Evolutionary biologists solve puzzle of evolutionary relationships among vertebrates

Fishes, amphibians, mammals, snakes, turtles, lizards, crocodiles and birds are all groups of animals that include thousands of species and are morphologically very different from each other. These animal lineages show huge differences in species richness, life history, behaviour and many other aspects of their biology. Notwithstanding these differences, they all possess a backbone and jaws. Since their origin about 470 million years ago, jawed vertebrates have diversified extraordinarily: they include more than 68,000 described species, not counting those that went extinct. Some of them evolved key innovations that enabled their ancestors during the Devonian age to leave water and conquer terrestrial environments on all continents. They even learned to fly on more than once.

The evolution of jawed vertebrates is also part of our own history as humans. Understanding the evolutionary relationships between jawed vertebrates has thus been one of the major unsolved puzzles in biology. Despite decades of investigations, attempting to determine how some of these animal groups are related to each other has remained difficult. Estimating a robust tree that depicts evolutionary relationships is the first requirement for understanding the evolution, and also of jawed vertebrates. Their history includes astonishing examples of repeated evolution such as flight (in birds and bats) and echolocation (bats and whales). However, such convergences can only be recognised if the relationships among organisms are estimated with confidence.

The study reconstructs a new phylogenetic tree of jawed vertebrates using the largest and most informative dataset ever analysed. A total of 7,189 genes from 100 species are employed, providing one million nucleotides each to retrace their evolutionary history. Inferring evolutionary relationships by means of statistical methods could be viewed as "molecular archaeology," as the signals left by evolution in the DNA of our genomes are used to reconstruct events that happened millions of years ago.

The new tree of jawed vertebrates resolves several key relationships that have remained controversial despite decades of research, including the identification of lungfishes as the closest living relatives of land vertebrates, the close association of turtles with crocodilians and birds (the Archosaurs), or the relationships among amphibian groups (salamanders, frogs, caecilians) (supporting the Batrachia hypothesis). The phylogenetic tree was time-calibrated using fossils as anchors, which allowed testing of temporal relationship of diversification with major geological events. For example, two major groups of birds and mammals had been hypothesised to have diversified as a consequence of the extinction of dinosaurs (67 million years ago). The new study invalidates this hypothesis by showing that both groups are in fact much older.

The strength of the study is a novel set of approaches for analysing new, large-scale genomic datasets. The newly developed analytical pipeline solves the most important challenges posed by the new genomic-scale data set and could thus be used to reconstruct the evolutionary relationship of other enigmatic groups of organisms that await resolution.