IN 1981 PIETRO and Rosemary Grant, a team of husband and wife evolutionary biologists, have noticed something odd about Daphne Major. Each year in the previous decade they had traveled from Princeton University to this Galapagos island to study its three endemic species of tanager, part of a group known colloquially as “Darwin’s finches”. On this occasion their eyes were drawn to an unusual male who sported dark feathers and sang a unique song. Genetic analysis later identified it as a large cactus finch, probably blown from Española, another part of the archipelago more than 1
Intrigued, the Grants followed the castaway as he explored his new home. They have seen him mate with a local female medium land finch. This produced five healthy and fit children. Those offspring were also surprisingly sexually selective. With the exception of a single male, they and their descendants only mated with each other, and have continued to do so ever since.
Despite this strong inbreeding, the hybrids (two of which are pictured above) have been successful. They have carved a niche in which they use their size and deep beak to take advantage of the large woody fruits of the Jamaican fever plant, which grows locally. They have effectively become another species of Darwin’s finch, of which 13 were previously recognized. Although they do not yet have a Latinized scientific name, they are known by all as the “Big Bird” lineage.
This story would once have been considered deeply implausible. The orthodox evolutionary narrative does not suggest that hybridization is how new animal species emerge. But, as genetic testing proliferated, biologists were faced with an unexpected fact. Hybrids are not an evolutionary bug. They are a feature.
This knowledge is changing the way people think about evolution. The ordered family trees imagined by Charles Darwin in one of his first notebooks (see image below) are turning into cobwebs, and the primacy of the mutation in generating the variation that natural selection then scrutinizes is questioned. The influx of genes that accompanies hybridization also creates that variation – and the more people look, the more important it seems to get. Hybridization also offers shortcuts on the long march to speciation that are not dependent on natural selection at all. As the example of the Big Bird lineage shows, instead of taking millennia to emerge, a new species can appear almost overnight.
Indeed, all of this had already been recognized for simple organisms such as bacteria. These genes are promiscuously exchanged between more and less related individuals. But bacteria were unknown when Darwin invented natural selection, and the subject of speciation has been dominated by examples from animals and plants ever since. Recognizing that what is true for bacteria is also true for these multicellular organisms has profound implications, not least for how humans understand their origins. It seems fitting, then, that the birds whose diversity helped inspire Darwin still have stories of evolution to tell.
The conventional view of evolution is that mutations occur randomly. The maladaptive ones are then eliminated by competitive pressure while the adaptive ones proliferate. The result, over long periods of time and witnessed by populations that are sometimes divided by external circumstances, is change that eventually crystallizes into new and separate species.
This process leaves the door open for hybrids. The genomes of closely related species can remain sufficiently similar to produce viable offspring. But these genes often do less well than those of parents of the same species. As a result, viable hybrids are also often sterile (think mules) and are also at increased risk for developmental and other diseases. In fact, infertility in male hybrids is so common that it has a name: Haldane’s rule. This sort of thing was enough to persuade most of Darwin’s twentieth-century disciples that the need to avoid hybridization was actually a driving force that caused natural selection to erect reproductive barriers between incipient species, encouraging so is speciation.
However, there is another way to look at hybridization. Mixing the traits of two parent species could actually leave their hybrid offspring in better condition. This is called hybrid vigor or heterosis. The interaction of the genes of two species can even produce traits shown by neither parent. This is known as transgressive segregation, and the resulting hybrid can be surprisingly well suited to an entirely new niche, as is the case with the Big Birds.
Both the evil and beneficial effects of hybridization are real. The question is who wins most often in practice? In plants, it is often the beneficial. This is a consequence of the unusually malleable genetics of plants. The nuclear genomes of complex organisms (animals, plants, fungi, and unicellular organisms such as amoebas) are divided into bundles of DNA called chromosomes. Such organisms are generally haploid or diploid, which means that each cell nucleus contains one or two copies of each chromosome. Humans are diploid. They have 23 chromosome pairs, for a total of 46 single chromosomes. But there are exceptions. Plants, for example, are often polyploid, which means that each nucleus contains copies in multiples greater than two. For example, Californian coastal redwoods have six copies. Since sequoia cell nuclei have 11 distinct types of chromosomes, they house a total of 66 chromosomes in all.
Sometimes, polyploidy is the result of spontaneous doubling of an organism’s genome. Often, however, it is a consequence of hybridization, with the chromosomes of both parents ending up in a single nucleus. However it turns out, polyploidy provides backup copies of genes that natural selection can work on while other versions continue with their original function. And if it is also the result of hybridization, it brings the further possibilities of heterosis and transgressive segregation.
Furthermore, by changing the chromosome count of an organism, polyploidy has another pertinent effect. Create an instant breeding barrier with both parent species. This gives a new incipient species the opportunity to establish itself without being reabsorbed into one of the parental populations. The results can be spectacular. Recent evidence suggests, for example, that hybridization between two plant species in the distant past, followed by a simple doubling of the number of chromosomes in their offspring, may be responsible for much of the extraordinary diversity in flowering plants that is seen. today.
Plants appear to be easy beneficiaries of hybridization. For many animals, however, and for mammals in particular, extra chromosomes do not serve to make things better, but to disturb them. Why, it’s not entirely clear. Cell division in animals seems more easily confused by superfluous chromosomes than in plants, so this could be a factor. Plants also have simpler cells, which are better able to accommodate extra chromosomes. Whatever the details, animal hybrids seem to suffer from the effects of genetic incompatibility much more acutely than plants, and are therefore less able to benefit from heterosis. Evolutionary biologists have therefore long assumed that hybridization plays a negligible role in animal evolution, and there was little evidence to suggest otherwise.
Advance in DNA sequencing changed that by allowing people to look under the hood of evolutionary history. This uncovered a steady stream of animals breathed alive entirely by hybrid speciation. They include some familiar names. The European bison, for example, is the result of hybridization, over 120,000 years ago, between two now extinct species: the Ice Age steppe bison and the aurochs. The latter were the wild antecedents of modern domestic cattle and survived in the Jaktorow Forest, Poland, until 1627.
Something similar is true of the Clymene Atlantic dolphin. Genetic analysis revealed that this cetacean, which roams the salt flats between West Africa, Brazil and the Gulf of Mexico, owes its existence to a hybridization that took place between two other globetrotting dolphins, the striped dolphin and the spinner dolphin. .
At least one hybrid animal also traces its ancestry back to three species. Genetic analysis proves this Artibeus schwartzi, a Caribbean fruit bat, is the result of hybridization over the past 30,000 years of the Jamaican fruit bat (Artibeus jamaicensis), the South American flat-faced fruit-eating bat (Artibeus planirostris) and a third animal, not yet identified, that researchers speculate may be extinct.
Another kettle of fish
It also appears that, as in the case of flowering plants, hybridization may fuel the explosive radiation of new animals. The best known example is the case of cichlids from the African Great Lakes, in particular Lake Victoria, Lake Tanganyika and Lake Malawi. Great Lake cichlids are a group of thousands of closely related fish, famous for their panoply of shapes, sizes and colors (see photo). Each is adapted to a different depth and ecological niche.
The evolutionary history of cichlids has long puzzled biologists. Lake Victoria, in particular, comes and goes with the climate. Its current instantiation is less than 15,000 years old. In evolutionary terms this is a blink of an eye, but lake cichlids diversified into more than 500 species during that time.
The reason is hybridization. Using genetic analysis to place Lake Victoria cichlids within the larger cichlid family tree, the researchers found that they descended from an encounter between two distinct parental lineages, one swimming in the Congo and the other in the Nile.
The value of being such a genetic mosaic is evident from the story of one of the best-studied cichlid genes, which codes for a long-wave sensitive protein called opsin found in the retina of the eye. This protein determines the sensitivity of the eye to red light. This is important because red light levels drop rapidly in deeper waters. Consequently, fish living at different depths need eyes that are tuned differently from each other.
The Congo cichlid lineage had eyes optimized for clear and shallow water. The lineage view of the Nile was more in tune with the deep and dark. The hybrids were able to cut and modify these genetic variants to produce a range of light sensitivity. This allowed them to colonize the full depth of the water column in Lake Victoria as it developed. The new lake, for its part, offered cichlids a myriad of empty ecological niches to fill. The result was a sudden and explosive process called “combinatorial speciation”.
Elsewhere in the natural world, combinatorial speciation appears to have contributed to the surprising diversity of Sporophila, a genus of 41 neotropical songbirds, and the munias, mannikin, and silverbills of the genus Lonchura, a group of 31 estrildid finches that range across Africa and Southeast Asia. Nor is it only in vertebrates that this phenomenon raises its head. Heliconius, a genus of 39 flaming New World butterflies, also owes its captivating diversity to combinatorial speciation.
It’s raining cats, dogs and bears
These findings confuse Darwin’s concept of speciation as a slow and gradual process. Biologists now know that under the right circumstances, and with the help of hybridization, new species can emerge and consolidate over a handful of generations. This is an important amendment to evolutionary theory.
However, it is true that hybrid speciation in its full form remains rare for animals. It requires an unlikely congruence of factors to maintain a new hybrid population reproductively isolated from both parental species. The survival of the Galapagos Big Bird lineage, for example, involved physical isolation from one and strong sexual selection against the other.
Most commonly, an incipient hybrid population is reabsorbed by one or both parental species before it can establish itself properly. The result is a percolation of genes from one species to another, rather than a complete hybrid. This is called introgressive hybridization or, simply, introgression. DNA analysis of a long list of closely related animals shows that this version of hybridization is much more common than the complete form. It might even be ubiquitous.
The North American gray wolf, for example, owes its gene for melanism – the deep black fur shown by some wolves – to the introgression of domestic dogs brought from Asia 14,000 years ago by early American human settlers. In forest-dwelling wolves this gene has undergone strong positive selection, suggesting that it is adaptive. The most obvious explanation is that melanism provides better camouflage in the deep stygian woods of North America. Alternatively, female wolves may simply prefer their tall, dark, handsome males.
Panthera– the genus to which most big cats belong – is even more impressive in the scope of its introgressive weave. It has five members: lions, tigers, leopards, snow leopards and jaguars. It has long been known that these cross successfully in captivity, producing crosses called ligri (lion x tiger), jaglioni (jaguar x lion) and so on. But recent analyzes show that this also happened in nature. The researchers identified at least six past introgressive episodes in the genre, with each member involved in at least one of them.
The most promiscuous of the five appears to be the lion. Gene variants have spread among lions and tigers, lions and snow leopards, lions and jaguars. There is also evidence that at least some of this gene flow has been adaptive. Three lion genes incorporated into the jaguar genomes are known to have been heavily selected. Two of these are involved in vision, in particular they help guide the development of the optic nerve.
Genetic analysis also reveals a long history of hybridization between polar bears and grizzlies, the largest of their brown cousins. It is still unclear whether this had an adaptive value, but it may soon have a chance to prove itself. As climate change warms the polar bear’s Arctic home, the species may have to adapt quickly. A splash of grizzlies, a group accustomed to more temperate climates, could help achieve this.
The most studied case of introgression in animals is, however, closer to home than in wolves, big cats and bears. He’s looking at you from the mirror. The most up-to-date evidence suggests this Homo sapiens was born more than 315,000 years ago from gene flow between a series of interconnected population groups scattered across Africa. Whether these populations were different enough to be considered distinct species is still debated. In the African Pleistocene grasslands, however, these ancestral groups were not alone. Their world was interspersed with a menagerie of other hominins. And interspecies mating appears to have been widespread.
My family and other hominins
Several members of this human menagerie appear to have descended from Homo heidelbergensis, a species that spread to eastern and southern Africa about 700,000 years ago before crossing the Middle East to Europe and Asia. This species – a possible ancestor of the parent groups of Homo sapiens– also gave rise to at least two others, the Neanderthals (Homo neanderthalensis) and the Denisovians (Homo denisova). The former survived in Europe until 28,000 years ago, while the latter, an Asian group, lasted until about 50,000 years ago.
Other hominid species around at the time emerged directly from Homo erectus, a more primitive creature who was also the ancestor of Homo heidelbergensis and who, a million years earlier, had traced a transcontinental expansive path similar to that of heidelbergensis. Local descendants of erectus have been largely displaced from heidelbergensis when it arrived. But some resistance has survived in the corners of the Old World heidelbergensis never achieved. These included the islands of Flores in Indonesia and Luzon in the Philippines. Here was that diminutive Homo floresiensis is Homo luzonensis—The “hobbits” of the island – lasted, like the Denisovians, up to 50,000 years ago. There were probably isolated descendants of older cousins as well. At least one is known, Homo naledi, which preceded the emergence of Homo erectus and they still roamed southern Africa about 230,000 years ago.
Eventually this great hominid circus came to an abrupt end. The record in Africa is opaque. But in Europe, Asia and Oceania it is clear that the arrival of modern humans has coincided with a great disappearance of local hominids. Be it disease, competition for scarce resources or perhaps even genocide, a few thousand years of contact with Homo sapiens it was enough to extinguish every other hominid species.
Even a few millennia, however, have proved sufficient Homo sapiens to know his cousins intimately. The record of these romantic entanglements remains in the DNA of almost everyone alive today. In 2010 a team led by Svante Pääbo from the campus of the Max Planck Institute in Leipzig published the first draft sequence of the Neanderthal genome. This led to the extending discovery of Neanderthals DNA they make up 1-4% of the modern human genome in all populations outside sub-Saharan Africa. This is consistent with a series of hybridization reports in Europe, the Middle East and Central Asia dating back to around 65,000 years ago.
The Neanderthal legacy helped Homo sapiens adapt to the needs of the environments of these unknown places. There seems to have been a strong selection, for example, in favor of Neanderthal genes linked to skin and hair growth. These include bnc 2, a gene linked to skin pigment and freckles that is still present in two thirds of Europeans. There appears to have also been a selection for Neanderthal-derived genes that deal with pathogens. Some govern the immune system’s ability to detect bacterial infections. Others encode proteins that interact with viruses.
The Denisovians and their contribution a Homo sapiens, were another of Dr. Pääbo’s discoveries. In 2009, one of his teams was kidnapped DNA from a fossilized finger bone excavated from Denisova cave in the Altai Mountains of Siberia. This bone turned out to belong to a previously unknown species that got its name from the cave in which it was found. Physical specimens of this species remain rare. Examination of living people, however, reveals that it is Denisovan DNA they make up 3-6% of the genome of contemporary Papuans, Aboriginal Australians and Melanesians. Many Chinese and Japanese also bring Denisovan DNA, albeit at lower rates.
As with the Neanderthals, this inheritance brought benefits. The Denisovan version of a gene called epas1 modulates the production of red blood cells, which carry oxygen. This helps modern Tibetans survive at high altitudes. Denisovan tbx 15 is wars 2 likewise it helps the Inuit survive the intense cold of the Arctic by regulating the amount of metabolic heat they produce.
We count multitudes
That the Denisovans could hide in the modern human DNA yet leaving so few fossil traces left geneticists wondering what other ghosts they might have found. The genomes of sub-Saharan Africans, in particular, reveal evidence of at least one further intertwining. In 2012 a genomic analysis of members of the Baka, Hadza and Sandawe, three groups of people of ancient lineage, suggested an archaic introgression. In 2016 a deeper analysis focused on the Baka identified this aspect over the past 30,000 years. In February, a study of members of two other groups, the Yoruba and the Mende, confirmed that between 2% and 19% of their genomes can be traced back to an unidentified archaic species. It is unclear whether this is the same as what contributed to the Baka, Hadza and Sandawe, but it appears to have deviated from the line that leads directly to Homo sapiens not long before the Neanderthals and Denisovans, an African Neanderthal, if you will.
The same genetic tools also revealed deeper ghosts. The Denisovans show signs of hybridization with a “superarchaic” lineage, perhaps Homo erectus Yes. This constitutes 1% of the genome of the species. About 15% of this superarchaic heritage has, in turn, been passed on to modern humans. There is also evidence of a minuscule genetic contribution to African populations by an equally super-archaic relative.
To be human, therefore, is to be a multispecies bastard. However, as the example of the big cats in particular shows, Homo sapiens it is not, in this, an exception. Hybridization, once seen as a spear bearer in the great theater of evolution, is fast becoming a star of the show. Meanwhile, Darwin’s idea of a simple and universal family tree is relegated to wings.
In its place, some experts now prefer the idea of a tangled bush of interconnected branches. But even this is an imperfect comparison. A more appropriate analogy is a frayed rope. The species are intertwined with single threads. Where evolution proceeds in an orthodox Darwinian way, braids dissolve, strands split and new species result. But the rope doesn’t fray neatly. Introgression strands cross from braid to braid and occasionally two tangle to form a new braid altogether. This is a more complex conception of evolutionary history, but also richer. Few things in life are simple – why should life itself be? ■
This article appeared in the Science and Technology section of the print edition under the title “Match and Mix”