The New Horse Series: Genomes Confuse "Textbook Example of Evolution"

Horses, asses and zebras show evidence of gene flow despite extreme chromosome rearrangements.

An international team studying genomes of living members of the genus Equus (horses, asses and zebras) was astonished at how different species could share genes despite extreme chromosomal rearrangements.  In “Speciation with gene flow in equids despite extensive chromosomal plasticity,” published in PNAS, the team extended the story of horse evolution with new whole-genome data from six species of asses and zebras.  They were surprised by what they found.  The “Significance” paragraph says:

Strikingly, we find multiple instances of hybridization throughout the equine tree, despite extremely divergent chromosomal structures. This contrasts with theories promoting chromosomal incompatibilities as drivers for the origin of equine species.

The Abstract makes the same point in more scholarly lingo, except for the shared word “Strikingly”:

Strikingly, we also find evidence for gene flow involving three contemporary equine species despite chromosomal numbers varying from 16 pairs to 31 pairs. These findings challenge the claim that the accumulation of chromosomal rearrangements drive complete reproductive isolation, and promote equids as a fundamental model for understanding the interplay between chromosomal structure, gene flow, and, ultimately, speciation.

The finding, therefore, casts serious doubt on a common evolutionary claim: speciation occurs when chromosomes get rearranged in a population.  Some of these living species have double the number of chromosome pairs (Przewalski’s horse has 31, mountain zebras have 16), but many still show evidence of gene flow (hybridization).  This fact will undoubtedly lead to new thinking about the role of reproductive isolation in evolution.

The story of horse evolution is more complex than what was presented a century ago.  Today’s students, shown charts of horse evolution, may not realize that “Although the equine fossil record represents a textbook example of evolution, the succession of events that gave rise to the diversity of species existing today remains unclear.”  To get the new story to work, the authors proposed the following sequence of events:

1. Horse ancestors appeared 55 million years ago in the New World.  These had three or four toes.
2. The ancestors diversified into dozens of genera in the Old and New Worlds.  Most of this past diversity is now extinct.
3. All living equids belong to a single remaining genus, Equus, which “most likely” diverged 4 to 4.5 million years ago.
4. “Our analysis suggests that noncaballine equids did not emerge after a founder event into the Old World, but rather maintained gene flow in North America with caballine equids. We estimate that this gene flow ceased 2.1–3.4 Mya, which closely matches the paleontological evidence for the noncaballine dispersal out of America.”  How did these animals get across the ocean?
5. Asses and zebras have natural habitats spreading across Asia and Africa.  All zebra species live in Africa.

The succession of events is unclear, they say, “mainly because the paleontologic record has been split into an excessive number of taxonomic assemblages and is incomplete in some regions of the world.”  This may not only mean that the evolutionary picture is built on an incomplete set of pieces, but indicates an eagerness by some taxonomists to call fossils members of a new species when they are not.

They refer to “extreme karyotypic plasticity” (chromosomal flexibility) in early horse evolution, suggesting that existing genetic information can be shuffled between different numbers of chromosomes through fusion and fission.  Most of the chromosomal rearrangements appear downward.  Mountain zebras, for instance, “experienced almost four times more chromosome losses than gains, resulting in the smallest number of chromosomes in the entire genus,” 16 pairs.

Thus, we conclude that such massive karyotypic changes have not resulted in full reproductive isolation, in stark contrast with theories assuming that chromosomal impairment during meiosis is responsible for complete sterility in hybrids, but in agreement with the description of fertile offspring across equine species.

In fact, the authors mention a rare case: “Interestingly, although mules are generally sterile, a similar quartet involving a fertile female mule, a male donkey, and two offspring was reported recently.”  Since the “biological species concept” defines a species as capable of producing fertile offspring, this casts confusion into the taxonomy of Equus.  The authors found strong evidence of inbreeding in some of the genomes.

Although the team refers to evidence of “positive selection,” they only mention changes in regulation of existing systems like metabolism, olfaction, development and behavior as the species adapted to varying habitats.  The Tibetan kiang, for instance, lives at elevations as high as 5,400 m (17,700 ft), while burros and donkeys in North America and the middle east commonly live in low-elevation deserts.  The authors make no reference to “innovation” or “novel” features in their references to “positive selection.”

Clearly, a reduction in the number of toes does not count as an example of innovation, even if it proved to be adaptive.  Nor does size; living Shetland ponies and Clydesdale horses have organs and systems in common.  Strangely, the scientists identify one gene associated with autism in humans as having undergone “positive selection” in the extinct quagga, a once-abundant variety of plains zebra with a striped front and brown rear that “was driven to extinction in the early 1900s” (the authors sequenced its genes from hair samples).

In summary, the evolutionary picture of extinct equids over 55 million years is “unclear,” they said, and none of their new genetic work identifies a truly novel feature.  In addition, the living species indicate high levels of gene flow between populations despite “extreme” chromosomal rearrangements.  The evolutionary story is not complete:

High-resolution structural characterization will be required to fully explore the precise influence of chromosomal rearrangements on gene flow. For now, our study provides the first empirical evidence connecting gene flow and chromosomal rearrangements in equids. The extreme plasticity of their karyotype and the presence of multiple gene flows make equids a promising model for deciphering the role of chromosomal rearrangements in speciation.

So even though equids represent “one of the most famous examples of evolutionary transition,” the authors provided little evidence of actual Darwinian progress to maintain its status as a “textbook example” of evolution.  For comparison, see what evolutionists have said about horse evolution in the past decade (3/18/05, 12/11/09, 6/27/13).

Oh, the seductive power of visualization.  That horse series diagram that adorned biology textbooks throughout the 20th century was simple, elegant and wrong—just like Haeckel’s embryos, Darwin’s finches, and worst of all, the march from monkey to man.  The simplicity of the diagrams shields viewers from the complex truth.  Don’t be a sucker.  For fun, re-read our commentary from 3/18/05: “The horse evolution icon, like Rasputin, has been shot, stabbed and drowned, but is taking his time to get dead….”