Weinstock et al. have published a solid and interesting paper that attempts to resolve some issues in the recent evolution of horses. It's good work, and shows how molecular analysis of fossils can complement morphological studies to give a clearer picture of organismal history. Unsurprisingly, though, creationists are already spluttering out nonsense about it. I'm going to give a quick overview of the scientific results, and then show some of the creationist babble in response (not too much, though—you'll quickly see how dishonest and evasive creationists are).

First, what the paper is not: it is not a big picture view of all of the evolutionary history of horses. If you want that, I greatly recommend Kathleen Hunt's horse evolution FAQ. This paper, like most science papers, is very tightly focused on a specific, addressable problem…in this case, resolving the phylogeny of just American horse species within the last 3 million years. What Weinstock et al. were trying to figure out is how 3 major groups of horse species were related to one another, and how they were related to Old World horses. The method they are using is to extract ancient mitochondrial DNA from bone specimens, sequence a particularly informative stretch, and use established computer techniques to fit them into a phylogenetic tree.

The three groups they are trying to resolve are:

• The caballines, or the true horses, of which our modern Equus are representatives.
• The stilt-legged horses, species that resemble the true horses but were more slender limbed, and resemble Asian asses, such as the onager and kiang.
• Hippidion, a distinctive animal with a boxy skull and shorter, stouter limbs.

They have measurable, objective data to distinguish the three groups, as for example, in this plot of metatarsal dimensions.

Metatarsal Shape and Size in Pleistocene and Extant Equids. (A) Bivariate plot showing metatarsal shape and size in extant and extinct horses. Modern asses: kiang (E. kiang) = light blue circles; onager (E. hemionus onager) = dark blue; kulan (E. hemionus kulan) = purple. Pleistocene equids: stilt-legged from Alaska and the Yukon = black; E. lambei (Alaska) = red; stilt-legged from Natural Trap Cave (Wyoming) = yellow; caballines from Natural Trap Cave = orange; caballines from Alberta = green; H. saldiasi from southern Patagonia = grey. “A” and “B” above/beside points of caballine horses denote the phylogenetic clade to which the specimens belong. Not all of the specimens were genetically analyzed.

Prior hypotheses of the relationship of these three North American groups suggested that, because of their morphology similarity to Asian stock, the stilt-legged horses were related the Asian asses, and had migrated into the Americas by way of the Bering land bridge. Hippidion was so distinctly different from other horses that it was considered to have diverged from the equid lineage about 10 million years ago. These species were thought to have spread into South America during the Great American Biotic Interchange about 2.5 million years ago, when the Isthmus of Panama formed and allowed animals to move north and south between the continents. Two competing models of these relationships, based on morphological analyses, are shown below.

Diagrammatic Representation of North and South American Equid Taxonomy Superimposed on a Time Scale according to Paleontological Data. (A) represents MacFadden's view of hippidiform origins from a pliohippine, diversifying into two genera, Hippidion and Onohippidium, in North America during the Miocene. (B) shows Alberdi and Prado's view of hippidiforms as descendants of a pliohippine during the Miocene; the single genus, Hippidion, originates only after dispersal into South America (they do not recognize the genus Onohippidium as valid).

The molecular data revealed a surprise, though. The tree below was constructed by analysis of mtDNA, and it groups the animals very differently. The caballines of America and Europe form a single clade, as expected. The stilt-legged horses and Hippodion, though, cluster together; Hippodion diverged only recently, and the stilt-legged horses are more closely related to the caballines than to the Asian asses. The authors also suggest that many species within the caballines ought to be lumped together, are more likely to represent regional variants than true species.

Phylogeny of Recent and Pleistocene Equids The maximum likelihood tree was constructed with two fragments of the mitochondrial control region (583 bp and 133 bp in the HVR1 and HVR2 regions, respectively). Bayesian analysis produced a similar topology. The general time-reversible substitution model was used in both techniques. Black numbers above/beside nodes are posterior probabilities and bootstrap values, respectively (only values > 50% are shown). White numbers on black background are divergence times as calculated from the molecular data. Numbers/letters in bold at the beginning of each specimen's name are sample numbers or GenBank accession numbers. Labels of prehistoric specimens are followed by their age, if available, in thousands of years. The outgroup (Rhinoceros and Ceratotherium) is not shown.

It's a bit of a shakeup, and I'm sure taxonomists and phylogeneticists will be arguing about it for years. Here's their revised diagram of recent horse history:

Diagrammatic Representation of North and South American Equid Taxonomy Superimposed on a Time Scale according to Molecular Data. (C) represents the results of the molecular data presented in the Weinstock study; it shows Hippidion as originating during the Pliocene, c. 3-3.5 Ma ago. The stilt-legged horse is possibly a sister species of Hippidion.

Now what about those creationists? I was interested to discover a very recent response to this article, and I was curious to see how they would deal with it. The short answer: they didn't. They're quite sure it is wrong, of course, but they make no attempt at analysis—I suspect they just looked at it dull-eyed and uncomprehending, and did what all creationists do: went looking for some blanket disclaimer from a creationist authority that they could parrot. They found one at Apologetics Press, and it is amusingly bad. It's a rebuttal to an article by David Quammen in National Geographic that starts off this way:

In a section of his article that is an inexcusable gaffe on his part, and one that surely must represent a terrible embarrassment to his evolutionary colleagues, Quammen resurrected the long-dead concept of "horse evolution."

The concept of horse evolution isn't dead at all, and the Weinstock article is discussing at length and in some detail the evidence for evolution of several lineages. Where do creationists get this odd idea that evolutionary biologists would be embarrassed by someone discussing the evolution of horses?

It's all stone-cold ignorance, of course. The explanation comes a little further down.

Evolutionists themselves long ago abandoned horse evolution as an example of transitional forms, since they no longer believe the fossil record represents anything like a straightforward progression, but instead a bush with many varying branches.

How silly. The fossil history of horses is full of transitional forms. We don't think of evolution as simple linear progress, that is true…but even Darwin in the Origin drew a general picture of evolution as a branching tree. The idea of a linear progression is a common creationist misconception. What this article is basically doing, then, is complaining that evolutionary biologists' idea of horse history accurately reflects its complexity, while the creationists idea of simple lineages has been shown to be wrong…and they somehow mentally translate this into an example of biologists being wrong.

I really didn't need to read further. It's an excellent example of empty creationist noise against a rich (and growing richer) set of evolutionary data.

Weinstock J, Willerslev E, Sher A, Tong W, Ho SYW, et al. (2005) Evolution, systematics, and phylogeography of Pleistocene horses in the new world: A molecular perspective. PLoS Biol 3(8): e241.