Selective Sweep

Adaptation / Evolution / Selective Sweep

Single and independent mutations lead to an adaptive and complex color phenotype in deer mice living on the light-colored soils of the Nebraska Sand Hills

Pleiotropy of genes is often the main solution to explain genetic basis of complex phenotypes (i.e., those composed of multiple traits). But dissection of those genes or loci are rarely studied, and it remains unclear which of single pleiotropic mutations or multiple mutations with independent effects are responsible to elaborate complex phenotypes. Linnen et al. are interested in coloration of the deer mice (Peromyscus maniculatus) present on the light-colored soils of the Nebraska Sand Hills. Adaptation for crypsis is the strongest hypothesis to explain prevalence of the light morph compared to the black morph,  and they wanted to dissect the genetic basis of this adaptation. This study is composed of two main parts : first to understand and to evaluate the complexity of coloration phenotype and then to find the mutations responsible of those variation in traits and on which morph selection is acting on. First of all, they implemented an experimentation with plasticine models to count the number of attacks on each coloration morph. As they expected, statistical test reveals that the dark models are significantly more attacked than light models. Closer inspection reveals multiple pigmentation traits and pattern that differ between the light and the dark morph to compose complex coloration …

Read More
Evolution / Genomics / Selective Sweep

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. …

Read More
Adaptation / Evolution / Human / Selective Sweep

Hard selective sweeps do not seem to be the rule in human evolution.

by Ricardo Kanitz, based on the paper by Hernandez et al. published in Science (2011). One of the main topics in evolution is – as it has always been – human evolution. Many new methods are applied first to humans; other methods, which are not applied there, often come to humans at some point anyway. This is particularly true in the field of genomics and it is no surprise since we are talking about our own species’ evolution. The study commented here addresses an interesting general question in the subject. How selection shaped (if at all) our genomes? More specifically, Hernandez and colleagues are interested in the classic signature of selection in genomes, the “selective sweep”. This so-called sweep is simply the reduction of measured diversity in the (genomic) surroundings of a positively selected mutation. This is observed when (1st) a new beneficial mutation appears, (2nd) it rapidly becomes the most common variant in a population and, (3rd) because genomic positions are not physically independent, nearby positions also become more frequent. As we move further away from such positively selected position, we observe a decay of such pattern due to recombination (see cartoon below). Based on functional groundings, the authors …

Read More
Adaptation / Evolution / Genomics / Human / Science / Selective Sweep

Classic Selective Sweeps Were Rare in Recent Human Evolution

With the rise of genomics and the availability of whole genome sequences, geneticists hope to be able to understand the recent adaptations humans underwent. Classic selective sweeps, where a beneficial allele arises in a population and subsequently goes to fixation, leave a specific pattern. Indeed, all variation is erased as the selected allele invades the population, and the neighboring neutral variation is also partially swept, with an intensity depending on the linkage with the selected region. An example of classic selective sweep pattern. As the distance from the selected nucleotide increases, diversity increases. Fig. 2 from Hernandez et al. 2011. The selective sweep pattern was used to find evidence for recent adaptation in humans. Many candidate genes for recent adaptation in humans were found. Nevertheless, the preeminence of classic selective sweeps compared with other modes of adaptation (like background selection or recurrent a.k.a. “soft” sweeps) is still unknown. In this paper, the authors claim that classic selective sweeps are in fact a rare event in human recent evolution. They argue that the overall pattern found in genome scan studies can be explained with only nearly neutral mechanisms (neutral evolution plus some purifying selection), without any positive selection going on. This …

Read More