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Mallick, Swapan

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Mallick, Swapan
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    A Genetic History of the Pre-Contact Caribbean
    (Springer Nature, 2020-12-23) Fernandes, Daniel M.; Sirak, Kendra; Ringbauer, Harald; Sedig, Jakob; Rohland-Pinello, Nadin; Cheronet, Olivia; Mah, Matthew; Mallick, Swapan; Olalde, Inigo; Culleton, Brendan J.; Adamski, Nicole; Bernardos, Rebecca; Bravo, Guillermo; Broomandkhoshbacht, Nasreen; Callan, Kimberly; Candilio, Francesca; Demetz, Lea; Carlson, Kellie; Eccles, Laurie; Freilich, Suzanne; George, Richard J.; Lawson, Ann Marie; Mandl, Kirsten; Marzaioli, Fabio; McCool, Weston C.; Oppenheimer, Jonas; Özdogan, Kadir T.; Schattke, Constanze; Schmidt, Ryan; Stewardson, Kristin; Terrasi, Filippo; Zalzala, Fatma; Antúnez, Carlos Arredondo; Canosa, Ercilio Vento; Colten, Roger; Cucina, Andrea; Genchi, Francesco; Kraan, Claudia; La Pastina, Francesco; Lucci, Michaela; Maggiolo, Marcio Veloz; Marcheco-Teruel, Beatriz; Maria, Clenis Tavarez; Martínez, Christian; París, Ingeborg; Pateman, Michael; Simms, Tanya; Sivoli, Carlos Garcia; Vilar, Miguel; Kennett, Douglas J.; Keegan, William; Coppa, Alfredo; Lipson, Mark; Pinhasi, Ron; Reich, David
    Humans settled the Caribbean ~6,000 years ago, with ceramic use and intensified agriculture marking a shift from the Archaic to the Ceramic Age ~2,500 years ago. We report genome-wide data from 174 individuals from The Bahamas, Hispaniola, Puerto Rico, Curaçao, and Venezuela co-analyzed with published data. Archaic Age Caribbean people derive from a deeply divergent population closest to Central and northern South Americans; contrary to previous work, we find no support for ancestry contributed by a population related to North Americans. Archaic lineages were >98% replaced by a genetically homogeneous ceramic-using population related to Arawak-speakers from northeast South America who moved through the Lesser Antilles and into the Greater Antilles at least 1,700 years ago, introducing ancestry that is still present. Ancient Caribbean people avoided close kin unions despite limited mate pools reflecting small effective population sizes which we estimate to be a minimum of Ne=500-1500 and a maximum of Ne=1530-8150 on the combined islands of Puerto Rico and Hispaniola in the dozens of generations before the analyzed individuals lived. Census sizes are unlikely to be more than ten-fold larger than effective population sizes, so previous estimates of hundreds of thousands of people are too large. Confirming a small, interconnected Ceramic Age population, we detect 19 pairs of cross-island cousins, close relatives ~75 kilometers apart in Hispaniola, and low genetic differentiation across islands. Genetic continuity across transitions in pottery styles reveals that cultural changes during the Ceramic Age were not driven by migration of genetically-differentiated groups from the mainland but instead reflected interactions within an interconnected Caribbean world.
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    High continuity of forager ancestry in the Neolithic of the eastern Maghreb
    (SpringerNature) Reich, David; Lipson, Mark; Ringbauer, Harald; Mallick, Swapan; Rohland-Pinello, Nadin
    Ancient DNA from the Mediterranean region has revealed long-range connections and population transformations associated with the spread of food producing economies [1-6]. However, in contrast to Europe, genetic data from this key transition in northern Africa are limited, and have only been available from the far western Maghreb (Morocco) [1-3]. Here, we present genome-wide data for nine individuals from the Later Stone Age (LSA) through the Neolithic in Algeria and Tunisia. The earliest individuals cluster with pre-Neolithic people of the western Maghreb (~15000-7600 Before Present (BP)), showing that this “Maghrebi” ancestry profile had a substantial geographic and temporal extent. At least one individual from Djebba (Tunisia), dating to ~8000 BP, harbored ancestry from European hunter-gatherers, likely reflecting early Holocene movement across the Strait of Sicily. Later Neolithic people from the eastern Maghreb retained largely local forager ancestry together with smaller contributions from European farmers (by ~7000 BP) and Levantine groups (by ~6800 BP), and were thus far less impacted by external gene flow than were populations in other parts of the Neolithic Mediterranean.
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    Palaeo-Eskimo Genetic Ancestry and the Peopling of Chukotka and North America
    (Springer Science and Business Media LLC, 2019-06) Flegontov, Pavel; Rohland-Pinello, Nadin; Mallick, Swapan; Flegontova, Olga; Jeong, Choongwon; Keating, Denise; Lawson, Ann; Oppenheimer, Jonas; Raff, Jennifer; Skoglund, Pontus; Stewardson, Kristin; Vasilyev, Sergey; Veselovskaya, Elizaveta; Hayes, M. Geoffrey; Krause, Johannes; Pinhasi, Ron; Reich, David; Changmai, Piya; Adamski, Nicole; Bolnick, Deborah; Culleton, Brendan; Harper, Thomas; Kennett, Douglas; Kim, Alexander; Lamnidis, Thiseas; Olalde, Iñigo; Potter, Ben; Sattler, Robert; Vajda, Edwards; O’Rourke, Dennis; Schiffels, Stephan; Broomandkhoshbacht, Nasreen; Candilio, Francesca; Friesen, Max; Altınışık, Ezgi
    Paleo-Eskimos were the first people to settle vast regions of the American Arctic around 5,000 years ago, and were subsequently joined and largely displaced around 1,000 years ago by ancestors of present-day Inuit and Yup’ik1-3. The genetic relationship between Paleo-Eskimos and Native American, Inuit, Yup’ik and Aleut populations remains uncertain4-7. Here we present new genomic data for 48 ancient individuals from Chukotka, East Siberia, the Aleutian Islands, Alaska, and the Canadian Arctic. We co-analyze these data with new data from present-day Alaskan Iñupiat and West Siberian populations and published genomes. Employing new methods based on rare allele and haplotype sharing as well as established methods4,8-10, we show that Paleo-Eskimo-related admixture is ubiquitous among populations speaking Na-Dene and Eskimo-Aleut languages. We develop a comprehensive model for the Holocene peopling events of Chukotka and North America, and show that several key migrations connected to the origin of the Na-Dene peoples, the peopling of the Aleutian Islands, and the spread of Yup’ik and Inuit across the Arctic region are genetically linked to a single Siberian source related to Paleo-Eskimos.
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    Ancient West African Foragers in the Context of African Population History
    (Springer Science and Business Media LLC, 2020-01) Lipson, Mark; Rohland-Pinello, Nadin; Lawson, Ann; Lavachery, Philippe; Mindzie, Christophe Mbida; Orban, Rosine; Semal, Patrick; Van Neer, Wim; Veeramah, Krishna R.; Kennett, Douglas J.; Patterson, Nick; Hellenthal, Garrett; Lalueza-Fox, Carles; MacEachern, Scott; Prendergast, Mary E.; Reich, David; Ribot, Isabelle; Mallick, Swapan; Olalde, Inigo; Adamski, Nicole; Broomandkhoshbacht, Nadin; López, Saloa; Oppenheimer, Jonas; Stewardson, Kristin; Asombang, Raymond; Bocherens, Herve; Bradman, Neil; Culleton, Brendan; Cornelissen, Els; Crevecoeur, Isabelle; de Maret, Pierre; Fomine, Forka Leypey Mathew; Sawchuk, Elizabeth; Thomas, Mark
    We generated genome-wide DNA data from four children buried roughly 8000 and 3000 years ago at Shum Laka (Cameroon), one of the earliest archaeological sites within the probable homeland of Bantu languages. One individual carried the deeply divergent Y chromosome haplogroup A00, which is found today almost exclusively in the same region. However, all four individuals’ genome-wide ancestry profiles are most similar to West-Central African hunter-gatherers, implying that present-day populations in western Cameroon, as well as Bantu speakers across the continent, are not descended substantially from the population represented by these four people. We infer an Africa-wide phylogeny that features widespread admixture and three prominent radiations, including one giving rise to at least four major lineages deep in the history of modern humans.
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    A framework for the interpretation of de novo mutation in human disease
    (2014) Samocha, Kaitlin E.; Robinson, Elise; Sanders, Stephan J.; Stevens, Christine; Sabo, Aniko; McGrath, Lauren M.; Kosmicki, Jack; Rehnström, Karola; Mallick, Swapan; Kirby, Andrew; Wall, Dennis P.; MacArthur, Daniel; Gabriel, Stacey B.; dePristo, Mark; Purcell, Shaun M.; Palotie, Aarno; Boerwinkle, Eric; Buxbaum, Joseph D.; Cook, Edwin H.; Gibbs, Richard A.; Schellenberg, Gerard D.; Sutcliffe, James S.; Devlin, Bernie; Roeder, Kathryn; Neale, Benjamin; Daly, Mark
    Spontaneously arising (‘de novo’) mutations play an important role in medical genetics. For diseases with extensive locus heterogeneity – such as autism spectrum disorders (ASDs) – the signal from de novo mutations (DNMs) is distributed across many genes, making it difficult to distinguish disease-relevant mutations from background variation. We provide a statistical framework for the analysis of DNM excesses per gene and gene set by calibrating a model of de novo mutation. We applied this framework to DNMs collected from 1,078 ASD trios and – while affirming a significant role for loss-of-function (LoF) mutations – found no excess of de novo LoF mutations in cases with IQ above 100, suggesting that the role of DNMs in ASD may reside in fundamental neurodevelopmental processes. We also used our model to identify ~1,000 genes that are significantly lacking functional coding variation in non-ASD samples and are enriched for de novo LoF mutations identified in ASD cases.
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    Ancient human genomes suggest three ancestral populations for present-day Europeans
    (2014) Lazaridis, Iosif; Patterson, Nick; Mittnik, Alissa; Renaud, Gabriel; Mallick, Swapan; Kirsanow, Karola; Sudmant, Peter H.; Schraiber, Joshua G.; Castellano, Sergi; Lipson, Mark; Berger, Bonnie; Economou, Christos; Bollongino, Ruth; Fu, Qiaomei; Bos, Kirsten I.; Nordenfelt, Susanne; Li, Heng; de Filippo, Cesare; Prüfer, Kay; Sawyer, Susanna; Posth, Cosimo; Haak, Wolfgang; Hallgren, Fredrik; Fornander, Elin; Rohland-Pinello, Nadin; Delsate, Dominique; Francken, Michael; Guinet, Jean-Michel; Wahl, Joachim; Ayodo, George; Babiker, Hamza A.; Bailliet, Graciela; Balanovska, Elena; Balanovsky, Oleg; Barrantes, Ramiro; Bedoya, Gabriel; Ben-Ami, Haim; Bene, Judit; Berrada, Fouad; Bravi, Claudio M.; Brisighelli, Francesca; Busby, George B. J.; Cali, Francesco; Churnosov, Mikhail; Cole, David E. C.; Corach, Daniel; Damba, Larissa; van Driem, George; Dryomov, Stanislav; Dugoujon, Jean-Michel; Fedorova, Sardana A.; Romero, Irene Gallego; Gubina, Marina; Hammer, Michael; Henn, Brenna M.; Hervig, Tor; Hodoglugil, Ugur; Jha, Aashish R.; Karachanak-Yankova, Sena; Khusainova, Rita; Khusnutdinova, Elza; Kittles, Rick; Kivisild, Toomas; Klitz, William; Kučinskas, Vaidutis; Kushniarevich, Alena; Laredj, Leila; Litvinov, Sergey; Loukidis, Theologos; Mahley, Robert W.; Melegh, Béla; Metspalu, Ene; Molina, Julio; Mountain, Joanna; Näkkäläjärvi, Klemetti; Nesheva, Desislava; Nyambo, Thomas; Osipova, Ludmila; Parik, Jüri; Platonov, Fedor; Posukh, Olga; Romano, Valentino; Rothhammer, Francisco; Rudan, Igor; Ruizbakiev, Ruslan; Sahakyan, Hovhannes; Sajantila, Antti; Salas, Antonio; Starikovskaya, Elena B.; Tarekegn, Ayele; Toncheva, Draga; Turdikulova, Shahlo; Uktveryte, Ingrida; Utevska, Olga; Vasquez, René; Villena, Mercedes; Voevoda, Mikhail; Winkler, Cheryl; Yepiskoposyan, Levon; Zalloua, Pierre; Zemunik, Tatijana; Cooper, Alan; Capelli, Cristian; Thomas, Mark G.; Ruiz-Linares, Andres; Tishkoff, Sarah A.; Singh, Lalji; Thangaraj, Kumarasamy; Villems, Richard; Comas, David; Sukernik, Rem; Metspalu, Mait; Meyer, Matthias; Eichler, Evan E.; Burger, Joachim; Slatkin, Montgomery; Pääbo, Svante; Kelso, Janet; Reich, David; Krause, Johannes
    We sequenced the genomes of a ~7,000 year old farmer from Germany and eight ~8,000 year old hunter-gatherers from Luxembourg and Sweden. We analyzed these and other ancient genomes1–4 with 2,345 contemporary humans to show that most present Europeans derive from at least three highly differentiated populations: West European Hunter-Gatherers (WHG), who contributed ancestry to all Europeans but not to Near Easterners; Ancient North Eurasians (ANE) related to Upper Paleolithic Siberians3, who contributed to both Europeans and Near Easterners; and Early European Farmers (EEF), who were mainly of Near Eastern origin but also harbored WHG-related ancestry. We model these populations’ deep relationships and show that EEF had ~44% ancestry from a “Basal Eurasian” population that split prior to the diversification of other non-African lineages.
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    Genomic insights into the origin of farming in the ancient Near East
    (2016) Lazaridis, Iosif; Nadel, Dani; Rollefson, Gary; Merrett, Deborah C.; Rohland, Nadin; Mallick, Swapan; Fernandes, Daniel; Novak, Mario; Gamarra, Beatriz; Sirak, Kendra; Connell, Sarah; Stewardson, Kristin; Harney, Eadaoin; Fu, Qiaomei; Gonzalez-Fortes, Gloria; Jones, Eppie R.; Roodenberg, Songül Alpaslan; Lengyel, György; Bocquentin, Fanny; Gasparian, Boris; Monge, Janet M.; Gregg, Michael; Eshed, Vered; Mizrahi, Ahuva-Sivan; Meiklejohn, Christopher; Gerritsen, Fokke; Bejenaru, Luminita; Blüher, Matthias; Campbell, Archie; Cavalleri, Gianpiero; Comas, David; Froguel, Philippe; Gilbert, Edmund; Kerr, Shona M.; Kovacs, Peter; Krause, Johannes; McGettigan, Darren; Merrigan, Michael; Merriwether, D. Andrew; O'Reilly, Seamus; Richards, Martin B.; Semino, Ornella; Shamoon-Pour, Michel; Stefanescu, Gheorghe; Stumvoll, Michael; Tönjes, Anke; Torroni, Antonio; Wilson, James F.; Yengo, Loic; Hovhannisyan, Nelli A.; Patterson, Nick; Pinhasi, Ron; Reich, David
    We report genome-wide ancient DNA from 44 ancient Near Easterners ranging in time between ~12,000-1,400 BCE, from Natufian hunter-gatherers to Bronze Age farmers. We show that the earliest populations of the Near East derived around half their ancestry from a ‘Basal Eurasian’ lineage that had little if any Neanderthal admixture and that separated from other non-African lineages prior to their separation from each other. The first farmers of the southern Levant (Israel and Jordan) and Zagros Mountains (Iran) were strongly genetically differentiated, and each descended from local hunter-gatherers. By the time of the Bronze Age, these two populations and Anatolian-related farmers had mixed with each other and with the hunter-gatherers of Europe to drastically reduce genetic differentiation. The impact of the Near Eastern farmers extended beyond the Near East: farmers related to those of Anatolia spread westward into Europe; farmers related to those of the Levant spread southward into East Africa; farmers related to those from Iran spread northward into the Eurasian steppe; and people related to both the early farmers of Iran and to the pastoralists of the Eurasian steppe spread eastward into South Asia.
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    Parallel paleogenomic transects reveal complex genetic history of early European farmers
    (2017) Lipson, Mark; Szécsényi-Nagy, Anna; Mallick, Swapan; Pósa, Annamária; Stégmár, Balázs; Keerl, Victoria; Rohland-Pinello, Nadin; Stewardson, Kristin; Ferry, Matthew; Michel, Megan; Oppenheimer, Jonas; Broomandkhoshbacht, Nasreen; Harney, Eadaoin; Nordenfelt, Susanne; Llamas, Bastien; Mende, Balázs Gusztáv; Köhler, Kitti; Oross, Krisztián; Bondár, Mária; Marton, Tibor; Osztás, Anett; Jakucs, János; Paluch, Tibor; Horváth, Ferenc; Csengeri, Piroska; Koós, Judit; Sebők, Katalin; Anders, Alexandra; Raczky, Pál; Regenye, Judit; Barna, Judit P.; Fábián, Szilvia; Serlegi, Gábor; Toldi, Zoltán; Nagy, Emese Gyöngyvér; Dani, János; Molnár, Erika; Pálfi, György; Márk, László; Melegh, Béla; Bánfai, Zsolt; Domboróczki, László; Fernández-Eraso, Javier; Mujika-Alustiza, José Antonio; Fernández, Carmen Alonso; Echevarría, Javier Jiménez; Bollongino, Ruth; Orschiedt, Jörg; Schierhold, Kerstin; Meller, Harald; Cooper, Alan; Burger, Joachim; Bánffy, Eszter; Alt, Kurt W.; Lalueza-Fox, Carles; Haak, Wolfgang; Reich, David
    Ancient DNA studies have established that Neolithic European populations were descended from Anatolian migrants1–8 who received a limited amount of admixture from resident hunter-gatherers3–5,9. Many open questions remain, however, about the spatial and temporal dynamics of population interactions and admixture during the Neolithic period. Using the highest-resolution genome-wide ancient DNA data set assembled to date—a total of 180 samples, 130 newly reported here, from the Neolithic and Chalcolithic of Hungary (6000–2900 BCE, n = 100), Germany (5500–3000 BCE, n = 42), and Spain (5500–2200 BCE, n = 38)—we investigate the population dynamics of Neolithization across Europe. We find that genetic diversity was shaped predominantly by local processes, with varied sources and proportions of hunter-gatherer ancestry among the three regions and through time. Admixture between groups with different ancestry profiles was pervasive and resulted in observable population transformation across almost all cultural transitions. Our results shed new light on the ways that gene flow reshaped European populations throughout the Neolithic period and demonstrate the potential of time-series-based sampling and modeling approaches to elucidate multiple dimensions of historical population interactions.
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    Biological Sexing of a 4000-Year-Old Egyptian Mummy Head to Assess the Potential of Nuclear DNA Recovery from the Most Damaged and Limited Forensic Specimens
    (MDPI, 2018) Loreille, Odile; Ratnayake, Shashikala; Bazinet, Adam L.; Stockwell, Timothy B.; Sommer, Daniel D.; Rohland, Nadin; Mallick, Swapan; Johnson, Philip L.F.; Skoglund, Pontus; Onorato, Anthony J.; Bergman, Nicholas H.; Reich, David; Irwin, Jodi A.
    High throughput sequencing (HTS) has been used for a number of years in the field of paleogenomics to facilitate the recovery of small DNA fragments from ancient specimens. Recently, these techniques have also been applied in forensics, where they have been used for the recovery of mitochondrial DNA sequences from samples where traditional PCR-based assays fail because of the very short length of endogenous DNA molecules. Here, we describe the biological sexing of a ~4000-year-old Egyptian mummy using shotgun sequencing and two established methods of biological sex determination (RX and RY), by way of mitochondrial genome analysis as a means of sequence data authentication. This particular case of historical interest increases the potential utility of HTS techniques for forensic purposes by demonstrating that data from the more discriminatory nuclear genome can be recovered from the most damaged specimens, even in cases where mitochondrial DNA cannot be recovered with current PCR-based forensic technologies. Although additional work remains to be done before nuclear DNA recovered via these methods can be used routinely in operational casework for individual identification purposes, these results indicate substantial promise for the retrieval of probative individually identifying DNA data from the most limited and degraded forensic specimens.
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    Genetic origins of the Minoans and Mycenaeans
    (2017) Lazaridis, Iosif; Mittnik, Alissa; Patterson, Nick; Mallick, Swapan; Rohland, Nadin; Pfrengle, Saskia; Furtwängler, Anja; Peltzer, Alexander; Posth, Cosimo; Vasilakis, Andonis; McGeorge, P.J.P.; Konsolaki-Yannopoulou, Eleni; Korres, George; Martlew, Holley; Michalodimitrakis, Manolis; Özsait, Mehmet; Özsait, Nesrin; Papathanasiou, Anastasia; Richards, Michael; Roodenberg, Songül Alpaslan; Tzedakis, Yannis; Arnott, Robert; Fernandes, Daniel M.; Hughey, Jeffery R.; Lotakis, Dimitra M.; Navas, Patrick A.; Maniatis, Yannis; Stamatoyannopoulos, John A.; Stewardson, Kristin; Stockhammer, Philipp; Pinhasi, Ron; Reich, David; Krause, Johannes; Stamatoyannopoulos, George
    The origins of the Bronze Age Minoan and Mycenaean cultures have puzzled archaeologists for more than a century. We assembled genome-wide data from nineteen ancient individuals, including Minoans from Crete, Mycenaeans from mainland Greece, and their eastern neighbours from southwestern Anatolia. We show that Minoans and Mycenaeans were genetically similar, having at least three quarters of their ancestry from the first Neolithic farmers of western Anatolia and the Aegean1,2, and most of the remainder from ancient populations like those of the Caucasus3 and Iran4,5. However, the Mycenaeans differed from Minoans in deriving additional ancestry from an ultimate source related to the hunter-gatherers of eastern Europe and Siberia6–8, introduced via a proximal source related to either the inhabitants of either the Eurasian steppe1,6,9 or Armenia4,9. Modern Greeks resemble the Mycenaeans, but with some additional dilution of the early Neolithic ancestry. Our results support the idea of continuity but not isolation in the history of populations of the Aegean, before and after the time of its earliest civilizations.