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https://www.readbyqxmd.com/read/29040546/variation-and-functional-impact-of-neanderthal-ancestry-in-western-asia
#1
Recep Ozgur Taskent, 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 to other Eurasian populations. To better understand the genome-wide and phenotypic impact of Neanderthal introgression in the region, we sequenced whole genomes of 10 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...
October 13, 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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
https://www.readbyqxmd.com/read/26509580/early-holocenic-and-historic-mtdna-african-signatures-in-the-iberian-peninsula-the-andalusian-region-as-a-paradigm
#17
Candela L Hernández, Pedro Soares, Jean M Dugoujon, Andrea Novelletto, Juan N Rodríguez, Teresa Rito, Marisa Oliveira, Mohammed Melhaoui, Abdellatif Baali, Luisa Pereira, Rosario Calderón
Determining the timing, identity and direction of migrations in the Mediterranean Basin, the role of "migratory routes" in and among regions of Africa, Europe and Asia, and the effects of sex-specific behaviors of population movements have important implications for our understanding of the present human genetic diversity. A crucial component of the Mediterranean world is its westernmost region. Clear features of transcontinental ancient contacts between North African and Iberian populations surrounding the maritime region of Gibraltar Strait have been identified from archeological data...
2015: PloS One
https://www.readbyqxmd.com/read/26153446/analysis-of-ancient-human-mitochondrial-dna-from-the-xiaohe-cemetery-insights-into-prehistoric-population-movements-in-the-tarim-basin-china
#18
Chunxiang Li, Chao Ning, Erika Hagelberg, Hongjie Li, Yongbin Zhao, Wenying Li, Idelisi Abuduresule, Hong Zhu, Hui Zhou
BACKGROUND: The Tarim Basin in western China, known for its amazingly well-preserved mummies, has been for thousands of years an important crossroad between the eastern and western parts of Eurasia. Despite its key position in communications and migration, and highly diverse peoples, languages and cultures, its prehistory is poorly understood. To shed light on the origin of the populations of the Tarim Basin, we analysed mitochondrial DNA polymorphisms in human skeletal remains excavated from the Xiaohe cemetery, used by the local community between 4000 and 3500 years before present, and possibly representing some of the earliest settlers...
2015: BMC Genetics
https://www.readbyqxmd.com/read/25994871/genome-wide-signatures-of-male-mediated-migration-shaping-the-indian-gene-pool
#19
GaneshPrasad ArunKumar, Tatiana V Tatarinova, Jeff Duty, Debra Rollo, Adhikarla Syama, Varatharajan Santhakumari Arun, Valampuri John Kavitha, Petr Triska, Bennett Greenspan, R Spencer Wells, Ramasamy Pitchappan
Multiple questions relating to contributions of cultural and demographical factors in the process of human geographical dispersal remain largely unanswered. India, a land of early human settlement and the resulting diversity is a good place to look for some of the answers. In this study, we explored the genetic structure of India using a diverse panel of 78 males genotyped using the GenoChip. Their genome-wide single-nucleotide polymorphism (SNP) diversity was examined in the context of various covariates that influence Indian gene pool...
September 2015: Journal of Human Genetics
https://www.readbyqxmd.com/read/25731166/massive-migration-from-the-steppe-was-a-source-for-indo-european-languages-in-europe
#20
Wolfgang Haak, Iosif Lazaridis, Nick Patterson, Nadin Rohland, Swapan Mallick, Bastien Llamas, Guido Brandt, Susanne Nordenfelt, Eadaoin Harney, Kristin Stewardson, Qiaomei Fu, Alissa Mittnik, Eszter Bánffy, Christos Economou, Michael Francken, Susanne Friederich, Rafael Garrido Pena, Fredrik Hallgren, Valery Khartanovich, Aleksandr Khokhlov, Michael Kunst, Pavel Kuznetsov, Harald Meller, Oleg Mochalov, Vayacheslav Moiseyev, Nicole Nicklisch, Sandra L Pichler, Roberto Risch, Manuel A Rojo Guerra, Christina Roth, Anna Szécsényi-Nagy, Joachim Wahl, Matthias Meyer, Johannes Krause, Dorcas Brown, David Anthony, Alan Cooper, Kurt Werner Alt, David Reich
We generated genome-wide data from 69 Europeans who lived between 8,000-3,000 years ago by enriching ancient DNA libraries for a target set of almost 400,000 polymorphisms. Enrichment of these positions decreases the sequencing required for genome-wide ancient DNA analysis by a median of around 250-fold, allowing us to study an order of magnitude more individuals than previous studies and to obtain new insights about the past. We show that the populations of Western and Far Eastern Europe followed opposite trajectories between 8,000-5,000 years ago...
June 11, 2015: Nature
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