Seehausen believes that this kind of periodic mixing has happened often in the history of this lineage. “I started thinking about what that does to those lineages, and what speciation and re-mixing and re-speciation might do to the dynamics,” he said.

In 2004 he argued that hybridization between relatively distinct but still compatible lineages could inject large amounts of genetic diversity into a gene pool. Through recombination, this ancestral diversity gets sliced and diced into new configurations.

That rapid expansion of genetic possibility gives lineages traction in filling new ecological niches. Given an opportunity, such as a newly created lake, successful new combinations of old alleles shoot off from the hybrid swarm. Not all combinations work, of course, but selection can sometimes be weaker in newly formed environments. That relaxed selection can give a hybrid cichlid that has adapted a new way to scrape algae off rocks extra time to sort out any incompatibilities between its parents’ genomes that might otherwise become a handicap. At the same time, other unique combinations of old alleles elsewhere in the genome might be incompatible with those in other offshoots of the hybrid swarm, buffering the budding lineage from gene flow.

This view of speciation is gaining evidential weight as genomic sequencing reveals the ancestries involved in more speciation events. For instance, a study by Meier and her colleagues published in Nature Communications in 2017 confirmed that the rapid radiation of 500 species of cichlids in Lake Victoria stemmed from a hybrid swarm likely to be older than the lake.

Within the lake, all species descended from a common ancestor, probably within the past 15,000 years. But when the researchers tried to place the Lake Victoria group of fishes on the larger cichlid tree, they fell between two very ancient river species — one from the upper Nile, and one from the Congo River.

According to Meier, some parts of the Lake Victoria cichlid genomes more closely resemble that of the Nile species while others are closer to the Congo one. “They’re a genetic mosaic of these two species that hybridized at the origin of Lake Victoria cichlids,” she said. Those mosaic genomes seeded the ancestral hybrid swarm with enough genetic variation from the parental lineages to fuel the fishes’ rapid spread and speciation.

Same Gene, Different Combinations

This mosaic pattern is apparent in one of the most well-studied genes in cichlids — one that helps them see. The long-wave sensitive (LWS) opsin gene helps tune the eye to different levels of ambient light and is exceptionally diverse within Lake Victoria cichlids. That variety falls into two broad categories: one for shallow, clear water and one for deeper water where red light prevails. Seehausen says that variation in this gene helped African cichlids fill the full spectrum of available niches in newly formed lakes. It also helped to reproductively isolate emerging species, because different genotypes are associated with different coloration patterns in the males, a major sexual signal to females.

The exceptional variation in LWS opsin didn’t exist in a single gene pool until the Congo lineage, which possessed the shallow-water version, hybridized with the Nile lineage, which had the deep-water version. The smashing together of these two versions of the gene, and subsequent rearrangements within them, set off an explosion of new physical diversity within the hybrid population that “appears to have facilitated adaptation to an extreme range of light conditions and visual ecologies,” the authors wrote.

Patterns like this popped up elsewhere in the genome as well. As the researchers investigated genomic regions that had spearheaded the differentiation among the Lake Victoria cichlids, they found new combinations of variants from each parental lineage sorted into the newly emerged species.

Other Kinds of Combinations

The ancient admixture event that prompted the diversification of African cichlids is just one of the ways old alleles can be recombined to help form new species. Combinatorial speciation encompasses the classic mechanism of hybrid speciation that farmers and gardeners know so well: In plants, it’s common for hybridization to immediately create a new species that is reproductively isolated from its parents.

Combinatorial speciation also describes situations in which a large, highly genetically diverse population can sprout numerous offshoots over millennia, forged from new combinations of older rare alleles. That’s what Marques and other researchers say has happened with the three-spined stickleback, a tiny armored fish that lives in both marine and freshwater habitats. Since the last ice age, stickleback have repeatedly colonized lakes and streams across the northern hemisphere. Research shows that key genes associated with freshwater colonization, such as one that controls the reduction in the fishes’ armored plating, are frequently ancient marine variants. Some of these alleles may even predate the existence of three-spined stickleback themselves.