Month: November 2014

Adaptation / Evolution / Genomics

Population Genomics Reveal Recent Speciation and Rapid Evolutionary Adaptation in Polar Bears

The polar bear (Ursus maritimus) is a carnivorous species which is closely related to the brown bear (Ursus arctos) and is adapted to the severe living conditions of the High Arctic due to the great physiological changes happened during evolutionary speciation. Despite numerous researches it is still unclear when exactly this two species diverged. That’s why, Liu with colleagues in their work tried to determine a reliable divergence time of polar bear and brown bear populations and investigated demographic history as well as selection and adaptation of polar bears. Summary By applying a population genomic framework the authors analyzed 89 complete nuclear genomes of polar bears and brown bears. They showed that two species diverged 479-343 thousand years ago (kya) and found 16 genes under strong positive selection on the polar bear in comparison with the brown bear. They analyzed more precisely nine of these genes that are known to be associated with high risk of cardiomyopathy and vascular diseases in humans. However, in polar bears these genes are responsible for an important reorganization of the cardiovascular system which allowed them to survive in extreme life’s conditions within Arctic Circle (e.g. very low temperatures, high physical activity in cold water, high …

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Ancient human genomes suggest three ancestral populations for present-day Europeans

Introduction & Methods The demographic history of the human species has always fascinated us. It is known that the ancestral human lineage appeared in East Africa, and that it subsequently migrated out of Africa towards Eurasia, separating into distinct lineages through time. Although many studies have focused on human demographic history, some aspects remain unknown, partly due to the difficulty in finding ancient samples from wide geographic and temporal scales. Particularly, the specific origins of certain populations at more local scales, remains uncertain. For example, it is known that early European farmers originated at least in part from the Near-East, which was one of the centers of the development of agriculture, and that hunter-gatherers were already present in Europe when early farmers arrived. However, as Lazaridis et al (2014) mention, modeling present-day Europeans as a mixture of only these two ancestral populations does not account for all present genetic diversity. Their main goal was therefore to clarify the prehistory of present-day Europeans. To address this question, the authors sequenced the genomes of nine ancient Europeans: seven from Sweden and one from Luxembourg (hunter-gatherers), as well as one farmer from Stuttgart, Germany, a member of the first widespread farming culture in …

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Conservation / Evolution / Genomics

Comparative analysis of regulatory information and circuits across distant species

Development and homeostasis of all organisms is tightly controlled by transcription regulatory factors that are often highly conserved across deep phylogenies. However, it is unclear to what extend the basic components of these networks (e.g. network motifs and structure, binding frequencies, factor interactions) are preserved in distantly related species. Boyle and colleagues try to shed light on this question in a recent study published by nature in August 2014 (doi:10.1038/nature13668). Paper summary The scientists compare genome-wide binding locations of 165 human, 93 worm and 52 fly transcription regulatory factors in different cellular contexts (developmental stages and tissues) to identify the common properties of their underlying networks (data overview shown in Figure 1, taken from original publication). As already described in smaller-scale studies, they see that DNA binding motifs of orthologous regulatory factors remain similar in distantly related species. Furthermore, these orthologous factors are expressed in similar contexts. However, expression of the orthologous targets is only weakly correlated suggesting an extensive re-wiring of regulatory networks across human, worm and fly. Reconstructions of regulatory networks point to a higher number of master-regulators and upward-flowing edges in human when compared to worm and fly. In all three species, the most abundant network motif …

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