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https://www.readbyqxmd.com/read/29501328/population-turnover-in-remote-oceania-shortly-after-initial-settlement
#1
Mark Lipson, Pontus Skoglund, Matthew Spriggs, Frederique Valentin, Stuart Bedford, Richard Shing, Hallie Buckley, Iarawai Phillip, Graeme K Ward, Swapan Mallick, Nadin Rohland, Nasreen Broomandkhoshbacht, Olivia Cheronet, Matthew Ferry, Thomas K Harper, Megan Michel, Jonas Oppenheimer, Kendra Sirak, Kristin Stewardson, Kathryn Auckland, Adrian V S Hill, Kathryn Maitland, Stephen J Oppenheimer, Tom Parks, Kathryn Robson, Thomas N Williams, Douglas J Kennett, Alexander J Mentzer, Ron Pinhasi, David Reich
Ancient DNA from Vanuatu and Tonga dating to about 2,900-2,600 years ago (before present, BP) has revealed that the "First Remote Oceanians" associated with the Lapita archaeological culture were directly descended from the population that, beginning around 5000 BP, spread Austronesian languages from Taiwan to the Philippines, western Melanesia, and eventually Remote Oceania. Thus, ancestors of the First Remote Oceanians must have passed by the Papuan-ancestry populations they encountered in New Guinea, the Bismarck Archipelago, and the Solomon Islands with minimal admixture [1]...
February 26, 2018: Current Biology: CB
https://www.readbyqxmd.com/read/29466330/the-genomic-history-of-southeastern-europe
#2
Iain Mathieson, Songül Alpaslan-Roodenberg, Cosimo Posth, Anna Szécsényi-Nagy, Nadin Rohland, Swapan Mallick, Iñigo Olalde, Nasreen Broomandkhoshbacht, Francesca Candilio, Olivia Cheronet, Daniel Fernandes, Matthew Ferry, Beatriz Gamarra, Gloria González Fortes, Wolfgang Haak, Eadaoin Harney, Eppie Jones, Denise Keating, Ben Krause-Kyora, Isil Kucukkalipci, Megan Michel, Alissa Mittnik, Kathrin Nägele, Mario Novak, Jonas Oppenheimer, Nick Patterson, Saskia Pfrengle, Kendra Sirak, Kristin Stewardson, Stefania Vai, Stefan Alexandrov, Kurt W Alt, Radian Andreescu, Dragana Antonović, Abigail Ash, Nadezhda Atanassova, Krum Bacvarov, Mende Balázs Gusztáv, Hervé Bocherens, Michael Bolus, Adina Boroneanţ, Yavor Boyadzhiev, Alicja Budnik, Josip Burmaz, Stefan Chohadzhiev, Nicholas J Conard, Richard Cottiaux, Maja Čuka, Christophe Cupillard, Dorothée G Drucker, Nedko Elenski, Michael Francken, Borislava Galabova, Georgi Ganetsovski, Bernard Gély, Tamás Hajdu, Veneta Handzhyiska, Katerina Harvati, Thomas Higham, Stanislav Iliev, Ivor Janković, Ivor Karavanić, Douglas J Kennett, Darko Komšo, Alexandra Kozak, Damian Labuda, Martina Lari, Catalin Lazar, Maleen Leppek, Krassimir Leshtakov, Domenico Lo Vetro, Dženi Los, Ivaylo Lozanov, Maria Malina, Fabio Martini, Kath McSweeney, Harald Meller, Marko Menđušić, Pavel Mirea, Vyacheslav Moiseyev, Vanya Petrova, T Douglas Price, Angela Simalcsik, Luca Sineo, Mario Šlaus, Vladimir Slavchev, Petar Stanev, Andrej Starović, Tamás Szeniczey, Sahra Talamo, Maria Teschler-Nicola, Corinne Thevenet, Ivan Valchev, Frédérique Valentin, Sergey Vasilyev, Fanica Veljanovska, Svetlana Venelinova, Elizaveta Veselovskaya, Bence Viola, Cristian Virag, Joško Zaninović, Steve Zäuner, Philipp W Stockhammer, Giulio Catalano, Raiko Krauß, David Caramelli, Gunita Zariņa, Bisserka Gaydarska, Malcolm Lillie, Alexey G Nikitin, Inna Potekhina, Anastasia Papathanasiou, Dušan Borić, Clive Bonsall, Johannes Krause, Ron Pinhasi, David Reich
Farming was first introduced to Europe in the mid-seventh millennium bc, and was associated with migrants from Anatolia who settled in the southeast before spreading throughout Europe. Here, to understand the dynamics of this process, we analysed genome-wide ancient DNA data from 225 individuals who lived in southeastern Europe and surrounding regions between 12000 and 500 bc. We document a west-east cline of ancestry in indigenous hunter-gatherers and, in eastern Europe, the early stages in the formation of Bronze Age steppe ancestry...
February 21, 2018: Nature
https://www.readbyqxmd.com/read/29356938/reconstructing-the-demographic-history-of-the-himalayan-and-adjoining-populations
#3
Rakesh Tamang, Gyaneshwer Chaubey, Amrita Nandan, Periyasamy Govindaraj, Vipin Kumar Singh, Niraj Rai, Chandana Basu Mallick, Vishwas Sharma, Varun Kumar Sharma, Anish M Shah, Albert Lalremruata, Alla G Reddy, Deepa Selvi Rani, Pilot Doviah, Neetu Negi, Yarin Hadid, Veena Pande, Satti Vishnupriya, George van Driem, Doron M Behar, Tikaram Sharma, Lalji Singh, Richard Villems, Kumarasamy Thangaraj
The rugged topography of the Himalayan region has hindered large-scale human migrations, population admixture and assimilation. Such complexity in geographical structure might have facilitated the existence of several small isolated communities in this region. We have genotyped about 850,000 autosomal markers among 35 individuals belonging to the four major populations inhabiting the Himalaya and adjoining regions. In addition, we have genotyped 794 individuals belonging to 16 ethnic groups from the same region, for uniparental (mitochondrial and Y chromosomal DNA) markers...
February 2018: Human Genetics
https://www.readbyqxmd.com/read/29222464/the-irish-dna-atlas-revealing-fine-scale-population-structure-and-history-within-ireland
#4
Edmund Gilbert, Seamus O'Reilly, Michael Merrigan, Darren McGettigan, Anne M Molloy, Lawrence C Brody, Walter Bodmer, Katarzyna Hutnik, Sean Ennis, Daniel J Lawson, James F Wilson, Gianpiero L Cavalleri
The extent of population structure within Ireland is largely unknown, as is the impact of historical migrations. Here we illustrate fine-scale genetic structure across Ireland that follows geographic boundaries and present evidence of admixture events into Ireland. Utilising the 'Irish DNA Atlas', a cohort (n = 194) of Irish individuals with four generations of ancestry linked to specific regions in Ireland, in combination with 2,039 individuals from the Peoples of the British Isles dataset, we show that the Irish population can be divided in 10 distinct geographically stratified genetic clusters; seven of 'Gaelic' Irish ancestry, and three of shared Irish-British ancestry...
December 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29040546/variation-and-functional-impact-of-neanderthal-ancestry-in-western-asia
#5
Recep Ozgur Taskent, Nursen Duha Alioglu, Evrim Fer, Handan Melike Donertas, Mehmet Somel, Omer Gokcumen
Neanderthals contributed genetic material to modern humans via multiple admixture events. Initial admixture events presumably occurred in Western Asia shortly after humans migrated out of Africa. Despite being a focal point of admixture, earlier studies indicate lower Neanderthal introgression rates in some Western Asian populations as compared with other Eurasian populations. To better understand the genome-wide and phenotypic impact of Neanderthal introgression in the region, we sequenced whole genomes of nine present-day Europeans, Africans, and the Western Asian Druze at high depth, and analyzed available whole genome data from various other populations, including 16 genomes from present-day Turkey...
December 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28844488/the-genetic-legacy-of-zoroastrianism-in-iran-and-india-insights-into-population-structure-gene-flow-and-selection
#6
Saioa López, Mark G Thomas, Lucy van Dorp, Naser Ansari-Pour, Sarah Stewart, Abigail L Jones, Erik Jelinek, Lounès Chikhi, Tudor Parfitt, Neil Bradman, Michael E Weale, Garrett Hellenthal
Zoroastrianism is one of the oldest extant religions in the world, originating in Persia (present-day Iran) during the second millennium BCE. Historical records indicate that migrants from Persia brought Zoroastrianism to India, but there is debate over the timing of these migrations. Here we present genome-wide autosomal, Y chromosome, and mitochondrial DNA data from Iranian and Indian Zoroastrians and neighboring modern-day Indian and Iranian populations and conduct a comprehensive genome-wide genetic analysis in these groups...
September 7, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28734067/range-instability-leads-to-cytonuclear-discordance-in-a-morphologically-cryptic-ground-squirrel-species-complex
#7
Mark A Phuong, Ke Bi, Craig Moritz
The processes responsible for cytonuclear discordance frequently remain unclear. Here, we employed an exon capture data set and demographic methods to test hypotheses generated by species distribution models to examine how contrasting histories of range stability vs. fluctuation have caused cytonuclear concordance and discordance in ground squirrel lineages from the Otospermophilus beecheyi species complex. Previous studies in O. beecheyi revealed three morphologically cryptic and highly divergent mitochondrial DNA lineages (named the Northern, Central and Southern lineages based on geography) with only the Northern lineage exhibiting concordant divergence for nuclear genes...
September 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28714974/genetic-analysis-in-uk-biobank-links-insulin-resistance-and-transendothelial-migration-pathways-to-coronary-artery-disease
#8
Derek Klarin, Qiuyu Martin Zhu, Connor A Emdin, Mark Chaffin, Steven Horner, Brian J McMillan, Alison Leed, Michael E Weale, Chris C A Spencer, François Aguet, Ayellet V Segrè, Kristin G Ardlie, Amit V Khera, Virendar K Kaushik, Pradeep Natarajan, Sekar Kathiresan
UK Biobank is among the world's largest repositories for phenotypic and genotypic information in individuals of European ancestry. We performed a genome-wide association study in UK Biobank testing ∼9 million DNA sequence variants for association with coronary artery disease (4,831 cases and 115,455 controls) and carried out meta-analysis with previously published results. We identified 15 new loci, bringing the total number of loci associated with coronary artery disease to 95 at the time of analysis. Phenome-wide association scanning showed that CCDC92 likely affects coronary artery disease through insulin resistance pathways, whereas experimental analysis suggests that ARHGEF26 influences the transendothelial migration of leukocytes...
September 2017: Nature Genetics
https://www.readbyqxmd.com/read/28712569/extensive-farming-in-estonia-started-through-a-sex-biased-migration-from-the-steppe
#9
Lehti Saag, Liivi Varul, Christiana Lyn Scheib, Jesper Stenderup, Morten E Allentoft, Lauri Saag, Luca Pagani, Maere Reidla, Kristiina Tambets, Ene Metspalu, Aivar Kriiska, Eske Willerslev, Toomas Kivisild, Mait Metspalu
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...
July 24, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/27848937/reconstructing-druze-population-history
#10
Scarlett Marshall, Ranajit Das, Mehdi Pirooznia, Eran Elhaik
The Druze are an aggregate of communities in the Levant and Near East living almost exclusively in the mountains of Syria, Lebanon and Israel whose ~1000 year old religion formally opposes mixed marriages and conversions. Despite increasing interest in genetics of the population structure of the Druze, their population history remains unknown. We investigated the genetic relationships between Israeli Druze and both modern and ancient populations. We evaluated our findings in light of three hypotheses purporting to explain Druze history that posit Arabian, Persian or mixed Near Eastern-Levantine roots...
November 16, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27633963/maternal-genetic-ancestry-and-legacy-of-10-th-century-ad-hungarians
#11
Aranka Csősz, Anna Szécsényi-Nagy, Veronika Csákyová, Péter Langó, Viktória Bódis, Kitti Köhler, Gyöngyvér Tömöry, Melinda Nagy, Balázs Gusztáv Mende
The ancient Hungarians originated from the Ural region in today's central Russia and migrated across the Eastern European steppe, according to historical sources. The Hungarians conquered the Carpathian Basin 895-907 AD, and admixed with the indigenous communities. Here we present mitochondrial DNA results from three datasets: one from the Avar period (7(th)-9(th) centuries) of the Carpathian Basin (n = 31); one from the Hungarian conquest-period (n = 76); and a completion of the published 10(th)-12(th) century Hungarian-Slavic contact zone dataset by four samples...
2016: Scientific Reports
https://www.readbyqxmd.com/read/27507099/a-genomic-view-of-the-peopling-of-the-americas
#12
REVIEW
Pontus Skoglund, David Reich
Whole-genome studies have documented that most Native American ancestry stems from a single population that diversified within the continent more than twelve thousand years ago. However, this shared ancestry hides a more complex history whereby at least four distinct streams of Eurasian migration have contributed to present-day and prehistoric Native American populations. Whole genome studies enhanced by technological breakthroughs in ancient DNA now provide evidence of a sequence of events involving initial migrations from a structured Northeast Asian source population with differential relatedness to present-day Australasian populations, followed by a divergence into northern and southern Native American lineages...
December 2016: Current Opinion in Genetics & Development
https://www.readbyqxmd.com/read/27453128/east-eurasian-ancestry-in-the-middle-of-europe-genetic-footprints-of-steppe-nomads-in-the-genomes-of-belarusian-lipka-tatars
#13
Vasili Pankratov, Sergei Litvinov, Alexei Kassian, Dzmitry Shulhin, Lieve Tchebotarev, Bayazit Yunusbayev, Märt Möls, Hovhannes Sahakyan, Levon Yepiskoposyan, Siiri Rootsi, Ene Metspalu, Maria Golubenko, Natalia Ekomasova, Farida Akhatova, Elza Khusnutdinova, Evelyne Heyer, Phillip Endicott, Miroslava Derenko, Boris Malyarchuk, Mait Metspalu, Oleg Davydenko, Richard Villems, Alena Kushniarevich
Medieval era encounters of nomadic groups of the Eurasian Steppe and largely sedentary East Europeans had a variety of demographic and cultural consequences. Amongst these outcomes was the emergence of the Lipka Tatars-a Slavic-speaking Sunni-Muslim minority residing in modern Belarus, Lithuania and Poland, whose ancestors arrived in these territories via several migration waves, mainly from the Golden Horde. Our results show that Belarusian Lipka Tatars share a substantial part of their gene pool with Europeans as indicated by their Y-chromosomal, mitochondrial and autosomal DNA variation...
2016: Scientific Reports
https://www.readbyqxmd.com/read/27420957/hvsi-polymorphism-indicates-multiple-origins-of-mtdna-in-the-hazarewal-population-of-northern-pakistan
#14
N Akbar, H Ahmad, M S Nadeem, B E Hemphill, K Muhammad, W Ahmad, M Ilyas
Mitochondrial DNA (mtDNA) is an important tool used to explore ethnogenetics and the evolutionary history of human populations. In this study, hypervariable segment I (HVSI) from mtDNA was analyzed to establish the genetic lineage of the Hazarewal populations residing in the Mansehra and Abbottabad districts of Northern Pakistan. HVSI was extracted from genetic specimens obtained from 225 unrelated male and female individuals belonging to seven distinct Pakistani ethnic groups (31 Abbassis, 44 Awans, 38 Gujars, 16 Jadoons, 23 Karlals, 33 Syeds, and 40 Tanolis)...
June 24, 2016: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/27135931/the-genetic-history-of-ice-age-europe
#15
Qiaomei Fu, Cosimo Posth, Mateja Hajdinjak, Martin Petr, Swapan Mallick, Daniel Fernandes, Anja Furtwängler, Wolfgang Haak, Matthias Meyer, Alissa Mittnik, Birgit Nickel, Alexander Peltzer, Nadin Rohland, Viviane Slon, Sahra Talamo, Iosif Lazaridis, Mark Lipson, Iain Mathieson, Stephan Schiffels, Pontus Skoglund, Anatoly P Derevianko, Nikolai Drozdov, Vyacheslav Slavinsky, Alexander Tsybankov, Renata Grifoni Cremonesi, Francesco Mallegni, Bernard Gély, Eligio Vacca, Manuel R González Morales, Lawrence G Straus, Christine Neugebauer-Maresch, Maria Teschler-Nicola, Silviu Constantin, Oana Teodora Moldovan, Stefano Benazzi, Marco Peresani, Donato Coppola, Martina Lari, Stefano Ricci, Annamaria Ronchitelli, Frédérique Valentin, Corinne Thevenet, Kurt Wehrberger, Dan Grigorescu, Hélène Rougier, Isabelle Crevecoeur, Damien Flas, Patrick Semal, Marcello A Mannino, Christophe Cupillard, Hervé Bocherens, Nicholas J Conard, Katerina Harvati, Vyacheslav Moiseyev, Dorothée G Drucker, Jiří Svoboda, Michael P Richards, David Caramelli, Ron Pinhasi, Janet Kelso, Nick Patterson, Johannes Krause, Svante Pääbo, David Reich
Modern humans arrived in Europe ~45,000 years ago, but little is known about their genetic composition before the start of farming ~8,500 years ago. Here we analyse genome-wide data from 51 Eurasians from ~45,000-7,000 years ago. Over this time, the proportion of Neanderthal DNA decreased from 3-6% to around 2%, consistent with natural selection against Neanderthal variants in modern humans. Whereas there is no evidence of the earliest modern humans in Europe contributing to the genetic composition of present-day Europeans, all individuals between ~37,000 and ~14,000 years ago descended from a single founder population which forms part of the ancestry of present-day Europeans...
June 9, 2016: Nature
https://www.readbyqxmd.com/read/27014585/first-report-on-hla-dpa1-gene-allelic-distribution-in-the-general-lebanese-population
#16
Joseph Haddad, Dina Shammaa, Fatmeh Abbas, Rami A R Mahfouz
AIMS: HLA-DPA1 is an important marker in bone marrow and organ transplantation and a highly emerging screening parameter in histocompatibility laboratories. Being highly polymorphic, it has another significant value in detecting population origins and migrations. This is the first study to assess DPA1 allele frequencies in an Arab population. METHODS: The HLA DPA1 alleles were identified using the One-Lambda assays on a Luminex reverse SSO DNA typing system. Our study included 101 individuals coming from different Lebanese geographical areas representing the different communities and religious sects of the country...
June 2016: Meta Gene
https://www.readbyqxmd.com/read/27003890/palaeogenomics-mitogenomes-and-migrations-in-europe-s-past
#17
COMMENT
Martin B Richards, Pedro Soares, Antonio Torroni
The latest in a series of transformative studies of DNA from prehistoric Europeans focuses on mitochondrial DNA, bringing fresh surprises and filling in important details of the early stages of a European ancestry stretching back more than 40,000 years.
March 21, 2016: Current Biology: CB
https://www.readbyqxmd.com/read/26799213/genetic-diversity-and-phylogeny-of-aedes-aegypti-the-main-arbovirus-vector-in-the-pacific
#18
Elodie Calvez, Laurent Guillaumot, Laurent Millet, Jérôme Marie, Hervé Bossin, Vineshwaran Rama, Akata Faamoe, Sosiasi Kilama, Magali Teurlai, Françoise Mathieu-Daudé, Myrielle Dupont-Rouzeyrol
BACKGROUND: The Pacific region is an area unique in the world, composed of thousands of islands with differing climates and environments. The spreading and establishment of the mosquito Aedes aegypti in these islands might be linked to human migration. Ae. aegypti is the major vector of arboviruses (dengue, chikungunya and Zika viruses) in the region. The intense circulation of these viruses in the Pacific during the last decade led to an increase of vector control measures by local health authorities...
January 2016: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/26781090/resolving-the-ancestry-of-austronesian-speaking-populations
#19
Pedro A Soares, Jean A Trejaut, Teresa Rito, Bruno Cavadas, Catherine Hill, Ken Khong Eng, Maru Mormina, Andreia Brandão, Ross M Fraser, Tse-Yi Wang, Jun-Hun Loo, Christopher Snell, Tsang-Ming Ko, António Amorim, Maria Pala, Vincent Macaulay, David Bulbeck, James F Wilson, Leonor Gusmão, Luísa Pereira, Stephen Oppenheimer, Marie Lin, Martin B Richards
There are two very different interpretations of the prehistory of Island Southeast Asia (ISEA), with genetic evidence invoked in support of both. The "out-of-Taiwan" model proposes a major Late Holocene expansion of Neolithic Austronesian speakers from Taiwan. An alternative, proposing that Late Glacial/postglacial sea-level rises triggered largely autochthonous dispersals, accounts for some otherwise enigmatic genetic patterns, but fails to explain the Austronesian language dispersal. Combining mitochondrial DNA (mtDNA), Y-chromosome and genome-wide data, we performed the most comprehensive analysis of the region to date, obtaining highly consistent results across all three systems and allowing us to reconcile the models...
March 2016: Human Genetics
https://www.readbyqxmd.com/read/26591010/update-of-phylogenetic-and-genetic-diversity-of-sporothrix-schenckii-sensu-lato
#20
Lucía Rangel-Gamboa, Fernando Martínez-Hernandez, Pablo Maravilla, Roberto Arenas-Guzmán, Ana Flisser
Sporothrix schenckii sensu lato causes subcutaneous mycosis. In this article we analysed its phylogeny and genetic diversity using calmodulin DNA sequences deposited in GenBank database. Population genetics indices were calculated, plus phylogenetic and haplotype network trees were built. Five clades with high values of posterior probability, 47 haplotypes and high diversity in the complex were found. Analysis of partial calmodulin sequences alignment revealed conserved and polymorphic regions that could be used as reference for taxonomic identification...
March 2016: Medical Mycology: Official Publication of the International Society for Human and Animal Mycology
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