Posts Tagged ‘selection’

Did natural selection make the Dutch the tallest people on the planet?

Tuesday, June 16th, 2015

Did natural #selection make the Dutch the tallest people on the
planet? Height spurt in last century not all nurture

“This study drives home the message that the human population is still subject to natural selection,” says Stephen Stearns, an evolutionary biologist at Yale University who wasn’t involved in the study. “It strikes at the core of our understanding of human nature, and how malleable it is.” It also confirms what Stearns knows from personal experience about the population in the northern Netherlands, where the study took place: “Boy, they are tall.”

“For many years, the U.S. population was the tallest in the world. In the 18th century, American men were 5 to 8 centimeters taller than those in the Netherlands. Today, Americans are the fattest, but they lost the race for height to northern Europeans—including Danes, Norwegians, Swedes, and Estonians—sometime in the 20th century.

Just how these peoples became so tall isn’t clear, however. Genetics has an important effect on body height: Scientists have found at least 180 genes that influence how tall you become. Each one has only a small effect, but together, they may explain up to 80% of the variation in height within a population. Yet environmental factors play a huge role as well. The children of Japanese immigrants to Hawaii, for instance, grew much taller than their parents. Scientists assume that a diet rich in milk and meat played a major role.

The Dutch have become so much taller in such a short period that scientists chalk most of it up to their changing environment. As the Netherlands developed, it became one of the world’s largest producers and consumers of cheese and milk. An increasingly egalitarian distribution of wealth and universal access to health care may also have helped.”

Extensive evolutionary changes in regulatory element activity during human origins are associated with altered gene expression and positive selection. PLoS Genet. 2012

Sunday, April 12th, 2015

Changes in [DHS] #regulatory element activity…[over 3 primates] associated w/ altered…expression & pos. selection

DHS across 3 primates finds species specific sites associated with differential expression & positive selection

Shibata Y, Sheffield NC, Fedrigo O, Babbitt CC, Wortham M, Tewari AK, London D, Song L, Lee BK, Iyer VR, Parker SC, Margulies EH, Wray GA, Furey TS, Crawford GE*. Extensive evolutionary changes in regulatory element activity during human origins are
associated with altered gene expression and positive selection. PLoS Genet. 2012 Jun; 8(6):e1002789. doi: 10.1371/journal.pgen.1002789. Epub 2012 Jun 28. PubMed PMID: 22761590; PubMed Central PMCID: PMC3386175

SUMMARY (from csds):

The study is focused on analyzing genotype-phenotype correlation by looking at the evolution of DHS sites across three primate genomes: human, chimp and macaque. By comparing the data they were able to identify common DHS sites across the three species (sites that show similar DHS levels) and also species-specific sites. All the assays were supported by ChiP experiments. The study identified >2000 regulatory elements that were gained/lost since the divergence of
human and chimp. Looking at DNase and RNAseq data the authors show that the enrichment of regulatory elements next to genes with species-specific expression, suggests that the gain or loss of DHS sites impacts transcript abundance. The human DHS sites were enhanced for chromatin marks predictive of enhancers, while common regions were preferentially associated with promoters and insulators. By looking at species specificity, they found that species-specific DHS gains are cell type specific while both species specific DHS gains and losses are subject to positive selection. The common DHS sites are conserved and are suggested to have roles involving transcription and general housekeeping.

The genomic landscape of Neanderthal ancestry in present-day humans : Nature : Nature Publishing Group

Saturday, November 1st, 2014

The genomic landscape of #Neanderthal ancestry in…humans Regions enriched & depleted in ancient alleles, from 1000G

1004 indiv. => 1000G phase 1

Here, we have systematically inferred Neandertal haplotypes in the genomes of 1,004 present-day humans. Regions that harbor a high frequency of Neandertal alleles in modern humans are enriched for genes affecting keratin filaments suggesting that Neandertal alleles may have helped modern humans adapt to non-African environments. Neandertal alleles also continue to shape human biology, as we identify multiple Neandertal-derived alleles that confer risk for disease. We also identify regions of millions of base pairs that are nearly devoid of Neandertal ancestry and enriched in genes, implying selection to remove genetic material derived from Neandertals. “}}

Genome-wide signals of positive selection in human evolution

Sunday, April 6th, 2014

“We further demonstrate that the observed signatures of positive selection correlate better with the presence of regulatory sequences, as predicted by the ENCODE Project Consortium, than with the positions of amino acid substitutions. Our results suggest that adaptation was frequent in human evolution and provide support for the hypothesis of King and Wilson that adaptive divergence is primarily driven by regulatory changes.”

Similar to conclusion positive-section section in FunSeq paper