Analyses of pig genomes provide insight into porcine demography and evolution

Pig domestication has started over 10 000 years ago and has had important consequences on human life, changing our agricultural and medical practices. Much has been argued on whether pig was domesticated independently across multiple locations or it was adopted by humans only once and then transported elsewhere. Originally, pig (Sus scrofa) has emerged in the South East Asia during the early Pliocene (~5.3–3.5 Myr ago) and then spread across most of the Eurasian continent. Yet, unraveling the true story of the pig domestication has become possible only recently, with a publication of a near complete pig genome by Groenen et al. featuring the Nature front cover in the November issue 7424, 2012.  Genome assembly The research team (RT hereafter) made impressive efforts on genome sequencing and assembly. The genome was sequenced with both BAC and NGS technologies. For NGS the RT used 44bp paired-end Illumina library, which was likely the headliner technology from Illumina at the time of the initiation of the porcine genome project. In total, the RT obtained 2.60 Gb of sequencing data and thanks to BAC could assign scaffolds (2.5 Gb) quite precisely to 20 (18+X and Y) chromosomes, leaving only 212 Mb of unplaced scaffolds. …

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Genomic analysis of a key innovation in an experimental Escherichia coli population

In this paper Richard E. Lenski and colleague are showing an example of how efficient adaptation by natural selection is. During 20 year they have been growing twelve populations of Escherichia coli in glucose medium containing also abundant citrate, this famous long-term evolution experiment called LTEE allowed the evolution to run for 40’000 generations in controlled laboratory conditions. Surprisingly after 31’000 generations some mutants appeared that were able to use citrate, as a source of carbon instead of glucose, the inability to use citrate is one of the frame that define E.coli as a species. Researcher Zachary D. Blount dissected all the mechanism in using whole genome re-sequencing of 29 clones along the population history (Fig.1). Three steps are analyzed in details, as they were necessary to permit the evolution of Cit+ trait, potentiation, actualization and refinement. The phylogeny (Fig.1) highlight two clades that coevolved and were maintain with the new Cit+ clade around generation 20’000 (Fig 1.). Moreover after the evolution of the citrate clade around 36’000, bacteria that have Cit+ phenotype have a SNP that is causing a defect in methyl directed mismatch DNA repair such that mutants accumulate SNPs much faster than any other clades. (Fig.1 inset). …

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Genome Patterns of Selection and Introgression of Haplotypes in Natural Populations of the House Mouse (Mus musculus)

  1. How genomes evolve in natural populations? is a question that, despite to be a long-standing search for geneticists, recent molecular genomic approaches may help to understand. Their evolution among natural populations may be shaped by forces derived from different processes, such as as mutation, neutral evolution, negative or positive selection and demographic changes (Nosil & Feder 2011). In addition, the study of population divergences and species formation has an important temporal context. That is, the point in time during the evolutionary trajectory of the set of populations or related species we aim to study, can display different patterns. For instance, during initial stages the level of genome differentiation may be low. Then, as divergence proceeds (by intrinsic or extrinsic forces) this level is expected to increase in the genome, in either a clustered or an interspersed way. Further, hybridization between differentiated populations may produce the secondary infiltration of genomic regions of one population into the other. The study of the genomic complexity in natural populations may shed light into the population dynamics and the relevant processes during species evolution. 2. Staubach et al. (2012) used natural populations of house mice (Mus musculus) subspecies (M. m. domesticus which does …

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