population biology; population genetics; evolutionary genomics; deep genome sequencing; bioinformatics; animals; plants; microorganisms; transcriptomics; ecological genomics
Wang John, Wurm Yannick, Nipitwattanaphon Mingkwan, Riba-Grognuz Oksana, Huang Yu-Ching, Shoemaker Dewayne, Keller Laurent (2013), A Y-like social chromosome causes alternative colony organization in fire ants., in Nature
, 493, 664-668.
Caseys Celine, Glauser G, Stölting KN, Christe C, Albrectsen BR, Lexer Christian (2012), Effects of interspecific recombination on functional traits in trees revealed by metabolomics and genotyping-by-resequencing, in Plant Ecology and Diversity
Lischer H E L, Excoffier L (2012), PGDSpider: an automated data conversion tool for connecting population genetics and genomics programs., in Bioinformatics (Oxford, England)
, 28(2), 298-9.
Riba-Grognuz Oksana, Keller Laurent, Falquet Laurent, Xenarios Ioannis, Wurm Yannick (2011), Visualization and quality assessment of de novo genome assemblies., in Bioinformatics (Oxford, England)
, 27(24), 3425-6.
Gharib Walid H, Robinson-Rechavi Marc (2011), When orthologs diverge between human and mouse., in Briefings in bioinformatics
, 12(5), 436-41.
Recent advances in sequencing technology (such as 454 titanium, Solexa, SOLiD, Helicos and Complete Genomics) allow the deep coverage of genomes and transcriptomes in a large number of individuals. These advances pave the way for the emerging field of population genomics, which combines the principles of population biology and genetics with deep genome and transcriptome sequencing, as well as the latest bioinformatics tools necessary to process the massive amount of data involved. This approach will allow us to understand, at an unprecedented level, the key micro-evolutionary processes of mutation, genetic drift, gene flow and natural selection,. It is these within-population processes that are ultimately responsible for the origin of new species and divergence of their genomic and phenotypic traits. The fundamentals of population genomics allow researchers to cross disciplinary boundaries because it is applicable to a wide variety of questions in biology and medicine. The technological developments also mean that genomics, including functional genomics, are no longer limited to a handful of model organisms. This technology now allows the observation of large-scale patterns of gene expression. For the first time, ecologists and evolutionary biologists have the possibly to understand the influence of the environment on which parts of the genome are expressed. The development of deep genome sequencing, coupled with major advances in quantitative DNA amplification technologies also add new possibilities in population genetics for looking at genome-wide gene expression differences within and among populations that will ultimately lead to identification of adaptive molecular variation.Switzerland’s future experts in population genomics need across-discipline training in population genetics, hands-on experience with up-to-date genomics and bioinformatics tools, for acquiring, organizing and analyzing large-scale population genomic data. We need to offer this training to our PhD students. The cross-disciplinary nature means it cannot be offered by one Swiss University. The training module in Population Genomics brings together applicants with experience in deep genome and transcriptome sequencing (Sanders, Ebert and Keller) with population genetics and bioinformatics (Goudet and Excoffier). It brings together leaders in ecology, evolution, includes bioinformatics expertise from 3 group leaders of the Swiss Institute of Bioinformatics (SIB: Excoffier, Robinson-Rechavi, Salamin) and state-of-the-art bioinformatics support from the SIB VitalIT platform (Xenarios). The combined expertise in these fields afforded by the universities of Lausanne, Bern and Basel would provide a perfect opportunity for PhD students to obtain the necessary training in population genomics that could not be obtained outside such a program.The training program is focussed on activities enabling PhD students to integrate the fields of population genetics, deep genome and transcriptome sequencing, bioinformatics and ecological and evolutionary genomics. Additional goals are:•To offer a coherent set of activities to improve the quality of the students research and develop additional scientific skills such as scientific communication and presentation•To enhance the sharing of ideas among Swiss research institutions and PhD students and increase the ability of these institutions to develop in the new field of population genomics•To attract and select top level PhD students through the international visibility of the school•To foster links with top international researchers and research institutes in these disciplines in order to maximize the doctoral students chance of subsequent employmentThe training program for the ProDoc in Population Genomics comprises activities for developing scientific skills, learning new techniques and methods and exchange of ideas among groups and disciplines. The activities comprise scientific seminars, workshops, methods courses in population genomics and scientific exchanges.It is clear that researchers of the future will be able to use population genomics approaches to solve a variety of scientific and practical problems in biology and medicine. As a leading country in technology and biotechnology it is essential that Switzerland develops a solid research base in population genomics. It is expected that doctoral students trained in this program will be widely sought after on the job market in fundamental research in biology and medicine, in biotechnology and in the biomedical and pharmaceutical industry.