene flow with Asians in northern populations. The earliest migrations occurred no earlier than 23,000 years ago from Siberian ancestors. Amerindians and Athabascans originated from a single population, splitting approximately 13,000 years ago. Science , this issue 10.1126/science.aab3884
Publisher: Wiley
Date: 07-2013
DOI: 10.1111/AHG.12028
Abstract: South Asian populations harbor a high degree of genetic ersity, due in part to demographic history. Two studies on genome-wide variation in Indian populations have shown that most Indian populations show varying degrees of admixture between ancestral north Indian and ancestral south Indian components. As a result of this structure, genetic variation in India appears to follow a geographic cline. Similarly, Indian populations seem to show detectable differences in diabetes and obesity prevalence between different geographic regions of the country. We tested the hypothesis that genetic variation at diabetes- and obesity-associated loci may be potentially related to different genetic ancestries. We genotyped 2977 in iduals from 61 populations across India for 18 SNPs in genes implicated in T2D and obesity. We examined patterns of variation in allele frequency across different geographical gradients and considered state of origin and language affiliation. Our results show that most of the 18 SNPs show no significant correlation with latitude, the geographic cline reported in previous studies, or by language family. Exceptions include KCNQ1 with latitude and THADA and JAK1 with language, which suggests that genetic variation at previously ascertained diabetes-associated loci may only partly mirror geographic patterns of genome-wide ersity in Indian populations.
Publisher: Springer Science and Business Media LLC
Date: 22-09-2013
Abstract: Many efforts have been made to detect signatures of positive selection in the human genome, especially those associated with expansion from Africa and subsequent colonization of all other continents. However, most approaches have not directly probed the relationship between the environment and patterns of variation among humans. We have designed a method to identify regions of the genome under selection based on Mantel tests conducted within a general linear model framework, which we call MAntel-GLM to Infer Clinal Selection (MAGICS). MAGICS explicitly incorporates population-specific and genome-wide patterns of background variation as well as information from environmental values to provide an improved picture of selection and its underlying causes in human populations. Our results significantly overlap with those obtained by other published methodologies, but MAGICS has several advantages. These include improvements that: limit false positives by reducing the number of independent tests conducted and by correcting for geographic distance, which we found to be a major contributor to selection signals yield absolute rather than relative estimates of significance identify specific geographic regions linked most strongly to particular signals of selection and detect recent balancing as well as directional selection. We find evidence of selection associated with climate (P 10 -5 ) in 354 genes, and among these observe a highly significant enrichment for directional positive selection. Two of our strongest 'hits’, however, ADRA2A and ADRA2C , implicated in vasoconstriction in response to cold and pain stimuli, show evidence of balancing selection. Our results clearly demonstrate evidence of climate-related signals of directional and balancing selection.
Publisher: Springer Science and Business Media LLC
Date: 07-10-2010
Publisher: American Association for the Advancement of Science (AAAS)
Date: 11-09-2015
Abstract: Duplications and deletions can lead to variation in copy number for genes and genomic loci among humans. Such variants can reveal evolutionary patterns and have implications for human health. Sudmant et al. examined copy-number variation across 236 in idual genomes from 125 human populations. Deletions were under more selection, whereas duplications showed more population-specific structure. Interestingly, Oceanic populations retain large duplications postulated to have originated in an ancient Denisovan lineage. Science , this issue 10.1126/science.aab3761
Publisher: Oxford University Press (OUP)
Date: 05-07-2016
Publisher: Proceedings of the National Academy of Sciences
Date: 28-07-2009
Abstract: Genetic studies of South Asia's population history have led to postulations of a significant and early population expansion in the subcontinent, dating to sometime in the Late Pleistocene. We evaluate this argument, based on new mtDNA analyses, and find evidence for significant demographic transition in the subcontinent, dating to 35–28 ka. We then examine the paleoenvironmental and, particularly, archaeological records for this time period and note that this putative demographic event coincides with a period of ecological and technological change in South Asia. We document the development of a new diminutive stone blade (microlithic) technology beginning at 35–30 ka, the first time that the precocity of this transition has been recognized across the subcontinent. We argue that the transition to microlithic technology may relate to changes in subsistence practices, as increasingly large and probably fragmented populations exploited resources in contracting favorable ecological zones just before the onset of full glacial conditions.
Publisher: Springer Science and Business Media LLC
Date: 21-09-2016
DOI: 10.1038/NATURE18964
Publisher: Springer Science and Business Media LLC
Date: 17-06-2021
Publisher: Elsevier BV
Date: 2004
DOI: 10.1086/380911
Abstract: We estimate an effective mutation rate at an average Y chromosome short-tandem repeat locus as 6.9x10-4 per 25 years, with a standard deviation across loci of 5.7x10-4, using data on microsatellite variation within Y chromosome haplogroups defined by unique-event polymorphisms in populations with documented short-term histories, as well as comparative data on worldwide populations at both the Y chromosome and various autosomal loci. This value is used to estimate the times of the African Bantu expansion, the ergence of Polynesian populations (the Maoris, Cook Islanders, and Samoans), and the origin of Gypsy populations from Bulgaria.
Publisher: Springer Science and Business Media LLC
Date: 09-2014
DOI: 10.1038/NATURE13673
Publisher: Springer Science and Business Media LLC
Date: 21-09-2016
DOI: 10.1038/NATURE19792
Publisher: Elsevier BV
Date: 07-2012
Publisher: Elsevier BV
Date: 12-2009
DOI: 10.1016/J.FSIGEN.2009.04.007
Abstract: Human identification systems such as criminal databases, forensic DNA testing and genetic genealogy require reliable and cost-effective genotyping of autosomal, mitochondrial and Y chromosome markers from different biological materials, including venous blood and saliva. Although many such assays are available, few systems are capable of simultaneously detecting all three targets in a single reaction. Employing the APEX-2 principle, we have characterized a novel 124-plex assay, using specific primer extension, universal primer lification and single base extension on an oligonucleotide array. The assay has been designed for simultaneous genotyping of SNPs from the single copy loci (46 autosomal and 29 Y chromosomal markers) side by side with SNPs from the mitochondrial genome (49 markers) that appears in up to thousands of copies per cell in certain tissue types. All the autosomal SNPs (from the SNPforID Consortium) included in the multiplex assay are unlinked and are distributed widely across autosomes, enabling genetic fingerprints to be distinguished. Mitochondrial DNA and Y chromosome polymorphisms that define haplogroups common in European populations are included to allow for maternity and paternity testing and for the analysis of genetic genealogies. After assay optimization we estimated the accuracy (99.83%) and call rate (99.66%) of the protocol on 17 mother-father-child/children families and five internal control DNAs. In addition, 79 unrelated Estonian and Swedish DNA s les were genotyped and the accuracy of mtDNA and Y chromosome haplogroup inference by the multiplex method was assessed using conventional genotyping methods and direct sequencing.
Publisher: Public Library of Science (PLoS)
Date: 05-07-2005
Publisher: Public Library of Science (PLoS)
Date: 02-09-2015
Publisher: Elsevier BV
Date: 06-2015
Publisher: Public Library of Science (PLoS)
Date: 07-11-2013
Publisher: Springer Science and Business Media LLC
Date: 03-10-2016
DOI: 10.1038/NATURE19844
Publisher: Elsevier BV
Date: 07-2017
DOI: 10.1016/J.CUB.2017.06.022
Abstract: The transition from hunting and gathering to farming in Europe was brought upon by arrival of new people carrying novel material culture and genetic ancestry. The exact nature and scale of the transition-both material and genetic-varied in different parts of Europe [1-7]. Farming-based economies appear relatively late in Northeast Europe, and the extent to which they involve change in genetic ancestry is not fully understood due to the lack of relevant ancient DNA data. Here we present the results from new low-coverage whole-genome shotgun sequence data from five hunter-gatherers and five first farmers of Estonia whose remains date to 4,500 to 6,300 years before present. We find evidence of significant differences between the two groups in the composition of autosomal as well as mtDNA, X chromosome, and Y chromosome ancestries. We find that Estonian hunter-gatherers of Comb Ceramic culture are closest to Eastern hunter-gatherers, which is in contrast to earlier hunter-gatherers from the Baltics, who are close to Western hunter-gatherers [8, 9]. The Estonian first farmers of Corded Ware culture show high similarity in their autosomes with European hunter-gatherers, Steppe Eneolithic and Bronze Age populations, and European Late Neolithic/Bronze Age populations, while their X chromosomes are in addition equally closely related to European and Anatolian and Levantine early farmers. These findings suggest that the shift to intensive cultivation and animal husbandry in Estonia was triggered by the arrival of new people with predominantly Steppe ancestry but whose ancestors had undergone sex-specific admixture with early farmers with Anatolian ancestry.
Publisher: Springer Science and Business Media LLC
Date: 16-05-2012
DOI: 10.1038/EJHG.2012.86
Publisher: Oxford University Press (OUP)
Date: 15-09-2009
Abstract: Relatively little is known about the genetic ersity of the Philippine population, and this is an important gap in our understanding of Southeast Asian and Oceanic prehistory. Here we describe mitochondrial DNA (mtDNA) variation in 423 Philippine s les and analyze them in the context of the genetic ersity of other Southeast Asian populations. The majority of Philippine mtDNA types are shared with Taiwanese aboriginal groups and belong to haplogroups of postglacial and pre-Neolithic origin that have previously been identified in East Asian and Island Southeast Asian populations. Analysis of hypervariable segment I sequence variation within in idual mtDNA haplogroups indicates a general decrease in the ersity of the most frequent types (B4a1a, E1a1a, and M7c3c) from the Taiwanese aborigines to the Philippines and Sulawesi, although calculated standard error measures overlap for these populations. This finding, together with the geographical distribution of ancestral and derived haplotypes of the B4a1a subclade including the Polynesian Motif, is consistent with southward dispersal of these lineages "Out of Taiwan" via the Philippines to Near Oceania and Polynesia. In addition to the mtDNA components shared with Taiwanese aborigines, complete sequence analyses revealed a minority of lineages in the Philippines that share their origins--possibly dating back to the Paleolithic--with haplogroups from Indonesia and New Guinea. Other rare lineages in the Philippines have no closely related types yet identified elsewhere.
No related grants have been discovered for Toomas Kivisild.