Search Results - "Malaspinas, Anna‐Sapfo"

Methods to characterize selective sweeps using time serial samples: an ancient DNA perspective by Malaspinas, Anna‐Sapfo

“…With hundreds of ancient genomes becoming available this year, ancient DNA research has now entered the genomics era. Utilizing the temporal aspect of these…”
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Genomic structure in Europeans dating back at least 36,200 years by Seguin-Orlando, Andaine, Korneliussen, Thorfinn S., Sikora, Martin, Malaspinas, Anna-Sapfo, Manica, Andrea, Moltke, Ida, Albrechtsen, Anders, Ko, Amy, Margaryan, Ashot, Moiseyev, Vyacheslav, Goebel, Ted, Westaway, Michael, Lambert, David, Khartanovich, Valeri, Wall, Jeffrey D., Nigst, Philip R., Foley, Robert A., Lahr, Marta Mirazon, Nielsen, Rasmus, Orlando, Ludovic, Willerslev, Eske

“…The origin of contemporary Europeans remains contentious. We obtained a genome sequence from Kostenki 14 in European Russia dating from 38,700 to 36,200 years…”
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Draft Sequence of the Neandertal Genome by Green, Richard E, Krause, Johannes, Briggs, Adrian W, Maricic, Tomislav, Stenzel, Udo, Kircher, Martin, Patterson, Nick, Li, Heng, Zhai, Weiwei, Fritz, Markus Hsi-Yang, Hansen, Nancy F, Durand, Eric Y, Malaspinas, Anna-Sapfo, Jensen, Jeffrey D, Marques-Bonet, Tomas, Alkan, Can, Prüfer, Kay, Meyer, Matthias, Burbano, Hernán A, Good, Jeffrey M, Schultz, Rigo, Aximu-Petri, Ayinuer, Butthof, Anne, Höber, Barbara, Höffner, Barbara, Siegemund, Madlen, Weihmann, Antje, Nusbaum, Chad, Lander, Eric S, Russ, Carsten, Novod, Nathaniel, Affourtit, Jason, Egholm, Michael, Verna, Christine, Rudan, Pavao, Brajkovic, Dejana, Kucan, Željko, Gušic, Ivan, Doronichev, Vladimir B, Golovanova, Liubov V, Lalueza-Fox, Carles, de la Rasilla, Marco, Fortea, Javier, Rosas, Antonio, Schmitz, Ralf W, Johnson, Philip L.F, Eichler, Evan E, Falush, Daniel, Birney, Ewan, Mullikin, James C, Slatkin, Montgomery, Nielsen, Rasmus, Kelso, Janet, Lachmann, Michael, Reich, David, Pääbo, Svante

“…Neandertals, the closest evolutionary relatives of present-day humans, lived in large parts of Europe and western Asia before disappearing 30,000 years ago. We…”
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Assessing the impact of post-mortem damage and contamination on imputation performance in ancient DNA by Garrido Marques, Antonio, Rubinacci, Simone, Malaspinas, Anna-Sapfo, Delaneau, Olivier, Sousa da Mota, Bárbara

“…Low-coverage imputation is becoming ever more present in ancient DNA (aDNA) studies. Imputation pipelines commonly used for present-day genomes have been shown…”
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Imputation of ancient human genomes by Sousa da Mota, Bárbara, Rubinacci, Simone, Cruz Dávalos, Diana Ivette, G. Amorim, Carlos Eduardo, Sikora, Martin, Johannsen, Niels N., Szmyt, Marzena H., Włodarczak, Piotr, Szczepanek, Anita, Przybyła, Marcin M., Schroeder, Hannes, Allentoft, Morten E., Willerslev, Eske, Malaspinas, Anna-Sapfo, Delaneau, Olivier

“…Due to postmortem DNA degradation and microbial colonization, most ancient genomes have low depth of coverage, hindering genotype calling. Genotype imputation…”
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Human bony labyrinth is an indicator of population history and dispersal from Africa by de León, Marcia S. Ponce, Koesbardiati, Toetik, Weissmann, John David, Milella, Marco, Reyna-Blanco, Carlos S., Suwa, Gen, Kondo, Osamu, Malaspinas, Anna-Sapfo, White, Tim D., Zollikofer, Christoph P. E.

“…The dispersal of modern humans from Africa is now well documented with genetic data that track population history, as well as gene flow between populations…”
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Coat Color Variation at the Beginning of Horse Domestication by Ludwig, Arne, Pruvost, Melanie, Reissmann, Monika, Benecke, Norbert, Brockmann, Gudrun A, Castaños, Pedro, Cieslak, Michael, Lippold, Sebastian, Llorente, Laura, Malaspinas, Anna-Sapfo, Slatkin, Montgomery, Hofreiter, Michael

“…The transformation of wild animals into domestic ones available for human nutrition was a key prerequisite for modern human societies. However, no other…”
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Genome-wide ancestry of 17th-century enslaved Africans from the Caribbean by Schroeder, Hannes, Ávila-Arcos, María C., Malaspinas, Anna-Sapfo, Poznik, G. David, Sandoval-Velasco, Marcela, Carpenter, Meredith L., Moreno-Mayar, José Víctor, Sikora, Martin, Johnson, Philip L. F., Allentoft, Morten Erik, Samaniego, José Alfredo, Haviser, Jay B., Dee, Michael W., Stafford, Thomas W., Salas, Antonio, Orlando, Ludovic, Willerslev, Eske, Bustamante, Carlos D., Gilbert, M. Thomas P.

“…Between 1500 and 1850, more than 12 million enslaved Africans were transported to the New World. The vast majority were shipped from West and West-Central…”
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A Complete Neandertal Mitochondrial Genome Sequence Determined by High-Throughput Sequencing by Green, Richard E., Malaspinas, Anna-Sapfo, Krause, Johannes, Briggs, Adrian W., Johnson, Philip L.F., Uhler, Caroline, Meyer, Matthias, Good, Jeffrey M., Maricic, Tomislav, Stenzel, Udo, Prüfer, Kay, Siebauer, Michael, Burbano, Hernán A., Ronan, Michael, Rothberg, Jonathan M., Egholm, Michael, Rudan, Pavao, Brajković, Dejana, Kućan, Željko, Gušić, Ivan, Wikström, Mårten, Laakkonen, Liisa, Kelso, Janet, Slatkin, Montgomery, Pääbo, Svante

“…A complete mitochondrial (mt) genome sequence was reconstructed from a 38,000 year-old Neandertal individual with 8341 mtDNA sequences identified among 4.8 Gb…”
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Influenza virus drug resistance: a time-sampled population genetics perspective by Foll, Matthieu, Poh, Yu-Ping, Renzette, Nicholas, Ferrer-Admetlla, Anna, Bank, Claudia, Shim, Hyunjin, Malaspinas, Anna-Sapfo, Ewing, Gregory, Liu, Ping, Wegmann, Daniel, Caffrey, Daniel R, Zeldovich, Konstantin B, Bolon, Daniel N, Wang, Jennifer P, Kowalik, Timothy F, Schiffer, Celia A, Finberg, Robert W, Jensen, Jeffrey D

“…The challenge of distinguishing genetic drift from selection remains a central focus of population genetics. Time-sampled data may provide a powerful tool for…”
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Mitochondrial genomes reveal an explosive radiation of extinct and extant bears near the Miocene-Pliocene boundary by Krause, Johannes, Unger, Tina, Noçon, Aline, Malaspinas, Anna-Sapfo, Kolokotronis, Sergios-Orestis, Stiller, Mathias, Soibelzon, Leopoldo, Spriggs, Helen, Dear, Paul H, Briggs, Adrian W, Bray, Sarah C E, O'Brien, Stephen J, Rabeder, Gernot, Matheus, Paul, Cooper, Alan, Slatkin, Montgomery, Pääbo, Svante, Hofreiter, Michael

“…Despite being one of the most studied families within the Carnivora, the phylogenetic relationships among the members of the bear family (Ursidae) have long…”
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Proboscidean mitogenomics: chronology and mode of elephant evolution using mastodon as outgroup by Rohland, Nadin, Malaspinas, Anna-Sapfo, Pollack, Joshua L, Slatkin, Montgomery, Matheus, Paul, Hofreiter, Michael

“…We have sequenced the complete mitochondrial genome of the extinct American mastodon (Mammut americanum) from an Alaskan fossil that is between 50,000 and…”
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Inference of natural selection from ancient DNA by Dehasque, Marianne, Ávila‐Arcos, María C., Díez‐del‐Molino, David, Fumagalli, Matteo, Guschanski, Katerina, Lorenzen, Eline D., Malaspinas, Anna‐Sapfo, Marques‐Bonet, Tomas, Martin, Michael D., Murray, Gemma G. R., Papadopulos, Alexander S. T., Therkildsen, Nina Overgaard, Wegmann, Daniel, Dalén, Love, Foote, Andrew D.

“…Evolutionary processes, including selection, can be indirectly inferred based on patterns of genomic variation among contemporary populations or species…”
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bammds: a tool for assessing the ancestry of low-depth whole-genome data using multidimensional scaling (MDS) by Malaspinas, Anna-Sapfo, Tange, Ole, Moreno-Mayar, José Víctor, Rasmussen, Morten, DeGiorgio, Michael, Wang, Yong, Valdiosera, Cristina E, Politis, Gustavo, Willerslev, Eske, Nielsen, Rasmus

“…We present bammds, a practical tool that allows visualization of samples sequenced by second-generation sequencing when compared with a reference panel of…”
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In-solution Y-chromosome capture-enrichment on ancient DNA libraries by Cruz-Dávalos, Diana I, Nieves-Colón, María A, Sockell, Alexandra, Poznik, G David, Schroeder, Hannes, Stone, Anne C, Bustamante, Carlos D, Malaspinas, Anna-Sapfo, Ávila-Arcos, María C

“…As most ancient biological samples have low levels of endogenous DNA, it is advantageous to enrich for specific genomic regions prior to sequencing. One…”
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Comparative performance of two whole‐genome capture methodologies on ancient DNA Illumina libraries by Ávila‐Arcos, María C., Sandoval‐Velasco, Marcela, Schroeder, Hannes, Carpenter, Meredith L., Malaspinas, Anna‐Sapfo, Wales, Nathan, Peñaloza, Fernando, Bustamante, Carlos D., Gilbert, M. Thomas P., Bunce, Michael

“…Summary Application of whole‐genome capture (WGC) methods to ancient DNA (aDNA) promises to increase efficiency of ancient genome sequencing. We compared the…”
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Identification of Polynesian mtDNA haplogroups in remains of Botocudo Amerindians from Brazil by Gonçalves, Vanessa Faria, Stenderup, Jesper, Rodrigues-Carvalho, Cláudia, Silva, Hilton P., Gonçalves-Dornelas, Higgor, Líryo, Andersen, Kivisild, Toomas, Malaspinas, Anna-Sapfo, Campos, Paula F., Rasmussen, Morten, Willerslev, Eske, Pena, Sergio Danilo J.

“…There is a consensus that modern humans arrived in the Americas 15,000–20,000 y ago during the Late Pleistocene, most probably from northeast Asia through…”
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Decline of genetic diversity in ancient domestic stallions in Europe by Wutke, Saskia, Sandoval-Castellanos, Edson, Benecke, Norbert, Döhle, Hans-Jürgen, Friederich, Susanne, Gonzalez, Javier, Hofreiter, Michael, Lõugas, Lembi, Magnell, Ola, Malaspinas, Anna-Sapfo, Morales-Muñiz, Arturo, Orlando, Ludovic, Reissmann, Monika, Trinks, Alexandra, Ludwig, Arne

“…Present-day domestic horses are immensely diverse in their maternally inherited mitochondrial DNA, yet they show very little variation on their paternally…”
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Ancient nuclear genomes enable repatriation of Indigenous human remains by Wright, Joanne L, Wasef, Sally, Heupink, Tim H, Westaway, Michael C, Rasmussen, Simon, Pardoe, Colin, Fourmile, Gudju Gudju, Young, Michael, Johnson, Trish, Slade, Joan, Kennedy, Roy, Winch, Patsy, Pappin, Sr, Mary, Wales, Tapij, Bates, William Badger, Hamilton, Sharnie, Whyman, Neville, van Holst Pellekaan, Sheila, McAllister, Peter J, Taçon, Paul S C, Curnoe, Darren, Li, Ruiqiang, Millar, Craig, Subramanian, Sankar, Willerslev, Eske, Malaspinas, Anna-Sapfo, Sikora, Martin, Lambert, David M

“…After European colonization, the ancestral remains of Indigenous people were often collected for scientific research or display in museum collections. For many…”
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Estimating allele age and selection coefficient from time-serial data by Malaspinas, Anna-Sapfo, Malaspinas, Orestis, Evans, Steven N, Slatkin, Montgomery

“…Recent advances in sequencing technologies have made available an ever-increasing amount of ancient genomic data. In particular, it is now possible to target…”
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