Thu, 07 Aug 2008 21:21:59 BST CiteULike: Author Balloux http://www.citeulike.org/author/Balloux CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/jyuh/article/1095215 <i>Nature</i> An African origin for the intimate association between humans and Helicobacter pylori Bodo Linz François Balloux Yoshan Moodley Andrea Manica Hua Liu Philippe Roumagnac Daniel Falush Christiana Stamer Franck Prugnolle Schalk van der Merwe Yoshio Yamaoka David Graham Emilio Perez-Trallero Torkel Wadstrom Sebastian Suerbaum Mark Achtman doi:10.1038/nature05562 Nature 2007-02-08T19:36:11-00:00 Nature 0028-0836 Nature Publishing Group no-tag http://www.citeulike.org/user/balicea/article/1465869 <i>Nature, Vol. 448, No. 7151., pp. 346-348.</i> The effect of ancient population bottlenecks on human phenotypic variation Andrea Manica William Amos François Balloux Tsunehiko Hanihara doi:10.1038/nature05951 Nature, Vol. 448, No. 7151., pp. 346-348. 2007-07-18T23:12:57-00:00 Nature 0028-0836 448 7151 346 348 Nature Publishing Group anthropometry cultural-evolution evolution evolutionary-genomics evolution-of-intelligence genome-variation pop-gen http://www.citeulike.org/user/joepickrell/article/1577030 <i>Trends in Genetics, Vol. 23, No. 9. (September 2007), pp. 432-439.</i><br /><br />Global human genetic variation is greatly influenced by geography, with genetic differentiation between populations increasing with geographic distance and within-population diversity decreasing with distance from Africa. In fact, these 'clines' can explain most of the variation in human populations. Despite this, population genetics inferences often rely on models that do not take geography into account, which could result in misleading conclusions when working at global geographic scales. Geographically explicit approaches have great potential for the study of human population genetics. Here, we discuss the most promising avenues of research in the context of human settlement history and the detection of genomic elements under natural selection. We also review recent technical advances and address the challenges of integrating geography and genetics. Going the distance: human population genetics in a clinal world Lori Handley Andrea Manica Jerome Goudet Francois Balloux doi:10.1016/j.tig.2007.07.002 Trends in Genetics, Vol. 23, No. 9. (September 2007), pp. 432-439. 2007-08-20T15:38:14-00:00 2007 Trends in Genetics 23 9 432 439 genetics population http://www.citeulike.org/user/ryanraaum/article/1552512 <i>Human Genetics, Vol. 118, No. 3. (18 December 2005), pp. 366-371.</i><br /><br />Abstract Individuals differ genetically in their susceptibility to particular diseases and their response to drugs. However, personalized treatments are difficult to develop, because disease susceptibility and drug response generally have poorly characterized genetic architecture. It is thus tempting to use the ethnicity of patients to capture some of the variation in allele frequencies at the genes underlying a clinical trait. The success of such a strategy depends on whether human populations can be accurately classified into discrete genetic ethnic groups. Despite the heated discussions and controversies surrounding this issue, there has been essentially no attempt so far to quantify the relative power of ethnic groups and geography at predicting the proportion of shared alleles between human populations. Here, we present the first such quantification using a dataset of 51 populations typed at 377 autosomal microsatellite markers, and show that pair-wise geographic distances across landmasses constitute a far better predictor than ethnicity. Allele-sharing between human populations worldwide decays smoothly with increasing physical distance. We discuss the relevance of these patterns for the expected distribution of variants of medical interest. The distribution patterns of gene coding for simple traits are expected to be highly heterogeneous, as most such genes experienced strong natural selection. However, variants involved in complex traits are expected to behave essentially neutrally, and we expect them to fit closely our predictions based on microsatellites. We conclude that the use of ethnicity alone will often be inadequate as a basis for medical treatment. Geography is a better determinant of human genetic differentiation than ethnicity Andrea Manica Franck Prugnolle François Balloux doi:10.1007/s00439-005-0039-3 Human Genetics, Vol. 118, No. 3. (18 December 2005), pp. 366-371. 2007-08-10T20:34:38-00:00 2005 Human Genetics 118 3 366 371 geographic-structure population-structure race str http://www.citeulike.org/user/ryanraaum/article/1530515 <i>Trends in Ecology & Evolution, Vol. 20, No. 4. (April 2005), pp. 194-201.</i><br /><br />Many clonal organisms experience occasional events of sexual recombination, with profound consequences for their population dynamics and evolutionary trajectories. With the recent development of polymorphic genetic markers and new statistical methods, we now have an unprecedented ability to detect recombination in organisms that are thought to reproduce strictly, or essentially asexually. However, it is not always obvious which methodology to apply. Consequently, biologists might decide how to analyse their data without clear guidelines. Here, we discuss the available methods, focusing on those best suited when working with limited genetic information, such as a few genetic markers or DNA sequences. We conclude by commenting on the prospects offered by some recent conceptual advances and the access to high throughput technologies in an increasing number of model organisms. Tackling the population genetics of clonal and partially clonal organisms Fabien Halkett Jean-Christophe Simon Francois Balloux doi:10.1016/j.tree.2005.01.001 Trends in Ecology & Evolution, Vol. 20, No. 4. (April 2005), pp. 194-201. 2007-08-02T12:18:36-00:00 2005 Trends in Ecology & Evolution 20 4 194 201 bacterial-pop-gen http://www.citeulike.org/user/lp2/article/1468558 <i>Current Biology, Vol. 15, No. 5. (8 March 2005), pp. R159-R160.</i><br /><br />A leading theory for the origin of modern humans, the `recent African origin' (RAO) model [], postulates that the ancestors of all modern humans originated in East Africa and that, around 100,000 years ago, some modern humans left the African continent and subsequently colonised the entire world, displacing previously established human species such as Neanderthals in Europe [ and ]. This scenario is supported by the observation that human populations from Africa are genetically the most diverse [] and that the genetic diversity of non-African populations is negatively correlated with their genetic differentiation towards populations from Africa []. Geography predicts neutral genetic diversity of human populations Franck Prugnolle Andrea Manica Francois Balloux Current Biology, Vol. 15, No. 5. (8 March 2005), pp. R159-R160. 2007-07-20T09:56:59-00:00 2005 Current Biology 15 5 R159 R160 no-tag http://www.citeulike.org/user/lp2/article/944844 <i>Heredity, Vol. aop, No. current.</i> Is urbanization scrambling the genetic structure of human populations? A case study M Ashrafian-Bonab Lawson Handley F Balloux doi:10.1038/sj.hdy.6800918 Heredity, Vol. aop, No. current. 2006-11-15T15:50:17-00:00 Heredity 0018-067X aop current Nature Publishing Group no-tag http://www.citeulike.org/user/rhyax/article/893706 <i>Molecular Ecology, Vol. 11, No. 2. (2002), pp. 155-165.</i><br /><br />Abstract Microsatellite markers are routinely used to investigate the genetic structuring of natural populations. The knowledge of how genetic variation is partitioned among populations may have important implications not only in evolutionary biology and ecology, but also in conservation biology. Hence, reliable estimates of population differentiation are crucial to understand the connectivity among populations and represent important tools to develop conservation strategies. The estimation of differentiation is c from Wright's FST and/or Slatkin's RST, an FST-analogue assuming a stepwise mutation model. Both these statistics have their drawbacks. Furthermore, there is no clear consensus over their relative accuracy. In this review, we first discuss the consequences of different temporal and spatial sampling strategies on differentiation estimation. Then, we move to statistical problems directly associated with the estimation of population structuring itself, with particular emphasis on the effects of high mutation rates and mutation patterns of microsatellite loci. Finally, we discuss the biological interpretation of population structuring estimates. The estimation of population differentiation with microsatellite markers Francois Balloux Nicolas Lugon-Moulin doi:10.1046/j.0962-1083.2001.01436.x Molecular Ecology, Vol. 11, No. 2. (2002), pp. 155-165. 2006-10-12T00:34:38-00:00 2002 Molecular Ecology 11 2 155 165 fst review rst stepwisemodel http://www.citeulike.org/user/Yanno/article/4674 <i>Nature, Vol. 432, No. 7020. (23 December 2004), pp. 980-987.</i> Genome-wide survey of protein kinases required for cell cycle progression M Bettencourt-Dias R Giet R Sinka A Mazumdar WG Lock F Balloux PJ Zafiropoulos S Yamaguchi S Winter RW Carthew M Cooper D Jones L Frenz DM Glover doi:10.1038/nature03160 Nature, Vol. 432, No. 7020. (23 December 2004), pp. 980-987. 2004-12-23T14:17:36-00:00 2004 Nature 432 7020 980 987 kinase http://www.citeulike.org/user/ladygoat/article/139226 <i>Curr Biol, Vol. 15, No. 5. (8 March 2005)</i> Geography predicts neutral genetic diversity of human populations. F Prugnolle A Manica F Balloux doi:10.1016/j.cub.2005.02.038 Curr Biol, Vol. 15, No. 5. (8 March 2005) 2005-03-24T15:45:06-00:00 2005 Curr Biol 0960-9822 15 5 no-tag