A closer genetic look at the quagga, an extinct zebra

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A quagga-like zebra named Freddy grazes with his offspring in October last year.
A quagga-like zebra named Freddy grazes with his offspring in October last year.

New DNA evidence confirms that the recently extinct quagga is, indeed, a plains zebra. Science writer Ricki Lewis, who has a PhD in genetics, discusses the latest Danish research and a fascinating project in southern Africa to breed quagga-like zebras. Her piece was originally published by PLOS Blogs.

Like the dodo bird, heath hen, and woolly mammoth, the quagga vanished so recently that glimpsing its evolution is possible, using DNA from museum specimens and breeding modern relatives to select individuals bearing ancestral traits.

Samuel Daniell (1775-1811) captured the elegant quagga (Smithsonian)
Samuel Daniell (1775-1811) captured the elegant quagga. Image: Smithsonian

Named and described in 1788, a quagga looks like someone took an eraser to the rear end and hind legs of a zebra, brushing away the telltale stripes. Charles Darwin deemed the quagga a separate species, but today Equus quagga quagga is considered an extinct subspecies of the plains zebra. The living five subspecies roam south and eastern Africa, while the other zebra species, mountain and Grevy’s, live in more limited areas. When I visited Cape Town a few years ago, I was amazed to see zebras standing in ordinary backyards, like deer appear here in the US.

The sequenced genomes of six living species of zebras and asses, published in 2014, catalogued not only great genetic diversity, but the ability of horse relatives with different chromosome numbers to produce offspring. Today’s equids – horses, asses, and zebras – descend from an ancestor that lived 4.0 to 4.5 million years ago in the New World, and spread to the Old World 2.1 to 3.4 million years ago.

This week researchers from the University of Copenhagen published in Nature Ecology & Evolution analysis of 68,000 to 168,000 single-base places in the genome (SNPs) that vary, in the genomes of 65 plains zebras, including one museum quagga. The report fleshes out a study from 2008 that looked only at mitochondrial and short repeated DNA sequences.

The new DNA evidence confirms that the quagga is a plains zebra and also reveals nine genetically-defined groups, or “evolutionary units,” that don’t jibe with the traits used to distinguish subspecies – stripe pattern, body size, and head shape.

Nina’s stripelessness and brown background make her very similar to quaggas. She is expecting.
Nina’s stripelessness and brown background make her very similar to quaggas. She is expecting.

The Quagga Project

The last quagga, a female, died in the Amsterdam zoo on August 12, 1883. Charles Darwin may have seen a live quagga at the London Zoo, where the last one perished in 1870. The animals were hunted to extinction to preserve grasslands for goats and sheep.

The Quagga Project began with the taxidermy efforts of Reinhold Rau, a German expert in natural history who meticulously described the animals from 23 museum specimens. Controlled breeding to bring back a semblance of the quagga started in 1987, with plains zebras selected from wild populations for the absence of stripes on their hindquarters and legs, against a darker background. Striping pattern is more consistently inherited than background color; the bands persist even in albino zebras.

FD17, born last year, has lost the leg stripes that mom has.
FD17, born last year, has lost the leg stripes that mom has.

Each new generation springs from the least stripy animals of the previous one, with the striped animals removed from the grazing areas in the Western Cape region of South Africa. “We continue to select on both criteria (stripes and background color), and get ‘better’ results from each generation; we are, genetically speaking, in our 5th and 6th generations. In a domestic breeding situation, with a purebred individual to work from, we would have gotten there by now. But it still remains an uncertain enterprise,” says March Turnbull, coordinator of the Quagga Project. Here’s a progress report from 2008, at generation four.

Mating stripe-deficient zebras isn’t like crossing fruit flies or arranging the conception of a labradoodle or racehorse. The animals call the shots.

“Our stallions mate with whoever stands for them and the mares stand for any dominant stallion, regardless of morphology. Zebras are always pregnant. All matings are done in free-range herds on properties of between 1000 and 4000 hectares.

FD17, born last year, has lost the leg stripes that mom has.
FD17.

Plains zebras live in harems of a dominant stallion, perhaps five mares, and a few young hangers-on.  Every now and then the DNA proves that an interloper slipped in under cover of darkness, but it’s unusual,” explains Turnbull. And sometimes a throwback will just appear, a carefully selected newbie with leg stripes, like Nonnie. But even Charles Darwin noticed this.

Moving stallions to influence mating doesn’t always go smoothly. Battling adults may trample foals. “Eventually the mares and stallions work out who is going to settle with whom, after a hiatus that might lose a breeding season,” Turnbull adds.

The project has so far spawned about a dozen “Rau Quaggas,” named for the founder. These animals are the most quagga-like, lacking leg and rump stripes. Live cells would be required for cloning a quagga.

A pioneer species

The new DNA evidence supports the Quagga Project’s conclusion that “the striping pattern does not come from unique mutations in the quagga, but from standing genetic variation in the plains zebra. This means that we don’t need to invoke new mutations to explain at least one quite conspicuous change of phenotype in the quagga,” explains Rasmus Heller, assistant professor at the University of Copenhagen and co-author of the new paper.

Did the quagga’s loss of stripes doom it? It’s tempting to speculate, but impossible to tell from one specimen. “We do not know whether the quagga had specific adaptations in addition to the deviant striping pattern. To answer that we would probably need a population-level sampling of quaggas at a genomic scale,” says Heller.

While we await further data from preserved quaggas, the nine underlying genetic subgroups of the plains zebra illuminate unusual aspects of their evolution. The groups don’t show gradual changes in gene variant frequencies (clines), nor do they indicate a few individuals giving rise to genetically distinct populations (founder effects).

Instead, the subspeciation may be a consequence of the role of plains zebras as a pioneer species: the animals move all over Africa because they’re not too fussy about food, and are among the first to colonize damaged or disrupted grasslands. They’re hardy, adaptable mammals. The genetic groupings might indicate the consequences of past periods of climate change that transiently isolated small populations that then came together again, restoring the gene flow that kept variation in genomes.

Grant’s zebras are smaller than the other subspecies.
Grant’s zebras are smaller than the other subspecies.

The genetic partitioning doesn’t have much to do with the traditional subspecies designations. Populations of the smallish Grant’s zebra, for example, include individuals from two, three, or four genetically defined groups.

On origins

According to the new genetic analysis, zebras originated in the Zambezi river basin-Okavango delta area in Zambia and Botswana. They may have shared a refugium (a region that persists during environmental upheaval) with elands, impalas, and wildebeests, spreading throughout the grasslands as the glaciers receded.

The researchers traced the plains zebra populations back to about 800,000 to 900,000 years ago, and deduced that quaggas split off, along with other southern zebra populations, about 340,000 years ago. Whenever it happened, quaggas likely came from Namibia, says postdoctoral researcher Casper-Emil T. Pedersen, first author of the new paper. (Unicorns came from Nambia.) Quaggas mingled with other plains zebras near the basin of the Orange River, which extends from South Africa north into Namibia and Botswana.

Although the genetic data remain incomplete, today’s plains zebras seem like a mellow bunch. Their genomes are variable, yet many of the mutations are neutral, not affecting natural selection. Perhaps this means that instead of hanging around threatening environments until natural selection left only those animals whose inherited quirks enabled them to survive, stressed zebras just left, seeking new grasslands.

Makes sense to me!

(Amazon offers a nice selection of stuffed quaggas and I highly recommend the Evolution of the Horse Coloring Book, by Patricia Wynne.)

Thank you to the Quagga Project for providing photos.

Ricki Lewis’s blog, originally published by PLOS Blogs, is republished under a Creative Commons License.

Ricki Lewis is a science writer with a PhD in genetics. The author of several textbooks and thousands of articles in scientific, medical, and consumer publications, Ricki’s first narrative nonfiction book, The Forever Fix: Gene Therapy and the Boy Who Saved It, was published by St. Martin’s Press in March 2012. In addition to writing, Ricki provides genetic counseling for parents-to-be at CareNet Medical Group in Schenectady, NY and teaches “Genethics” an online course for master’s degree students at the Alden March Bioethics Institute of Albany Medical Center.

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