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But in the past couple decades, new doubt has emerged in some circles. Microbiologists have gained a better understanding of genetic behavior of simple life forms, which can be much more amorphous than the typical, vertical transfer of genes from one generation to the next. The ability of microbes such as bacteria and viruses to exchange genes laterally among individuals—and even among species—changes some of the basic structural understanding of the map of evolution. With horizontal gene transfers, genetic signatures can move swiftly between branches, quickly turning a traditional tree into a tangled web. This dynamic "throws doubt on this tree of life model," Theobald says. And "once you throw doubt on that, it kind of throws doubt on common ancestry as well."
The Proof Is in the Proteins: Test Supports Universal Common Ancestor for All LifeOne researcher put the basic biological assumption of a single common ancestor to the test--and found that advanced genetic analysis and sophisticated statistics back up Darwin's age-old proposition
Echo Your post and the choice of section of the SciAm article you have quoted gives the impression that Douglas Theobald's Nature article casts more doubt on the existence of a common ancestor; whereas his quantitative statistical analysis provides ever more proof for existence of a common ancestor.I will quote the title of the SciAm article and subtitle which I believe gives a better idea of the contentsQuoteThe Proof Is in the Proteins: Test Supports Universal Common Ancestor for All LifeOne researcher put the basic biological assumption of a single common ancestor to the test--and found that advanced genetic analysis and sophisticated statistics back up Darwin's age-old propositionhttp://www.scientificamerican.com/article.cfm?id=universal-common-ancestor&page=2 The full article from nature is herehttp://www.nature.com/nature/journal/v465/n7295/full/nature09014.html
By plugging these sequences into various relational and evolutionary models, he found that a universal common ancestor is at least 10^2,860 more likely to have produced the modern-day protein sequence variances than even the next most probable scenario (involving multiple separate ancestors).