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Population genomics

Plenary lecture 2

Sunday, 11 September, 09:00 - 10:30

Room: Musensaal (Saal 2.0)

Brian Charlesworth UK

University of Edinburgh

Sex, flies and molecular evolution
Population genetics theory predicts that sexual reproduction and genetic recombination facilitate adaptive evolution. In addition, the X chromosome may experience faster rates of adaptive evolution relative to the autosomes, because of the exposure of beneficial X-linked partially recessive mutations to selection in males. Methods have for estimating the incidence of adaptive evolution at nonsynonymous sites, using genome-wide data on variation within a species combined with data on divergence from related species.Analyses of such data from Drosophila melanogaster show that genes located in genomic regions with higher rates of genetic recombination are under more effective selection in favour of beneficial mutations and against deleterious one than genes in low recombination regions. In addition, genes on the X chromosome show faster rates of adaptive evolution than genes on the autosomes; this effect is not caused by the higher effective X chromosomal recombination rate, or by differences in patterns of sex-biased gene expression.

Biography

Brian Charlesworth is a Senior Honorary Professorial Fellow at the University of Edinburgh. He obtained his PhD in genetics at Cambridge in 1969, and was a postdoctoral fellow with Richard Lewontin at the University of Chicago. He subsequently worked at the Universities of Liverpool, Sussex and Chicago, moving to Edinburgh as a Royal Society Research Professor in 1997. He is a Fellow of the Royal Society, Honorary Fellow of the American Academy of Arts and Sciences, and Foreign Associate of the US National Academy of Sciences. He received the Darwin Medal of the Royal Society in 2000, the Darwin-Wallace medal of the Linnean Society in 2010, and the Thomas Hunt Morgan Medal of the Genetics Society of America. His current research interests are in population genetics theory, molecular evolution and genome evolution. He has published over 300 papers and three books (two co-authored with Deborah Charlesworth).


Charles H. Langley US

University of California, Davis

Natural Selection on the Interactions of DNA Polymorphisms with Elements of Chromatin
Much of our understanding of polymorphism and divergence centers on downstream fitness consequences of associated effects on gene expression. But differences in structural interactions of DNA sequence variants in chromatin can lead to selection far upstream or independently. The scale of chromatin mediated selection ranges from that of a dinucleotide with an amino acid in a core histone to an entire centromeric region in where both the molecular and evolutionary mechanism remain largely obscure.80% of genomic DNA in eukaryotes is packaged as nucleosomes the fundamental unit of chromatin. A ~10 bp periodicity is readily observed in AA, TT and GC dinucleotide frequencies in the 147 bp DNA sequences in nucleosomes.  Many structural studies support a functional interpretation of these repeated elements in wrapping the DNA around the core histones. Yet the relative roles of mutation bias, gene conversion and natural selection in shaping this ubiquitous periodicity has been controversial.  To address this question the nucleosomal DNA from embryos of 3 Drosophila species was juxtaposed to genomic polymorphism and divergence data.  The levels of both exhibited the expected periodicities consistent with all hypotheses.  But also observed were periodicities in the frequency spectra of SNPs - “preferred” SNPs occurred in higher frequencies.  These same dinucleotide periodicities are also observed in nucleosomal DNA from coding regions.  Could they play a role in the apparent codon bias in Drosophila? And linkage disequilibrium occurs on short scale in Drosophila melanogaster, approximately that of three nucleosomes.  Interactions among adjacent nucleosomes may generate this LD.Genomic polymorphism and divergence in Drosophila show periodicities that parallel the commonly observed dinucleotide periodicities in nucleosomal DNAs. The observation of excess frequencies of “preferred” alleles favors the hypothesis of natural selection on function over one of mutational bias.

Biography

Charles H. Langley is Professor of Genetics in the Department of Evolution and Ecology at the University of California - Davis.  He received his Ph.D. at the University of Texas - Austin under the mentorship of K. Kojima in 1971.  After two years as a postdoctoral researcher with J.F. Crow at the University of Wisconsin - Madison Professor Langley joined the National Institute of Environmental Health Science (NIH) where he established a productive population genetics research environment.  In 1990 he join the faculty of UC-Davis and has focused much of his research on the forces that shape genomic polymorphism and divergence, especially in Drosophila and forest trees.  Professor Langley received the Genetics Society of America Medal in 1999 and was elected a Fellow of the American Academy of Arts and Sciences in 2007.


Anna Di Rienzo US

University of Chicago

Adaptations to high altitude in human populations
The ascent to high altitude presents formidable challenges to physiological processes, including hypoxia as well as cold stress and resource-poor habitats; these environmental features pose severe constraints on work capacity and reproduction.  Therefore, the history of initial settlement at high altitude and subsequent population movements is intertwined with the history of adaptations. Studies of human populations from the Tibetan region have revealed a complex history of mixing among modern human populations as well as evidence that a key adaptive allele was introduced into the Tibetan genome through admixture with a Denisova-like population.  This history provides novel opportunities for mapping locally beneficial alleles and for learning about the genetic architecture of high altitude adaptations. We are studying a large cohort of Tibetans and Sherpa from Nepal using approaches to detect selective sweeps as well as polygenic adaptation signals. We complement these approaches with standard genome-wide association mapping of physiological and reproductive phenotypes measured at high altitude, to gain insights into phenotypes and genetic variation with fitness effects.

Biography

Anna Di Rienzo was trained in Human Genetics and Medical Genetics at the University of Rome “La Sapienza”, Italy. After a postdoctoral training period at the Institute of Cell Biology of the National Research Council, she moved to the US where she did further postdoctoral training at University of California in Berkeley and in UC San Francisco. In 1993, she took an Assistant Professor position in the Department of Anthropology at Northwestern University, moving to the University of Chicago in 1996. She is now a Professor in the Department of Human Genetics and a member of the Institute for Genomics and Systems Biology, the Committee on Genetics, Genomics and Systems Biology, the Committee on Clinical Pharmacology and Pharmacogenomics, and the Committee on Molecular Metabolism and Nutrition.