But animal species seemed more discrete, at least for a while. Most zoologists supported the biological species concept proposed in 1942 by the legendary biologist Ernst Mayr, who was one of the architects of the modern synthesis, the version of evolution theory that combined Darwin’s natural selection with the science of genetics. Mayr’s biological species concept was based on reproductive isolation: A species was defined as a population that could not or did not breed with other populations. Even when exceptions to that rule started to emerge in the 1970s, many biologists considered hybridization to be too rare to be important in animals. “We had a blinkered attitude,” said James Mallet, an evolutionary biologist at Harvard University. Today, he added, saying that such hybridizations don’t affect reconstructions of evolutionary history or “that this wasn’t useful in adaptive evolution—that’s no longer tenable.”

This is especially true now that computational and genomic tools prove just how prolific introgression is—even in our own species. Since 2009, studies have revealed that approximately 50,000 to 60,000 years ago, some modern humans spreading out of Africa interbred with Neanderthals; they later did so with another ancestral human group, the Denisovans, as well. The children in both cases went on to mate with other modern humans, passing the genes they acquired down to us. At present, researchers estimate that some populations have inherited 1 to 2 percent of their DNA from Neanderthals, and up to 6 percent of it from Denisovans—fractions that amount to hundreds of genes.

In 2012, Mallet and his colleagues showed a large amount of gene flow between two hybridizing species of Heliconius butterfly. The following year, they determined that approximately 40 percent of the genes in one species had come from the other. Mallet’s team is now working with another pair of butterfly species that exchange even more of their genes: something like 98 percent, he said. Only the remaining 2 percent of the genome carries the information that separates the species and reflects their “true” evolutionary trajectory. A similar blurring of species lines has already been found in malaria-carrying mosquitoes of the Anopheles genus.

Other types of organisms, from fish and birds to wolves and sheep, experience their share of introgression, too. “The boundaries between species are now known to be less rigid than previously thought,” said Peter Grant, an evolutionary biologist at Princeton University who, along with his fellow Princeton biologist (and wife) Rosemary Grant, has been studying the evolution of Galápagos finches for decades. “Phylogenetic reconstructions depict treelike patterns as if there is a clear barrier between species that arises instantaneously and is never breached. This may be misleading.”

Arnold concurred. “It’s a web of life,” he said, “rather than a simple bifurcating tree of life.” That also means it’s more necessary than ever before to examine the entire genome, and not just selected genes, to understand a species’ evolutionary relationships and generate the correct phylogeny. And even that might not be enough. “It may well be,” Mallet said, “that some actual evolutionary patterns are still completely irrecoverable.”

Restless Genes Make Themselves Felt

Genomic studies can’t create a complete picture of the introgressive movements of genes. Whenever one species inherits genes from another, the outcome can be either deleterious, neutral or adaptive. Natural selection tends to weed out the first, although some of the genes we have inherited from Neanderthals, for example, may be involved in disorders such as diabetes, obesity or depression. Neutral introgressed regions drift, so it’s possible for them to remain in the genome for very long periods of time without having an observable effect.

But it’s the beneficial introgressions that particularly fascinate researchers. Take the Neanderthal and Denisovan DNA again: Those genes have allowed people to adapt to the harsh environs of places like the Tibetan plateau, protecting them against the harmful effects of high altitudes and low oxygen saturation, which in nonlocals can cause stroke, miscarriage and other health risks. Variants from interbreeding with archaic humans have also conferred immunity to certain infections and made skin and hair pigmentation more suitable for Eurasian climes.