Adaptation

Adaptation / Evolution / Genomics / Human

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

“ 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 …

Read More
Adaptation / Yak

The yak genome and adaptation to life at high altitude

The domestic yak (Bos grunniens) is an important domesticated species for Tibetans. Domestic yaks provide meat and other basic resources of necessity. The analysis of yak genome provides important insights into adaptation to a high altitude. Here discussed study was published in Nature Genetics. The study compares the yak genome with the genome of taurine cattle (B. taurus). Yak and cattle are cross-fertile, that means that they are genetically very similar. However the cattle suffer from hypertension when living in the yak habitat, thus, comparing this two species can provide the information about evolutionary adaptation to high altitude. In the study, researches sequenced genome of a female yak. They found three genes that help the animal to deal with a low concentration of oxygen that is typical for high altitude. Five further genes provide a better nutritional assimilation, as a consequence of the limited herbal resources available in the mountains where they live. Fig.1 Qiu et al., The yak genome and adaptation to life at high altitude., Nature Genetics 44, 2012 Venn diagram showing unique and shared gene families between the yak, cattle, dog and human genoms. One the Fig.1 unique and shared gene families from four different species (yak, …

Read More
Adaptation / Bears / Conservation / Evolution / Genomics / PNAS / Science

The evolutionary history of polar bears

The study of the Ursus lineage, including brown bear (Ursus arctos), black bear (Ursus americanus) and polar bear (Ursus maritimus), provides the ability of addressing the subject of adaptation to extreme (salty and glacial) environments in mammals. Moreover, in last few decades, polar bears won public and media attention, being one of the most charismatic species endangered by global warming and Arctic ice melting. To trace history of innovations and determine response to environmental changes in populations of polar bears, two articles published in Science and Proceedings of the National Academy of Sciences in April and June 2012 provide new data and insights to resolve this question. The absence of fossil of polar bears dating before the late Pleistocene (circa 126 000 years ago) and mitochondrial data, suggesting that polar bear were very closely related to a group of brown bear living in Admiralty, Baranof and Chichagof (ABC) islands in Alaska, previously led to believe that polar bears recently emerged from brown bears. The consequences of this hypotheses would be : Polar bear underwent a very rapid and recent (less than 200 ky ago) adaptation to extreme environment (previously not seen in mammals) Brown bear is a paraphyletic taxon, as …

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