Natural selection was particularly inventive in the appendage and accessory department during the evolution of placentalsan
expansive category of mammals that bear live, fully developed offspring. A placental might sport webbed wings, a prehensile tail, flippers, fangs, tusks, cloven hooves, paws, claws, floppy ears, horns, or any number of other specialized structures. While such morphological characteristics shed light on
evolutionary relationships, they can also confound classifications because animals might independently acquire the same traits without sharing a common ancestor.
With an ever-growing repository of genome sequence data, scientists have increasingly turned to molecular techniques to help resolve evolutionary relationships. Several recent molecular analyses offer support for placing recent placentals into four major groups: Afrotheria (mostly African species, including elephants and aardvarks), Xenarthra (New World species such as armadillos and sloths), Laurasiatheria (includes carnivores, whales, and horses), and the newly reclustered Supraprimates (includes rodents and primates). Supraprimates and Laurasiatheria are further grouped together as sister taxa in a larger group called Boreotheria. Molecular approaches have also tried to resolve the hotly debated issue of where to draw the base of the placental tree, though no consensus has emerged. These studies arrived at these conclusions by analyzing different datasets of nuclear and mitochondrial genes under different models of DNA sequence evolution.
But such molecular approaches have their own limitations, as genomes can also contain confounding features (called homoplasies), similar elements that look alike but do not represent common ancestry. In a new study, Jan Ole Kriegs, Jrgen Schmitz, and their colleagues used a different molecular strategy to infer the evolutionary history of placentals, relying on retroposons to signal kinship. Unlike mitochondrial or nuclear genes, retroposons are virtually free from homoplasies. They are reliable markers for inferring evolutionary history, the researchers explain, because their integration into the genome is randommaking it highly unlikely for the same element to integrate independently into a conserved region of the genome (called an
orthologous position) in two different species. In addition to finding significant support for the previously identified divisions, they offer strong support for placing Xenarthraarmadillos and their kinat the base of the placental tree.
Using specialized computer software, Kriegs et al. searched the mouse, dog, and human genome databases for the presence (or absence) of retroposons. From the 237 candidates identified in the scan, they designed PCR primers (a technique to identify and generate sufficient amounts of specific sequence for analysis) to amplify the equivalent sequences from organisms representing each placental superorder. When size differences between amplified and original sequences (indicating the presence or absence of a retroposed element) occurred within orthologous genome sites, the researchers repeated the analysis with loci from different taxa. (For example, an element might be present in all boreotherian species, but absent in afrotherians and xenarthrans, which diverged before the insertion occurred.) Twenty-eight loci showing size shifts within orthologous sequences were identified for further sequence analysis.
Kriegs et al. next studied the presence/absence patterns of these loci to determine how the various placental representatives were related. This analysis yielded markers that provided solid evidence for the divergence of several superordinal groups, as well as the base branch on the placental tree. Four markers occupied the same orthologous location in every species sampled except for the opossum, demonstrating the power of retroposons to reveal evolutionary splits, even as long as 100 million years ago. Eleven markers were p