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1. Distinct variants at LIN28B influence growth in height from birth to adulthood

Author

Widen, Elisabeth, Ripatti, Samuli, Cousminer, Diana L., Surakka, Ida, Lappalainen, Tuuli, Jarvelin, Marjo-Riitta, Eriksson, Johan G., Raitakari, Olli, Salomaa, Veikko, Sovio, Ulla, Hartikainen, Anna-Liisa, Pouta, Anneli, McCarthy, Mark I., Osmond, Clive, Kajantie, Eero, Lehtimaki, Terho, Viikari, Jorma, Kahonen, Mika, Tyler-Smith, Chris, Freimer, Nelson, Hirschhorn, Joel N., Peltonen, Leena, and Palotie, Aarno

Subjects
Human growth -- Research, Stature -- Genetic aspects, Genetic regulation -- Analysis, Human population genetics -- Research, Biological sciences
Abstract

A unique resource of longitudinal childhood height data available in Finnish population cohorts was used to study the largely unknown genetic underpinnings of height growth. The partially correlated variants at LIN28B which influence the entire period of postnatal growth implied a critical role for LIN28B in the regulation of human growth.

Published
2010

2. Origins and functional impact of copy number variation in the human genome

Author

Conrad, Donald F., Pinto, Dalila, Redon, Richard, Feuk, Lars, Gokcumen, Omer, Zhang, Yujun, Aerts, Jan, Andrews, T. Daniel, Barnes, Chris, Campbell, Peter, Fitzgerald, Tomas, Hu, Min, Ihm, Chun Hwa, Kristiansson, Kati, MacArthur, Daniel G., MacDonald, Jeffrey R., Onyiah, Ifejinelo, Pang, Andy Wing Chun, Robson, Sam, Stirrups, Kathy, Valsesia, Armand, Walter, Klaudia, Wei, John, Tyler-Smith, Chris, Carter, Nigel P., Lee, Charles, Scherer, Stephen W., and Hurles, Matthew E.

Subjects
Genetic variation -- Research, Human genome -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Structural variations of DNA greater than 1 kilobase in size account for most bases that vary among human genomes, but are still relatively under-ascertained. Here we use tiling oligonucleotide microarrays, comprising 42 million probes, to generate a comprehensive map of 11,700 copy number variations (CNVs) greater than 443 base pairs, of which most (8,599) have been validated independently. For 4,978 of these CNVs, we generated reference genotypes from 450 individuals of European, African or East Asian ancestry. The predominant mutational mechanisms differ among CNV size classes. Retrotransposition has duplicated and inserted some coding and non-coding DNA segments randomly around the genome. Furthermore, by correlation with known trait-associated single nucleotide polymorphisms (SNPs), we identified 30 loci with CNVs that are candidates for influencing disease susceptibility. Despite this, having assessed the completeness of our map and the patterns of linkage disequilibrium between CNVs and SNPs, we conclude that, for complex traits, the heritability void left by genome-wide association studies will not be accounted for by common CNVs., Genomes vary from one another in multifarious ways, and the totality of this genetic variation underpins the heritability of human traits. Over the past two years, the human reference sequence [...]

Published
2010
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3. Population differentiation as an indicator of recent positive selection in humans: an empirical evaluation

Author

Yali Xue, Xuelong Zhang, Huang, Ni, Daly, Allan, Gillson, Christopher J., MacArthur, Daniel G., Yngvadottir, Bryndis, Nica, Alexandra C., Woodwark, Cara, Yuan Chen, Conrad, Donald F., Ayub, Qasim, Mehdi, S. Qasim, Pu Li, and Tyler-Smith, Chris

Subjects
Gene mutations -- Research, Genetic polymorphisms -- Research, Mass spectrometry -- Usage, Population genetics -- Research, Biological sciences
Abstract

We have evaluated the extent to which SNPs identified by genomewide surveys as showing unusually high levels of population differentiation in humans have experienced recent positive selection, starting from a set of 32 nonsynonymous SNPs in 27 genes highlighted by the HapMap1 project. These SNPs were genotyped again in the HapMap samples and in the Human Genome Diversity Project-Centre d'Etude du Polymorphisme Humain (HGDP-CEPH) panel of 52 populations representing worldwide diversity; extended haplotype homozygosity was investigated around all of them, and full resequence data were examined for 9 genes (5 from public sources and 4 from new data sets). For 7 of the genes, genotyping errors were responsible for an artifactual signal of high population differentiation and for 2, the population differentiation did not exceed our significance threshold. For the 18 genes with confirmed high population differentiation, 3 showed evidence of positive selection as measured by unusually extended haplotypes within a population, and 7 more did in between-population analyses. The 9 genes with resequence data included 7 with high population differentiation, and 5 showed evidence of positive selection on the haplotype carrying the nonsynonymous SNP from skewed allele frequency spectra; in addition, 2 showed evidence of positive selection on unrelated haplotypes. Thus, in humans, high population differentiation is (apart from technical artifacts) an effective way of enriching for recently selected genes, but is not an infallible pointer to recent positive selection supported by other lines of evidence.

Published
2009

4. A genome-wide survey of the prevalence and evolutionary forces acting on human nonsense SNPs

Author

Yngvadottir, Bryndis, Yali Xue, Searle, Steve, Hunt, Sarah, Delgado, Marcos, Morrison, Jonathan, Whittaker, Pamela, Deloukas, Panos, and Tyler-Smith, Chris

Subjects
Single nucleotide polymorphisms -- Research, Human genome -- Research, Evolution -- Research, Population genetics -- Research, Biological sciences
Abstract

A large-scale genome-wide survey of the nonsense SNPs is carried out to examine the prevalence and the various evolutionary forces acting on them in the human genome. These nonsense SNPs are proved to be slightly disadvantageous over the evolutionary timescales.

Published
2009

5. Maximum-likelihood estimation of site-specific mutation rates in human mitochondrial DNA from partial phylogenetic classification

Author

Rosset, Saharon, Wells, R. Spencer, Soria-Hernanz, David F., Tyler-Smith, Chris, Royyuru, Ajay K., and Behar, Doron M.

Subjects
Maximum likelihood estimates (Statistics) -- Methods, Gene mutations -- Identification and classification, Cladistic analysis -- Methods, Mitochondrial DNA -- Properties, Biological sciences
Abstract

The mitochondrial DNA hypervariable segment I (HVS-I) is widely used in studies of human evolutionary genetics, and therefore accurate estimates of mutation rates among nucleotide sites in this region are essential. We have developed a novel maximum-likelihood methodology for estimating site-specific mutation rates from partial phylogenetic information, such as haplogroup association. The resulting estimation problem is a generalized linear model, with a nonstandard link function. We develop inference and bias correction tools for our estimates and a hypothesis-testing approach for site independence. We demonstrate our methodology using 16,609 HVS-I samples from the Genographic Project. Our results suggest that mutation rates among nucleotide sites in HVS-I are highly variable. The 16,400-16,500 region exhibits significantly lower rates compared to other regions, suggesting potential functional constraints. Several loci identified in the literature as possible termination-associated sequences (TAS) do not yield statistically slower rates than the rest of HVS-I, casting doubt on their functional importance. Our tests do not reject the null hypothesis of independent mutation rates among nucleotide sites, supporting the use of site-independence assumption for analyzing HVS-I. Potential extensions of our methodology include its application to estimation of mutation rates in other genetic regions, like Y chromosome short tandem repeats.

Published
2008

6. Adaptive evolution of UGT2B17 copy-number variation

Author

Yali Xue, Tyler-Smith, Chris, Donglin Sun, Daly, Allan, Fengtang Yang, Mengyao Zhao, Xue Zhou, Ni Huang, Zerjal, Tatiana, Lee, Charles, Carter, Nigel P., and Hurles, Matthew E.

Subjects
Adaptation (Biology) -- Analysis, Biological diversity -- Analysis, Biological sciences
Abstract

Several technical analyses are conducted to explain the biological significance and the adaptative evolution of the UGT2B17 copy-number variation (CNV) in humans, which varies from zero to two per individual. The observed diversity in the observed CNV is shown to be low in East Asia.

Published
2008

7. The dawn of human matrilineal diversity

Author

Behar, Doron M., Villems, Richard, Soodyall, Himla, Blue-Smith, Jason, Pereira, Luisa, Metspalu, Ene, Scozzari, Rosaria, Makkan, Heeran, Tzur, Shay, Comas, David, Bertranpetit, Jaume, Quintana-Murci, Lluis, Tyler-Smith, Chris, Wells, R. Spencer, and Rosset, Saharon

Subjects
Cladistic analysis -- Usage, Human genetics -- Research, Mitochondrial DNA -- Research, Population genetics -- Research, Biological sciences
Abstract

A matrilineal tree is developed and used to study the diversity and the structure of the mitochondrial DNA phylogeny at dawn of Homo sapiens. The early settlement of humans in Africa was shown to be matrilineally structured with small and separately evolving isolated populations.

Published
2008

8. Y-chromosomal diversity in Lebanon is structured by recent historical events

Author

Zalloua, Pierre A., Yali Xue, Khalife, Jade, Makhoul, Nadine, Debiane, Labib, Platt, Daniel E., Royyuru, Ajay K., Herrera, Rene J., Hernaz, David F. Soria, Blue-Smith, Jason, Wells, R. Spencer, Comas, David, Bertranpetit, Jaume, and Tyler-Smith, Chris

Subjects
Y chromosome -- Research, Population genetics -- Research, Human genome -- History, Human genome -- Research, Biological sciences
Abstract

The influence of various historical events and religion on the observed Y-chromosomal diversity and other current patrilienal variations are explained. The Islamic and Crusader activities in the country were found to be the reason behind the invasion of the Arabian and European lineages among its people.

Published
2008

9. Relative impact of nucleotide and copy number variation on gene expression phenotypes

Author

Stranger, Barbara E., Forrest, Matthew S., Dunning, Mark, Ingle, Catherine E., Beazley, Claude, Thorne, Natalie, Redon, Richard, Bird, Christine P., de Grassi, Anna, Lee, Charles, Tyler-Smith, Chris, Carter, Nigel, Scherer, Stephen W., Tavare, Simon, Deloukas, Panagiotis, Hurles, Matthew E., and Dermitzakis, Emmanouil T.

Subjects
Genetic regulation -- Analysis, Nucleotides -- Analysis, Nucleotides -- Research, Gene expression -- Research, Genetic research -- Reports, Genetic variation -- Research, Genetic variation -- Identification and classification, Single nucleotide polymorphisms -- Research
Published
2007

10. Global variation in copy number in the human genome

Author

Redon, Richard, Ishikawa, Shumpei, Fitch, Karen R., Feuk, Lars, Perry, George H., Andrews, T. Daniel, Fiegler, Heike, Shapero, Michael H., Carson, Andrew R., Chen, Wenwei, Cho, Eun Kyung, Dallaire, Stephanie, Freeman, Jennifer L., Gonzalez, Juan R., Gratacos, Monica, Huang, Jing, Kalaitzopoulos, Dimitrios, Komura, Daisuke, MacDonald, Jeffrey R., Marshall, Christian R., Mei, Rui, Montgomery, Lyndal, Nishimura, Kunihiro, Okamura, Kohji, Shen, Fan, Somerville, Martin J., Tchinda, Joelle, Valsesia, Armand, Woodwark, Cara, Yang, Fengtang, Zhang, Junjun, Zerjal, Tatiana, Zhang, Jane, Armengol, Lluis, Conrad, Donald F., Estivill, Xavier, Tyler-Smith, Chris, Carter, Nigel P., Aburatani, Hiroyuki, Lee, Charles, Jones, Keith W., Scherer, Stephen W., and Hurles, Matthew E.

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Richard Redon [1]; Shumpei Ishikawa [2, 3]; Karen R. Fitch [4]; Lars Feuk [5, 6]; George H. Perry [7]; T. Daniel Andrews [1]; Heike Fiegler [1]; Michael H. Shapero [...]

Published
2006
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11. Nepalese populations show no association between the distribution of malaria and protective alleles

Author

Caetano, Catia P., Kraaijenbrink, Thirsa, Tuladhar, Nirmal M., van Driem, George L., de Knijff, Peter, Tyler-Smith, Chris, and Carvalho-Silva, Denise R.

Subjects
Nepal -- Health aspects, Malaria -- Genetic aspects, Single nucleotide polymorphisms -- Research, Genetic susceptibility, Biological sciences
Abstract

ABSTRACT Malaria is perhaps the most important parasitic infection and strongest known force for selection in the recent evolutionary history of the human genome. Genetically-determined resistance to malaria has been [...]

Published
2006

12. Hotspots for copy number variation in chimpanzees and humans

Author

Perry, George H., Tchinda, Joelle, McGrath, Sean D., Zhang, Junjun, Picker, Simon R., Caceres, Angela M., Iafrate, A. John, Tyler-Smith, Chris, Scherer, Stephen W., Eichler, Evan E., Stone, Anne C., and Lee, Charles

Subjects
Chimpanzees -- Research, Human evolution -- Research, Genomics -- Research, Science and technology
Abstract

Copy number variation is surprisingly common among humans and can be involved in phenotypic diversity and variable susceptibility to complex diseases, but little is known of the extent of copy number variation in nonhuman primates. We have used two array-based comparative genomic hybridization platforms to identify a total of 355 copy number variants (CNVs) in the genomes of 20 wild-born chimpanzees (Pan troglodytes) and have compared the identified chimpanzee CNVs to known human CNVs from previous studies. Many CNVs were observed in the corresponding regions in both chimpanzees and humans; especially those CNVs of higher frequency. Strikingly, these loci are enriched 20-fold for ancestral segmental duplications, which may facilitate CNV formation through nonallelic homologous recombination mechanisms. Therefore, some of these regions may be unstable 'hotspots' for the genesis of copy number variation, with recurrent duplications and deletions occurring across and within species. chimpanzee genome | human evolution | structural genomic variation

Published
2006

13. Male demography in East Asia:a North-South contrast in human population expansion times

Author

Xue, Yali, Zerjal, Tatiana, Bao, Weidong, Zhu, Suling, Shu, Qunfang, Xu, Jiujin, Du, Ruofu, Fu, Songbin, Li, Pu, Hurles, Matthew E., Yang, Huanming, and Tyler-Smith, Chris

Subjects
Demographic surveys -- Analysis, Population -- Growth, Population -- Analysis, Biological sciences
Abstract

The human population has increased greatly in size in the last 100,000 years, but the initial stimuli to growth, the times when expansion started, and their variation between different parts of the world are poorly understood. We have investigated male demography in East Asia, applying a Bayesian full-likelihood analysis to data from 988 men representing 27 populations from China, Mongolia, Korea, and Japan typed with 45 binary and 16 STR markers from the Y chromosome. According to our analysis, the northern populations examined all started to expand in number between 34 (18-68) and 22 (12-39) thousand years ago (KYA), before the last glacial maximum at 21-18 KYA, while the southern populations all started to expand between 18 (6-47) and 12 (1-45) KYA, but then grew faster. We suggest that the northern populations expanded earlier because they could exploit the abundant megafauna of the 'Mammoth Steppe,' while the southern populations could increase in number only when a warmer and more stable climate led to more plentiful plant resources such as tubers.

Published
2006

15. Recent spread of a Y-chromosomal lineage in northern China and Mongolia

Author

Xue, Yali, Zerjal, Tatiana, Bao, Weidong, Zhu, Suling, Lim, Si-Keun, Shu, Qunfang, Xu, Jiujin, Du, Roufu, Fu, Songbin, Li, Pu, Yang, Huanming, and Tyler-Smith, Chris

Subjects
Human beings -- Genetic aspects, Man -- Genetic aspects, Human chromosome abnormalities -- Research, Biological sciences
Published
2005

17. A predominantly Neolithic origin for Y-chromosomal DNA variation in North Africa

Author

Arredi, Barbara, Poloni, Estella S., Paracchini, Silvia, Zerjal, Tatiana, Fathallah, Dahmani M., Makrelouf, Mohamed, Pascali, Vincenzo L., Novelletto, Andrea, and Tyler-Smith, Chris

Subjects
Northern Africa -- Research, Northern Africa -- Reports, Y chromosome -- Research, Y chromosome -- Varieties, Genetic variation -- Research, DNA testing, Biological sciences
Published
2004

18. A comprehensive survey of human Y-chromosomal microsatellites

Author

Kayser, Manfred, Kittler, Ralf, Erler, Axel, Hedman, Minttu, Lee, Andrew C., Mohyuddin, Aisha, Mehdi, S. Qasim, Rosser, Zoe, Stoneking, Mark, Jobling, Mark A., Sajantila, Antti, and Tyler-Smith, Chris

Subjects
Human genetics -- Research, Biological sciences
Published
2004

19. Where west meets east: the complex mtDNA landscape of the Southwest and Central Asian corridor

Author

Quintana-Murci, Lluis, Chaix, Raphaelle, Wells, R. Spencer, Behar, Doron M., Sayar, Hamid, Scozzari, Rosaria, Rengo, Chiara, Al-Zahery, Nadia, Semino, Ornella, Santachiara-Benerecetti, A. Silvana, Coppa, Alfredo, Ayub, Qasim, Mohyuddin, Aisha, Tyler-Smith, Chris, Mehdi, S. Qasim, Torroni, Antonio, and McElreavey, Ken

Subjects
Human genetics -- Research, Elamites, Biological sciences
Published
2004

20. The genetic legacy of the Mongols. (Report)

Author

Zerjal, Tatiana, Xue, Yali, Bertorelle, Giorgio, Wells, R. Spencer, Bao, Weidong, Zhu, Suling, Qamar, Raheel, Ayub, Qasim, Mohyuddin, Aisha, Fu, Songbin, Li, Pu, Yuldasheva, Nadira, Ruzibakiev, Ruslan, Xu, Jiujin, Shu, Qunfang, Du, Ruofu, Yang, Huanming, Hurles, Matthew E., Robinson, Elizabeth, Gerelsaikhan, Tudevdagva, Dashnyam, Bumbein, Mehdi, S. Qasim, and Tyler-Smith, Chris

Subjects
Mongols -- Genetic aspects, Natural selection -- Case studies, Natural selection -- Genetic aspects, Genetic research, Biological sciences
Published
2003

22. Y-chromosomal DNA variation in Pakistan

Author

Qamar, Raheel, Ayub, Qasim, Mohyuddin, Aisha, Helgason, Agnar, Mazhar, Kehkashan, Mansoor, Atika, Zerjal, Tatiana, Tyler-Smith, Chris, and Mehdi, S. Qasim

Subjects
Pakistanis -- Physiological aspects, Genetic research -- Analysis, Y chromosome -- Research, Chromosome replication -- Demographic aspects, Biological sciences
Published
2002

23. Recent Male-Mediated Gene Flow over a Linguistic Barrier in Iberia, Suggested by Analysis of a Y-Chromosomal DNA Polymorphism

Author

Hurles, Matthew E., Veitia, Reiner, Arroyo, Eduardo, Armenteros, Manuel, Bertranpetit, Jaume, Perez-Lezaun, Anna, Bosch, Elena, Shlumukova, Maria, Cambon-Thomsen, Anne, McElreavey, Ken, Lopez de Munain, Adolfo, Rohl, Arne, Wilson, Ian J., Singh, Lalji, Pandya, Arpita, Santos, Fabricio R., Tyler-Smith, Chris, and Jobling, Mark A.

Subjects
Iberian Peninsula -- Health aspects, Genetic polymorphisms -- Demographic aspects, Biological sciences
Published
1999

24. Transmission of a fully functional human neocentromere through three generations

Author

Tyler-Smith, Chris, Gimelli, Giorgio, Giglio, Sabrina, Floridia, Giovanna, Pandya, Arpita, Terzoli, Gianluigi, Warburton, Peter E., Earnshaw, William C., and Zuffardi, Orsetta

Subjects
DNA -- Research, Chromosome replication -- Research, Meiosis -- Research, Genetic research -- Research, Evolution -- Genetic aspects, Biological sciences
Abstract

A fully functional human neocentromere has been transmitted through three generations. Neocentromeres can be normally transmitted at meiosis. An unusual Y chromosome with a primary constriction inside the long-arm heterochromatin was discovered in amniocytes of a woman aged 38. Since it was also found in her husband and brother-in-law, it was present in the father. The Y chromosome seems to have been deleted for part of the alphoid DNA, likely silencing the normal centromere. Neocentromere activation might have taken place first and brought on inactivation of the normal centromere through partial deletion.

Published
1999

25. The central Siberian origin for Native American Y chromosomes

Author

Santos, Fabricio R., Pandya, Arpita, Tyler-Smith, Chris, Pena, Sergio D.J., Schanfield, Moses, Leonard, William R., Osipova, Ludmila, Crawford, Michael H., and Mitchell, R. John

Subjects
Siberia -- Emigration and immigration, North America -- Emigration and immigration, South America -- Emigration and immigration, Eurasia -- Emigration and immigration, Chromosome mapping -- Usage, Native Americans -- Genetic aspects, Caucasian race -- Genetic aspects, Human beings -- Migrations, Biological sciences
Abstract

Y chromosomal DNA polymorphisms have been used to study Pleistocene migrations to the American continent. In a sample of 306 men from all over the world, 32 haplotypes were established with the variations from 30 distinct polymorphic sites. The major Y haplotype in most Native Americans was followed back to recent ancestors common with Siberians, the Altaians and Kets from the Altai Mountains and the Yenissey River Basin, respectively, and then back to the next common ancestor. That one gave rise to Caucasoid Y chromosomes, likely from central Eurasia. The study indicates a mainly central Siberian origin for Native American paternal lineages for those who might have migrated to the Americas in the Upper Pleistocene.

Published
1999

26. Genomic analyses inform on migration events during the peopling of Eurasia

Author

Pagani, Luca, Lawson, Daniel John, Jagoda, Evelyn, Mrseburg, Alexander, Eriksson, Anders, Mitt, Mario, Clemente, Florian, Hudjashov, Georgi, DeGiorgio, Michael, Saag, Lauri, Wall, Jeffrey D., Cardona, Alexia, Mgi, Reedik, Sayres, Melissa A. Wilson, Kaewert, Sarah, Inchley, Charlotte, Scheib, Christiana L., Jrve, Mari, Karmin, Monika, Jacobs, Guy S., Antao, Tiago, Iliescu, Florin Mircea, Kushniarevich, Alena, Ayub, Qasim, Tyler-Smith, Chris, Xue, Yali, Yunusbayev, Bayazit, Tambets, Kristiina, Mallick, Chandana Basu, Saag, Lehti, Pocheshkhova, Elvira, Andriadze, George, Muller, Craig, Westaway, Michael C., Lambert, David M., Zoraqi, Grigor, Turdikulova, Shahlo, Dalimova, Dilbar, Sabitov, Zhaxylyk, Sultana, Gazi Nurun Nahar, Lachance, Joseph, Tishkoff, Sarah, Momynaliev, Kuvat, Isakova, Jainagul, Damba, Larisa D., Gubina, Marina, Nymadawa, Pagbajabyn, Evseeva, Irina, Atramentova, Lubov, Utevska, Olga, Ricaut, Franois-Xavier, Brucato, Nicolas, Sudoyo, Herawati, Letellier, Thierry, Cox, Murray P., Barashkov, Nikolay A., karo, Vedrana, Mulahasanovic, Lejla, Primorac, Dragan, Sahakyan, Hovhannes, Mormina, Maru, Eichstaedt, Christina A., Lichman, Daria V., Abdullah, Syafiq, Chaubey, Gyaneshwer, Wee, Joseph T. S., Mihailov, Evelin, Karunas, Alexandra, Litvinov, Sergei, Khusainova, Rita, Ekomasova, Natalya, Akhmetova, Vita, Khidiyatova, Irina, Marjanovi, Damir, Yepiskoposyan, Levon, Behar, Doron M., Balanovska, Elena, Metspalu, Andres, Derenko, Miroslava, Malyarchuk, Boris, Voevoda, Mikhail, Fedorova, Sardana A., Osipova, Ludmila P., Lahr, Marta Mirazn, Gerbault, Pascale, Leavesley, Matthew, Migliano, Andrea Bamberg, Petraglia, Michael, Balanovsky, Oleg, Khusnutdinova, Elza K., Metspalu, Ene, Thomas, Mark G., Manica, Andrea, Nielsen, Rasmus, Villems, Richard, Willerslev, Eske, Kivisild, Toomas, and Metspalu, Mait

Subjects
DNA sequencing -- Methods, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Luca Pagani (corresponding author) [1, 2, 3]; Daniel John Lawson [4]; Evelyn Jagoda [2, 5]; Alexander Mrseburg [2]; Anders Eriksson [6, 7]; Mario Mitt [8, 9]; Florian Clemente [2, [...]

Published
2016
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27. A genomic history of Aboriginal Australia

Author

Malaspinas, Anna-Sapfo, Westaway, Michael C., Muller, Craig, Sousa, Vitor C., Lao, Oscar, Alves, Isabel, Bergstrm, Anders, Athanasiadis, Georgios, Cheng, Jade Y., Crawford, Jacob E., Heupink, Tim H., Macholdt, Enrico, Peischl, Stephan, Rasmussen, Simon, Schiffels, Stephan, Subramanian, Sankar, Wright, Joanne L., Albrechtsen, Anders, Barbieri, Chiara, Dupanloup, Isabelle, Eriksson, Anders, Margaryan, Ashot, Moltke, Ida, Pugach, Irina, Korneliussen, Thorfinn S., Levkivskyi, Ivan P., Moreno-Mayar, J. Vctor, Ni, Shengyu, Racimo, Fernando, Sikora, Martin, Xue, Yali, Aghakhanian, Farhang A., Brucato, Nicolas, Brunak, Sren, Campos, Paula F., Clark, Warren, Ellingvg, Sturla, Fourmile, Gudjugudju, Gerbault, Pascale, Injie, Darren, Koki, George, Leavesley, Matthew, Logan, Betty, Lynch, Aubrey, Matisoo-Smith, Elizabeth A., McAllister, Peter J., Mentzer, Alexander J., Metspalu, Mait, Migliano, Andrea B., Murgha, Les, Phipps, Maude E., Pomat, William, Reynolds, Doc, Ricaut, Francois-Xavier, Siba, Peter, Thomas, Mark G., Wales, Thomas, Wall, Colleen Marun, Oppenheimer, Stephen J., Tyler-Smith, Chris, Durbin, Richard, Dortch, Joe, Manica, Andrea, Schierup, Mikkel H., Foley, Robert A., Lahr, Marta Mirazn, Bowern, Claire, Wall, Jeffrey D., Mailund, Thomas, Stoneking, Mark, Nielsen, Rasmus, Sandhu, Manjinder S., Excoffier, Laurent, Lambert, David M., and Willerslev, Eske

Subjects
Genetic research, Human genome -- Research, Aboriginal Australians -- Genetic aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

The population history of Aboriginal Australians remains largely uncharacterized. Here we generate high-coverage genomes for 83 Aboriginal Australians (speakers of PamaNyungan languages) and 25 Papuans from the New Guinea Highlands. We find that Papuan and Aboriginal Australian ancestors diversified 2540 thousand years ago (kya), suggesting pre-Holocene population structure in the ancient continent of Sahul (Australia, New Guinea and Tasmania). However, all of the studied Aboriginal Australians descend from a single founding population that differentiated 1032 kya. We infer a population expansion in northeast Australia during the Holocene epoch (past 10,000 years) associated with limited gene flow from this region to the rest of Australia, consistent with the spread of the PamaNyungan languages. We estimate that Aboriginal Australians and Papuans diverged from Eurasians 5172 kya, following a single out-of-Africa dispersal, and subsequently admixed with archaic populations. Finally, we report evidence of selection in Aboriginal Australians potentially associated with living in the desert., Author(s): Anna-Sapfo Malaspinas [1, 2, 3]; Michael C. Westaway [4]; Craig Muller [1]; Vitor C. Sousa [2, 3]; Oscar Lao [5, 6]; Isabel Alves [2, 3, 7]; Anders Bergstrm [8]; [...]

Published
2016
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28. The Simons Genome Diversity Project: 300 genomes from 142 diverse populations

Author

Mallick, Swapan, Li, Heng, Lipson, Mark, Mathieson, Iain, Gymrek, Melissa, Racimo, Fernando, Zhao, Mengyao, Chennagiri, Niru, Nordenfelt, Susanne, Tandon, Arti, Skoglund, Pontus, Lazaridis, Iosif, Sankararaman, Sriram, Fu, Qiaomei, Rohland, Nadin, Renaud, Gabriel, Erlich, Yaniv, Willems, Thomas, Gallo, Carla, Spence, Jeffrey P., Song, Yun S., Poletti, Giovanni, Balloux, Francois, van Driem, George, de Knijff, Peter, Romero, Irene Gallego, Jha, Aashish R., Behar, Doron M., Bravi, Claudio M., Capelli, Cristian, Hervig, Tor, Moreno-Estrada, Andres, Posukh, Olga L., Balanovska, Elena, Balanovsky, Oleg, Karachanak-Yankova, Sena, Sahakyan, Hovhannes, Toncheva, Draga, Yepiskoposyan, Levon, Tyler-Smith, Chris, Xue, Yali, Abdullah, M. Syafiq, Ruiz-Linares, Andres, Beall, Cynthia M., Di Rienzo, Anna, Jeong, Choongwon, Starikovskaya, Elena B., Metspalu, Ene, Parik, Jri, Villems, Richard, Henn, Brenna M., Hodoglugil, Ugur, Mahley, Robert, Sajantila, Antti, Stamatoyannopoulos, George, Wee, Joseph T. S., Khusainova, Rita, Khusnutdinova, Elza, Litvinov, Sergey, Ayodo, George, Comas, David, Hammer, Michael F., Kivisild, Toomas, Klitz, William, Winkler, Cheryl A., Labuda, Damian, Bamshad, Michael, Jorde, Lynn B., Tishkoff, Sarah A., Watkins, W. Scott, Metspalu, Mait, Dryomov, Stanislav, Sukernik, Rem, Singh, Lalji, Thangaraj, Kumarasamy, Pbo, Svante, Kelso, Janet, Patterson, Nick, and Reich, David

Subjects
Biodiversity -- Research, Genetic research, Genomes -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Here we report the Simons Genome Diversity Project data set: high quality genomes from 300 individuals from 142 diverse populations. These genomes include at least 5.8 million base pairs that are not present in the human reference genome. Our analysis reveals key features of the landscape of human genome variation, including that the rate of accumulation of mutations has accelerated by about 5% in non-Africans compared to Africans since divergence. We show that the ancestors of some pairs of present-day human populations were substantially separated by 100,000 years ago, well before the archaeologically attested onset of behavioural modernity. We also demonstrate that indigenous Australians, New Guineans and Andamanese do not derive substantial ancestry from an early dispersal of modern humans; instead, their modern human ancestry is consistent with coming from the same source as that of other non-Africans., Author(s): Swapan Mallick (corresponding author) [1, 2, 3]; Heng Li [2]; Mark Lipson [1]; Iain Mathieson [1]; Melissa Gymrek [2, 4, 5, 6]; Fernando Racimo [7]; Mengyao Zhao [1, 2, [...]

Published
2016
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29. Network analyses of Y-chromosomal types in Europe, Northern Africa, and Western Asia reveal specific patterns of geographic distribution

Author

Malaspina, Patrizia, Cruciani, Fulvio, Ciminelli, Bianca Maria, Terrenato, Luciano, Santolamazza, Piero, Alonso, Antonio, Banyko, Juraj, Brdicka, Radim, Garcia, Oscar, Gaudiano, Carlo, Guanti, Ginevra, Kidd, Kenneth K., Lavinha, Joao, Avila, Madalena, Mandich, Paola, Moral, Pedro, Qamar, Raheel, Mehdi, Syed Q., Ragusa, Angela, Stefanescu, Gheorghe, Caraghin, Maria, Tyler-Smith, Chris, Scozzari, Rosaria, and Novelletto, Andrea

Subjects
Human population genetics -- Research, Y chromosome -- Demographic aspects, Human geography -- Network analysis, Biological sciences
Abstract

Common descent followed by molecular radiation accounts for most of the phenetic relationships among haplotypes in four Y-linked dinucleotide microsatellites among 908 men from Europe, northern Africa, and western Asia. Six large networks and two small ones emerged. The complete diversity within a sample can be partitioned using this technique. A low level of homoplasy is found among dinucleotide microsatellite haplotypes. Populations are highly structured in terms of Y-chromosomal network frequencies.

Published
1998

30. Forensic genetic analysis of mitochondrial DNA hypervariable region I/II sequences: An expanded Korean population database.

Author

Jin, Han Jun, Kwak, Kyoung Don, Hong, Seung Bum, Shin, Dong Jik, Han, Myun Soo, Tyler-Smith, Chris, and Kim, Wook

Subjects
Forensic genetics -- Research -- Analysis, Haplotypes -- Research -- Analysis, Human population genetics -- Research -- Analysis, Mitochondrial DNA -- Analysis -- Research
Abstract

Abstract We have analyzed variation of the mitochondrial DNA (mtDNA) hypervariable segments I and II (HVS-I and HVS-II) in 185 randomly chosen individuals from Korea to provide an expanded and [...]

Published
2006

31. DNA Commission of the International Society of Forensic Genetics (ISFG): an update of the recommendations on the use of Y-STRs in forensic analysis.

Author

Gusmao, L., Butler, J.M., Carracedo, A., Gill, P., Kayser, M., Mayr, W.R., Morling, Niels, Prinz, M., Roewer, L., Tyler-Smith, Chris, and Schneider, Peter M.

Subjects
Mutation (Biology) -- Analysis -- Usage, Human population genetics -- Usage -- Analysis, Y chromosome -- Analysis -- Usage
Abstract

Abstract The DNA Commission of the International Society of Forensic Genetics (ISFG) regularly publishes guidelines and recommendations concerning the application of DNA polymorphisms to the problems of human identification. A [...]

Published
2006

32. Dodeca satellite: a conserved G+C-rich satellite from the centromeric heterochromatin of Drosophila melanogaster

Author

Abad, Jose P., Carmena, Mar, Baars, Sigrid, Saunders, Robert D.C., Glover, David M., Ludena, Paloma, Sentis, Carlos, Tyler-Smith, Chris, and Villasante, Alfredo

Subjects
Drosophila -- Genetic aspects, Satellite DNA -- Research, Chromatin -- Analysis, Centromeres -- Analysis, Science and technology
Abstract

A Drosophila melanogasted yeast artificial chromosome library was constructed and probed with a DNA sequence from the minichromosome Dp(1;f)1187 derived from the X chromosome. The Dpf(1;f)1187 minichromosome contains G+C-rich tandemly repeated dodeca satellite sequences. The results showed that dodeca satellite sequences are present in heterochromatin of the centromeric region in D. melanogaster autosomes. Cross-hybridization experiments further demonstrated the presence of these sequences in widely divergent species such as Arabidopsis thaliana and humans.

Published
1992

33. Y-chromosomal STR haplotypes in Pakistani populations.

Author

Mohyuddin, Aisha, Ayub, Qasim, Qamar, Raheel, Zerjal, Tatiana, Helgason, Agnar, Mehdi, S. Qasim, and Tyler-Smith, Chris

Subjects
Pakistanis -- Genetic aspects, Forensic genetics -- Conferences, meetings and seminars, Y chromosome -- Analysis, Haplotypes -- Analysis, Population genetics -- Research
Published
2001

34. IFITM3 restricts the morbidity and mortality associated with influenza

Author

Everitt, Aaron R., Clare, Simon, Pertel, Thomas, John, Sinu P., Wash, Rachael S., Smith, Sarah E., Chin, Christopher R., Feeley, Eric M., Sims, Jennifer S., Adams, David J., Wise, Helen M., Kane, Leanne, Goulding, David, Digard, Paul, Anttila, Verneri, Baillie, J. Kenneth, Walsh, Tim S., Hume, David A., Palotie, Aarno, Xue, Yali, Colonna, Vincenza, Tyler-Smith, Chris, Dunning, Jake, Gordon, Stephen B., Everingham, K., Dawson, H., Hope, D., Ramsay, P., Campbell, A., Kerr, S., Harrison, D., Rowan, K., Addison, J., Donald, N., Galt, S., Noble, D., Taylor, J., Dornan, R., Richard, C., Gilmour, D., Jardine, C., Quasim, T., Watson, V., Henry, P., Munro, F., Bell, L., Southward, J., Allcoat, P., Gray, S., Matheson, J., Alcorn, D., Sundaram, R., Bruce, J., McGuigan, K., Grant, J., Hughes, M., Harris, G., Paterson, R., Pollock, M., Antonelli, J., Duncan, A., Gibson, J., McCulloch, C., Murphy, L., Haley, C., Faulkner, G., Freeman, T., Hume, D. A., Chaussabel, D., Adamson, W. E., Carman, W. F., Thompson, C., Zambon, M. C., Aylin, P., Ashby, D., Barclay, W. S., Brett, S. J., Cookson, W. O., Drumright, L. N., Dunning, J., Elderfield, R. A., Garcia-Alvarez, L., Gazzard, B. G., Griffiths, M. J., Habibi, M. S., Hansel, T. T., Herberg, J. A., Holmes, A. H., Hussell, T., Johnston, S. L., Kon, O. M., Levin, M., Moffatt, M. F., Nadel, S., Openshaw, P. J., Warner, J. O., Aston, S. J., Gordon, S. B., Hay, A., McCauley, J., Banchereau, J., Hayward, A., Kellam, P., Baillie, J. K., Simmonds, P., McNamara, P. S., Semple, M. G., Smyth, R. L., Nguyen-Van-Tam, J. S., Ho, L.-P., McMichael, A. J., Smyth, Rosalind L., Openshaw, Peter J., Dougan, Gordon, Brass, Abraham L., and Kellam, Paul

Subjects
Swine influenza -- Research -- Analysis, Mortality -- Analysis -- United Kingdom, Membrane proteins -- Analysis, Morbidity -- Analysis, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Aaron R. Everitt [1]; Simon Clare [1]; Thomas Pertel [2]; Sinu P. John [2]; Rachael S. Wash [1]; Sarah E. Smith [1]; Christopher R. Chin [2]; Eric M. Feeley [...]

Published
2012
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35. Binary and microsatellite polymorphisms of the Y-chromosome in the Mbenzele Pygmies from the Central Africa Republic

Author

Coia, Valentina, Caglia, Alessandra, Arredi, Barbara, Donati, Francesco, Santos, Fabricio R., Tyler-Smith, Chris, Destro-Bisol, Giovanni, Pascall, Vincenzo, Paoli, Giorgio, Taglioli, Luca, and Pandya, Arpita

Subjects
Pygmies -- Genetic aspects, Pygmies -- Research, Y chromosome -- Research, Genetic polymorphisms -- Research, Biological sciences
Abstract

A study was conducted to examine the variation in six binary polymorphisms and six microsatellite polymorphisms existing in the Mbenzele Pygmies of Central Africa Republic. The results reported a similarity between the Mbenzele Pygmies and the Baika Pygmies owing to a close geographical proximity between the two civilizations.

Published
2004

36. Genetic Differentiation in South Amerindians Is Related to Environmental and Cultural Diversity: Evidence from the Y Chromosome

Author

Tarazona-Santos, Eduardo, Carvalho-Silva, Denise R., Pettener, Davide, Luiselli, Donata, De Stefano, Gian Franco, Labarga, Cristina Martinez, Rickards, Olga, Tyler-Smith, Chris, Pena, Sergio D. J., and Santos, Fabricio R.

Subjects
Y chromosome -- Research, South American native peoples -- Research, Human population genetics -- Research, Biological sciences
Published
2001

37. Y-Chromosome Lineages Trace Diffusion of People and Languages in Southwestern Asia

Author

Quintana-Murci, Lluis, Krausz, Csilla, Zerjal, Tatiana, Sayar, S. Hamid, Hammer, Michael F., Mehdi, S. Qasim, Ayub, Qasim, Qamar, Raheel, Mohyuddin, Aisha, Radhakrishna, Uppala, Jobling, Mark A., Tyler-Smith, Chris, and McElreavey, Ken

Subjects
Y chromosome -- Analysis, Nomads -- Genetic aspects, Human population genetics -- Social aspects, Human beings -- Migrations, Biological sciences
Published
2001

38. Y-Chromosomal Diversity in Europe Is Clinal and Influenced Primarily by Geography, Rather than by Language

Author

Rosser, Zoe H., Zerjal, Tatiana, Hurles, Matthew E., Adojaan, Maarja, Alavantic, Dragan, Amorim, Antonio, Amos, William, Armenteros, Manuel, Arroyo, Eduardo, Barbujani, Guido, Beckman, Gunhild, Beckman, Lars, Bertranpetit, Jaume, Bosch, Elena, Bradley, Daniel G., Brede, Gaute, Cooper, Gillian, Corte-Real, Helena B. S. M., de Knijff, Peter, Decorte, Ronny, Dubrova, Yuri E., Evgrafov, Oleg, Gilissen, Anja, Glisic, Sanja, Golge, Mukaddes, Hill, Emmeline W., Jeziorowska, Anna, Kalaydjieva, Luba, Kayser, Manfred, Kivisild, Toomas, Kravchenko, Sergey A., Krumina, Astrida, Kucinskas, Vaidutis, Lavinha, Joao, Livshits, Ludmila A., Malaspina, Patrizia, Maria, Syrrou, McElreavey, Ken, Meitinger, Thomas A., Mikelsaar, Aavo-Valdur, Mitchell, R. John, Nafa, Khedoudja, Nicholson, Jayne, Norby, Soren, Pandya, Arpita, Parik, Juri, Patsalis, Philippos C., Pereira, Luisa, Peterlin, Borut, Pielberg, Gerli, Prata, Maria Joao, Previdere, Carlo, Roewer, Lutz, Rootsi, Siiri, Rubinsztein, D. C., Saillard, Juliette, Santos, Fabricio R., Stefanescu, Gheorghe, Sykes, Bryan C., Tolun, Aslihan, Villems, Richard, Tyler-Smith, Chris, and Jobling, Mark A.

Subjects
Human genetics -- Research, Europeans -- Genetic aspects, Biological sciences
Published
2000

39. A Short Tandem Repeat-Based Phylogeny for the Human Y Chromosome

Author

Forster, Peter, Rohl, Arne, Lunnemann, Petra, Brinkmann, Catrin, Zerjal, Tatiana, Tyler-Smith, Chris, and Brinkmann, Bernd

Subjects
Human genetics -- Research, Gene mutations -- Research, Y chromosome -- Research, Biological sciences
Published
2000

41. Copy number variation: New insights in genome diversity

Author

Freeman, Jennifer L., Perry, George H., Feuk, Lars, Redon, Richard, McCarroll, Steven A., Altshuler, David M., Hiroyuki Aburatani, Jones, Keith W., Tyler-Smith, Chris, Hurles, Matthew E., Carter, Nigel P., Scherer, Stephen W., and Lee, Charles

Subjects
Genetic variation -- Research, Gene mutations -- Research, Genetic disorders -- Research, Health
Abstract

Copy number variants (CNVs) account for a substantial amount of genetic variation in humans, and since many CNVs include genes that result in differential levels of gene expression, CNVs may account for a significant proportion of normal phenotypic variation. Efforts are directed toward a more comprehensive cataloging and characterization of CNVs that will provide the basis for determining how genomic diversity impacts biological function, evolution and common human diseases.

Published
2006

42. Don't mix radiocarbon and calendar years

Author

Tyler-Smith, Chris, Hurles, Matthew E., and Jobling, Mark A.

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Chris Tyler-Smith [1]; Matthew E. Hurles [1]; Mark A. Jobling [2] Sir Your News Feature 'Skeleton keys' (Nature 433, 454-456; 2005) contains two statements that, together, are misleading. First, [...]

Published
2005
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