Flexibility is a key strength of evolution theory.  DailyTech recently chronicled a major evolution observed by American researchers, believed to be the first of its magnitude to be observed.  Now evolutionary biologists have made critical steps in revising the genetic side of evolutionary theory to help explain one of the most daunting questions of evolutionary history -- how prehistoric fish evolved over hundreds of millions of years into amphibians, then reptiles, and finally mammals, and eventually how apes evolved into humans.

European Molecular Biology Laboratory's European Bioinformatics Institute [EMBL-EBI] researchers have discovered and fixed critical errors in genetic comparisons between species.  Genetic comparisons are frequently used to draw evolutionary conclusions about heredity and common ancestors.  However, according to the EMBL-EBI researchers, these methods have been suffering silently under systematic errors.

Their findings are detailed in the journal Science this month.  They don't just point out the problem either -- they provide a solution.  The researchers have developed a computational tool which avoids the errors and offers key insight into how DNA and protein sequences have evolved over time.

The results suggest that sequence turnover, thought to be a key component of major evolutions, is discovered to be much more common than previously thought.  Nick Goldman, group leader at EMBL-EBI explains that while evolution may be occurring faster, it still occurs at a maddeningly slow pace by human standards.

Says Goldman, "Evolution is happening so slowly that we cannot study it by simply watching it. That's why we learn about the relationships between species and the course and mechanism of evolution by comparing genetic sequences."

Evolution is driven by changes in living organisms' DNA.  DNA code consists of sets of four "letter" bases, which code a sequence for a specific amino acid.  Mutation and thus evolution can occur when the DNA gets "messed up" during copying with individual or several letters incorrectly copied [substitution], lost [deletion] or gained [insertion].

The rather complex error is explained well in the researchers’ publications.  They detail genetic comparison and how they go awry, stating:

A comparison of multiple sequences starts with their alignment. Characters in different sequences that share common ancestry are matched and gains and losses of characters are marked as gaps. Since this procedure is computationally heavy, multiple alignments are often built progressively from several pairwise alignments. It is impossible, however, to judge if a length difference between two sequences is a deletion in one or an insertion in the other sequence. For correct alignment of multiple sequences, distinguishing between these two events is crucial. Existing methods, that fail to do that, lead to a flawed understanding of the course of evolution.

Ari Löytynoja, who developed the tool to correct these errors, states, "Our new method gets around these errors by taking into account what we already know about evolutionary relationships.  Say we are comparing the DNA of human and chimp and can't tell if a deletion or an insertion happened. To solve this, our tool automatically invokes information about the corresponding sequences in closely related species, such as gorilla or macaque. If they show the same gap as the chimp, this suggests an insertion in humans."

Researchers have thus discovered that insertions are much more prevalent than previously believed, while deletions are less common than previously believed.

The researchers believe that the errors came from adapting protein recognition tools to genetics, which is broader in scope.  They believe that for this reason, additional errors in current computational methods are likely to be found.  Fortunately for evolutionary theory, it has the flexibility to correct these errors, and some of the world's brightest minds to help with the corrections.