Although whole genome sequencing has defined many of the branches of the evolutionary “tree of life,” clarifying which species emerged when, it has also struggled with what might be called the evolutionary undergrowth. This consists of dense patches of speciation that defy analysis, with different genetic patterns suggesting different evolutionary paths.

To hack through the undergrowth, researchers at Uppsala University used the phylogenetic equivalent of a machete: a network analysis that accounted for the influence of incomplete lineage sorting (ILS), or the persistence of polymorphisms across multiple successive speciation events. Essentially, ILS can make sense of apparently contradictory genomic information by following retrotransposons, so-called jumping genes.

By following jumping genes, the Uppsala researchers made sense of a particularly tangled bit of phylogenetic history: the rise of modern birds. It began after the mass extinction of nonavian dinosaurs and archaic birds and was characterized by a period of super-rapid adaptive radiation. Characterizing this radiation has been difficult to resolve, even with whole genome sequences.

“[We could] see that the very rapid rate at which various bird species started evolving once the dinosaurs went extinct, around 65 million years ago, meant that the genome failed to split into separate lineages during the process of speciation,” said Hans Ellegren of the Uppsala University Evolutionary Biology Center. When Ellergren and colleagues analyzed this evolutionary period, they realized that when speciation events are particularly rapid, they may not resemble a fully bifurcating tree.

The Uppsala scientists published their findings August 18 in PLoS Biology, in an article entitled, “The Dynamics of Incomplete Lineage Sorting across the Ancient Adaptive Radiation of Neoavian Birds.”

“[We] show that genome-level analyses of 2,118 retrotransposon presence/absence markers converge at a largely consistent Neoaves phylogeny and detect a highly differential temporal prevalence of [ILS],” wrote the authors. “We found that ILS-derived incongruences are spread over the genome and involve 35% and 34% of the analyzed loci on the autosomes and the Z chromosome, respectively. Surprisingly, Neoaves diversification comprises three adaptive radiations, an initial near-K-Pg super-radiation with highly discordant phylogenetic signals from near-simultaneous speciation events, followed by two post-K-Pg radiations of core landbirds and core waterbirds with much less pronounced ILS.”

The advantage of using jumping genes is that they come in chunks, unlike single-nucleotide changes, and are hence more telling. Small variations can revert relatively easily, frustrating attempts to reconstruct resolve tangles in family trees.

By using the jumping genes, or so-called retrotransposed elements, the Uppsala researchers have found that, for instance, a cuckoo can be more closely related to a hummingbird than a pigeon in a certain part of its genome, while the opposite holds true in another part. The study found numerous examples to corroborate the existence of the phenomenon.

This is one of the first cases in evolutionary research where researchers have been able to document and quantify incomplete lineage sorting far back in time. It is likely a far more common occurrence than previously thought.

“The more complex kinship patterns that result from this phenomenon mean that the Tree of Life should often be understood as a Bush of Life,” the researchers concluded.