Human – Page 2 – Tutorial Genomics, Ecology, Evolution, etc

Humans and chimpanzees share about 95% of their DNA. Having this in mind the recently published paper of Prado-Martinez et al. 2013, focusing at identifying great-ape genetic variation and resolving great-ape population history (based on historical-effective population sizes) reflects a comprehensive catalogue of great-ape genetic diversity to which the human genome can be compared to. On the other hand, the paper provides a framework of genetically resources between and within species/populations that can be used to improve conservation-management and breeding programs for captive and wild great-ape populations, which suffer dramatic reductions in suitable habitat and are highly endangered. 79 wild and captive born individuals were sequenced, including all six great ape species and seven subspecies. Nine human genomes, three african and six non-african individuals complemented the study. Variant-calls were performed using GATK. Totally, they discovered 84 million fixed substitutions and 88.8 million SNPs. In general they provide very good genomic data, using several quality filters and having less than 2% contamination between samples. To test the quality of SNV-calls they applied three independent validation experiments leading to a concordance of 86-99%. A difference compared to previous discussed papers, in the GEE-tutorial, is that in this article they didn’t look at …

Adaptation / Evolution / Genomics / Human

Evolutionary History and Adaptation from High-Coverage Whole-Genome Sequences of Diverse African Hunter-Gatherers

June 19, 2013November 8, 2021

“ Hunting and gathering was humanity’s first and most successful adaptation, occupying at least 90 percent of human history. Until 12,000 years ago, all humans lived this way. ” [The Cambridge Encyclopedia of Hunters and Gatherers. Richard B. Lee and Richard Daly, 1999] Despite of playing a central role in human evolution, African populations remain one of the most understudied groups in human genomics. Furthermore, African human populations preserve the most genetic diversity in the world, and the study of this genetic diversity among the multitude of diverse African ethnic groups is crucial for reconstructing modern human origins. The succession of African hunter-gatherer societies is the longest and one of the most varied known, and African hunter-gatherer populations have some of the deepest divergence time of our species. In this work the genomes of 15 African hunter-gatherers were sequenced at high coverage, expanding the catalog of human genetic variation and increasing the few number of high coverage African genomes that have been analyzed to date. Samples and population features The 15 sequenced genomes were of male individuals coming from three different hunter-gatherer populations: 5 Pygmies from Cameroon, 5 Hadza and 5 Sandawe from Tanzania (Fig. 1). The Hadza and Sandawe …

Adaptation / Evolution / Human / Selective Sweep

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

December 16, 2011November 8, 2021

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 …

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

Classic Selective Sweeps Were Rare in Recent Human Evolution

November 30, 2011November 8, 2021

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 …