Evolution under the microscope

Evolution of horses

Outline of evolution of the modern horse (Equus)

The ancestry of the horse family (Equidae) over the last 55 million years is certainly the best-known example of sustained morphological change in the fossil record (fig. 1), mentioned in almost every textbook on evolution. Horse-like mammals were abundant through most of the Cenozoic Era, especially in North America where many fossils have been found, and it was in the 1870s that the American palaeontologist Othniel Charles Marsh proposed an evolutionary link between them. This was not long after Darwin’s Origin (1859), and it helped to persuade many of the truth of evolution. Marsh envisaged horse evolution as having been essentially linear, but as more fossils emerged it became apparent that it was bushy – better seen as a series of radiations with subsequent extinction of most of the terminal branches.

Figure 1. Schematic ancestry of the horse.

Eocene and Oligocene

The first horse-like animals, of a genus called Eohippus (or Hyracotherium [1]), appeared in the early Eocene, about 55 million years ago (Mya), and were about the size of a fox. They had long bones in their legs and toes, and the latter were held almost vertical so that they walked on the tips of their toes; all of which made them well suited for running. They had three and four toes respectively on their hind- and fore limbs. Although the toes ended in small hooves, it is thought they walked predominantly on toe pads (like a dog) rather than these hooves. Its teeth were relatively small, but clearly those of a herbivore, and they fed mainly by browsing for leaves and fruit (rather than the grazing of modern horses).

During the Eocene and Oligocene, in North America (see below for elsewhere) the early horses developed through intermediate genera known as Orohippus, Epihippus and Mesohippus, to Miohippus by about 35 Mya. Compared to Eohippus, Miohippus was somewhat larger and had longer legs and feet. Of particular note, the forelegs had lost their outermost toe, so there were three toes on each foot (tridactyl); and in each case the middle toe was now clearly larger than the outer ones. Also, its premolars were more like molars, and all the cheek teeth had higher crests. Miohippus persisted until about 20 Mya, well into the Miocene.

It should be noted that this evolution was not a simple linear succession, but there was some temporal overlapping of genera, indicating that species did not just evolve progressively into the next (anagenesis) but at least some speciation or splitting took place, with daughter species diverging.


This pattern was even more pronounced in the Miocene when the horses diversified widely, with at least a dozen genera living contemporaneously in North America. The main features of this evolution are as follows:

One line, Anchitherium, generally remained like Miohippus in both feet and teeth, but extended its range into the Old World where it gave rise to the much larger Sinohippus.

Of particular importance was Merychippus, which was about the size of a pony, and in which all the side toes were so small that it walked on only its middle toes, which now had a significant hoof. The teeth were more convoluted, with cement – providing improved abrasive surfaces for grinding siliceous plant material such as grasses; and it was probably the first of the horse family to feed predominantly by grazing.

Merychippus diverged, with one branch leading to the Hipparions which had more developed teeth, although with relatively unchanged feet. The Hipparions included various related genera (including Hipparion) which became widespread in both America and Europe where they survived until the Pleistocene.

The other important branch led to various genera including Dinohippus in which not only were the teeth more developed, but the side toes were so reduced that these animals effectively were single-toed (monodactyl). It became the most abundant equid in North America, and it is likely from Dinohippus that the modern horse, Equus, is derived.


It was during the Pliocene when the modern horse appeared. Almost all of the above horse evolution took place in North America, with occasional migrations of some genera to the Old World; but all of these became extinct there. Equus also migrated to the Old World, including Africa where it founded species such as the zebras, and to South America. Interestingly, after North America having been the birth-place of the horse, Equus became extinct there about 10,000 years ago, but was reintroduced from the Old World by man in the 16th century.

equine evolution

Figure 2. Main anatomical changes in the course of horse evolution. [a]


There are three major trends in passing from Eohippus to the modern horse:

equine evolution

Figure 2. Main anatomical changes in the course of horse evolution. [a]

What evolutionary processes were taking place?

The evolutionary paradigm is that

  1. mutations produce genetic variability,
  2. which (in the course of reproduction) is the basis for morphological (or phenotypic) variation,
  3. on which natural selection acts, to produce gradual change.

And in due course accumulation of small changes means that substantial change is achieved through repeated operation of these processes.

However, as amplified in what is the difference between micro- and macroevolution, all too often evolutionary biologists consider only (a) the production of variations (by mutation and in the course of reproduction) and (b) the selection of favourable variations; i.e. they generally conflate (1) and (2). It’s almost as if they do not actually recognise that there are these different processes operating, and certainly don't seem to consider which process(es) are occurring in any particular instance of evolution.

Consequently, when presented with the evidence about horse evolution, which clearly includes the production of variations and gradual change over millions of years, it seems they automatically assume that this demonstrates (and substantiates) the whole of the evolutionary process. For example:

All the morphological changes in the history of the Equidae can be accounted for by the neo-Darwinian theory of microevolution: genetic variation, natural selection, genetic drift, and speciation. [2]

Here, Douglas Futuyama, who is a world-renowned evolutionary biologist [3], simply lumps together the origin of useful genetic variability by mutation and the production of phenotypic variation through reproductive processes (as did Ernst Mayr).

However, it would be good science at least to ask what processes are taking place. And if we do this, it is clear that there are good reasons for thinking that all of the observed evolution of horses can be explained by, in fact is better explained by, segregation and selection of genes from an original gene pool (i.e. (2) and (3) above), rather than involving the production of new (useful) genes (i.e. (1) above).

Evidence indicates that the evolution of horses was due to selection from a gene pool rather than involving the production of new genes

1. The morphological changes were limited – entirely explicable by gene segregation

It is worth noting first that Eohippus was a thoroughgoing perissodactyl: It was fully herbivorous, with appropriate teeth and its intestines probably included a caecum (cf. human appendix) which accommodated bacteria for digesting cellulose and other plant material. [4] Also, it was lightly built, with slender legs and tip-toed gait, all of which made it well-suited for running.

All of the subsequent morphological changes were relatively minor modifications of characters already present in Eohippus. Even changes of the skull were only quantitative rather than qualitative, i.e. can be accounted for in terms of differential growth of various parts of it (termed allometry), rather than requiring fundamentally novel features. An indication that the differences between the various fossil and extant horses were rather limited is that all of the species are classified within a single family, Equidea. And, for example, one researcher commented on the ‘remarkable uniformity of anatomical features’ of all of the equids. [5] Also, whilst different characters are involved, the scale of the changes is comparable with those between the various breeds of dog (which we even regard as the same species).

So it is certainly reasonable to suggest that changes of the magnitude we see in horse evolution could be achieved by gene segregation alone.

2. The morphological change was limited – and cannot be retropolated to account for preceding evolution

Compared with Eohippus, modern horses are larger, with longer legs, longer and more convoluted teeth, and fewer toes. Yet these relatively minor changes took place over 50 million years or more.

This is approximately 10% of the time since the appearance of modern animal phyla (including chordates) in the Cambrian explosion; yet the morphological change is much less than 10% of that between the earliest chordate and Eohippus. So whatever evolutionary processes were taking place in the 50 million years of horse evolution will certainly not account for the preceding evolution (which necessarily would have required the production of new genes).

3a. Characters were very variable

As more horse fossils have become known, it is increasingly apparent not only that the evolution of the horse had not been simply linear but branched, but also that the ancestral horses showed a wide range of within-species and within-genera variation. This was true right from the start; for example, in a paper in which he argued that the European Hyracotherium was synonymous with the American Eohippis, George Gaylord Simpson concluded that:

Teeth of hyracotheres are extraordinarily variable. No two specimens are in really close agreement.

Specimens from the London Clay do not suffice to show whether their strong variation was segregated into two or more separate specific populations or was manifested in a series of interbreeding populations, perhaps with some progressive temporal change. [6]

Indeed, the earliest horses were so varied that in 2002 Froehlich [7] reclassified them into several genera (reversing the view of Simpson). But others have argued against at least some of Froehlich’s splitting, e.g.

We thus conclude that the diagnostic characteristics show intraspecific variation rather than taxonomically significant variation, so S. sandrae and M. jicarillai are the same genus and species. [8]

And at a recently discovered early Eocene (52/53 Mya) site in France the number of specimens of one species showed

a high degree of unsuspected variability within this taxon, including sexual dimorphism, thus permitting discussion of the reliability of commonly used characters [9]

That is, the characters often used to distinguish between species and genera may be too variable to be used for this purpose; the differences between character states may reflect variation of that character within the same species rather than distinguish between different species or genera.

This sort of variation was a persistent feature of the evolving horse lines, with Ann Forstén commenting

I see no advantage in splitting up the generic/specific taxonomy too much. On the contrary, the many synonyms bestowed on fossil equids in the last century indicates that over-splitting should be a thing of the past. It indicates underestimation of the variation within taxa and a lack of knowledge of the pertinent literature. [10]

Interestingly, with the advent of DNA analyses, these too have shown that recent equids show significant within-species morphological variation and have probably been over-split taxonomically.

Overall, the new genetic results suggest that we have underestimated how much a single species can vary over time and space, and mistakenly assumed more diversity among extinct species of megafauna. [11]

3b. Characters diversified rather than just proceeded in one direction

In addition to this widespread variation, it should be noted that characters diversified rather than just proceeded in one direction – part of the ‘bushy’ nature of the horse ancestry already noted. In particular, whereas the general view is of a gradual increase in the size of the horse, some lines became even larger than modern horses, and others became very small.

Therefore, for horses, the traditional interpretation of gradual increase in body size through time is oversimplified because: (1) although the exception to the rule, 5 of 24 species lineages studied are characterized by dwarfism; and (2) the general trend seems to have been a long period (32 ma) of relative stasis followed by 25 ma of diversification and progressive (although not necessarily gradual) change in body size. [12]

For example, some of the distant descendants of Eohippus, like the Pliocene horse Nannipus, were even smaller than the early horses. Similarly, although the usual trend was for lengthening of feet bones, some became shorter.

This variation and diversification of characters is the sort of pattern we get when a parent population with substantial genetic variability diversifies, and perhaps adapts to different environmental niches, such as the Galapagos finches.

4. The same characters evolved in different lineages

What carries particular weight is that the same morphological characters evolved in different lineages.

North America

Many morphological characters, which are considered advanced and used for taxonomic purposes and phylogeny reconstruction, evolved time and again in very different lineages of horses. Such characters are:

  • increased hypsodonty, which reached its peak (i.e. crown growth even after tooth eruption) in ... ;
  • straight enamel lines (the ‘cabballoid’ pattern) of the occlusal surface of the cheek teeth in …;
  • loss of cingular stylids in the lower cheek teeth, even in deciduous teeth, in … ;
  • development of a shallow ectoflexid in the lower molars in … ;
  • restriction and subsequent disappearance of the preorbital fossa in … ;
  • retraction and deepening of the nasal opening in … ;
  • development of a ‘monodactyl’ ligamental apparatus of the distal central toe (...), irrespective of reduction or not in the lateral toes, in … ;
  • gigantism/dwarfism in … ;
  • extremely elongated/shortened feet in … ; [13]

In addition, monodactyly developed independently in at least 4 distinct lineages. [14]

If the above features had arisen through the production of new genes it would require that the same many coordinated mutations required for each of these would need to have occurred independently in different evolving lines, which must surely be extremely unlikely.

Now we could choose to believe that somehow or other the horse-like mammals had some sort of propensity for these particular mutations. But surely a much more credible explanation is that the genetic bases for these features were already available within Eohippus. Then, through a combination of random mixing (in the course of reproduction) and selection, in various lines appropriate gene combinations arose, and the various traits emerged – analogous to the races of North American house sparrow or the various species of Galapagos finches (or the wide range of morphological features of different dog breeds, by artificial selection).

An observation that especially supports this latter view is that the monodactyl ligamental apparatus of the distal toe evolved in tridactyl genera (the 7th in Forstén's list). Given that this is supposed to be an adaptation to the single-toed status, it would be very odd if it evolved de novo in three-toed animals.

What takes it beyond any reasonable doubt is that, whereas Ann Forstén’s comments relate to the horses that evolved in North America, a similar pattern emerged in Europe.

The Old World

Accounts of horse evolution tend to focus on North America, because that is where it reached the modern horse. However, at the start of the Eocene, America was still joined to Europe and Eohippus lived there as well; but the two continents split soon afterwards and the two founding populations of Eohippus evolved separately. (Occasional land bridges occurred in the region of the Bering Strait from the Miocene onwards, allowing the migrations to the Old World mentioned above.) The European Eohippus diversified almost immediately into what are known as the Palaeotheriidae, reaching levels of diversity in the Eocene comparable with that occurring in North America in the Miocene (about 30 million years later), but became extinct early in the Oligocene (see Fig. 1).

Click to display Figure 1 again here.

What is particularly relevant is that this group developed many of the same characters as those in North America, notably large body size (Paleotherium magnum which lived as early as about 45 Mya was almost as large as a modern horse), more molarised teeth with cement, and reduction of the outer toes.

The variety of genera and species of equoids in the Eocene in Europe is comparable to the variety of equids during the Miocene in North America. [15]

These similar developments arose quite independently of those in North America, being separated by the nascent Atlantic, and the timing was very different anyway.

So, yet again, we have to propose that essentially the same mutations arose in completely different populations of Eohippus, or – surely much more likely – that the necessary genes were already present in the original Eohippus population.

In addition, the much earlier diversification would be all the more difficult to explain in terms of accumulating appropriate mutations in less time (given how unlikely useful new genes are), whereas there is no difficulty in achieving rapid diversification by gene segregation. In fact, the diversification is readily accounted for by the fact that, during the Eocene, Europe was an archipelago, and we are well aware that geographical separation, such as on islands, promotes gene segregation (such as the finches on the Galapagos Islands).

In the Paleogene [Paleocene-Eocene-Oligocene], Europe was an archipelago surrounded by sea. The great diversity of equoids in Europe in contrast to the sparsity of taxa in Asia and North America may have been due to the fragmentation of the European continent and the differentiation of species in isolation. [16]

5. Reduced adaptability following diversification

Diversification is generally seen by biologists as an indication of a species’ adaptability and hence actual and potential successfulness. Consequently, when the equids diversified – during the Eocene in Europe, and during the Miocene in N. America – this is perceived as indicating that the equids at the time were robust, successful and expected to continue flourishing. So biologists such as Forstén comment with some surprise at their subsequent demise:

At the time of their demise in Europe, in the Eocene, horses were generically diverse and flourishing, whereas at the same time in North America they survived despite being little differentiated. [17]

However, I think this is confusing morphological diversity among related groups with genetic diversity within each of those groups, and I suggest an alternative view:

The European horses were morphologically diverse because the original genetic diversity (in Eohippus) had been segregated (and some lost in the course of specialisation); although there was a variety of genera, the individual genera had reduced genetic variability. Consequently they were less adaptable, less tolerant of changing conditions, so more susceptible to extinction. In contrast, because the North American horses changed little during the Eocene and Oligocene, they retained their genetic variability, and survived. But then, having diversified (and specialised) from the beginning of the Miocene (possibly because their habitat, whilst still continental, also diversified), most were extinct by the end of the Miocene. Could this have been because, like their European cousins long before, in diversifying (and specialising), individually they had lost their genetic variability and adaptability?

A similar comment is made by Azzaroli about the demise of Equus in N. America:

In view of their remarkable capacity for adaptation, the dramatic decline in equids in number of species, and in the case of Eurasia in number of individuals of the surviving species, can hardly have been caused by climatic factors alone and is believed to be largely the result of prehistoric overkill. [18]

Again, an alternative view is that the Equus were susceptible to environmental challenges, not despite but because of the preceding diversification of the equids, which meant that Equus had become specialised, with limited genetic variability, and hence has limited scope for further adaptation.

In other words, this pattern of diversification being followed by extinction – occurring independently in Europe and N. America – is an indication that the diversifications were due to segregation of genes – and loss of genetic variability within any particular genus – rather than acquisition of new genetic variability.


It makes more sense that the evolution of the horse was due to segregation and selection from a gene pool already present in Eohippus, rather than involving the production of new genes, because:




Notes display in the main text when the cursor is on the Note number.

1. Eohippus was the name generally used for the early horse in America, Hyracotherium in Europe. George Gaylord Simpson [6] concluded that they are synonymous.

2. Futuyma, D.J., Evolutionary Biology. Sinauer Associates (1986), p409.

3. He is Distinguished Professor in the Department of Ecology and Evolution at Stony Brook University in Stony Brook, New York and a Research Associate on staff at the American Museum of Natural History in New York City. His research focuses on speciation and population biology. Futuyma is the author of a widely used undergraduate textbook on evolution. Source: Wikipedia, Douglas_J._Futuyma, accessed 20 Dec 2017.

4. Christine Janus, The evolutionary strategy of the Equidae and the origins of rumen and cecal digestion, Evolution 30:757-774 (1976).

5. A. Azzaroli, Ascent and decline of monodactyl equids: a case for prehistoric overkill, Ann. Zool. Fennici 28:151-163 (1992), p158.

6. G.G. Simpson, Notes on British Hyracotheres, Zoological Journal of the Linnean Society Vol 52 (1951), Issue 284, pp195-206.

7. David Froehlich; Quo vadis eohippus? The systematics and taxonomy of the early Eocene equids (Perissodactyla), Zoological Journal of te Linnean Society Vol 134 (2002), pp141-256

8. Julie E. Rej and Spencer Lucas, Morphological comparison of two early Eocene horse taxa: Minipuss of New Mexico and Sifrhippus of Wyoming, New Mexico Museum of Natural History and Science Bulletin 74 (2016), p223-230.

9. Laurie Danilo, Jean A. Remy, Monique Vianey-Liaud, Bernard Marandat, Jean Sudre and Fabrice Lihoreau; A new Eocene locality in Southern France sheds light on the basal radiation of Palaeotheriidae (Mammalia, Perissodactyla, Equoidea), Journal of Vertebrate Paleontology, Vol 33 (2013) pp195-215.

10. Ann Forstén; Horse Diversity through the ages, Biological Reviews of the Cambridge Philosophical Society, Vol 64 (1989), p282.

11. Ludovic Orlando, Jessica L. Metcalf, Maria T. Alberdi, Miguel Telles-Antunes, Dominiqu Bonjeane, Marcel Otte, Fabiana Martin, Véra Eisenmann, Marjan Mashkour, Flavia Morello, Jose L. Prado, Rodolfo Salas-Gismondi, Bruce J. Shockey, Patrick J. Wrinn, Sergei K. Vasil’ev, Nikolai D. Ovodov, Michael I. Cherry, Blair Hopwood, Dean Male, Jeremy J. Austin, Catherine Hänni, and Alan Cooper; Revising the recent evolutionary history of equids using ancient DNA, PNAS vol 106, No. 51 (2009) pp21754-21759.

12. B. Macfadden; Fossil Horses from 'Eohippus' (Hyracotherium) to Equus: Scaling, Cope’s Law, and the Evolution of Body Size, Paleobiology Vol 12, No. 4 (1986) pp 355-369.

13. Ann Forstén; Horse Diversity through the ages, Biological Reviews of the Cambridge Philosophical Society, Vol 64 (1989), p283; formatting added.

14. A. Azzaroli, Ascent and decline of monodactyl equids: a case for prehistoric overkill, Ann. Zool. Fennici 28:151-163 (1992), p151.

15. Ann Forstén; Horse Diversity through the ages, Biological Reviews of the Cambridge Philosophical Society, Vol 64 (1989), p285.

16. Ann Forstén; Horse Diversity through the ages, Biological Reviews of the Cambridge Philosophical Society, Vol 64 (1989), p285.

17. Ann Forstén; Horse Diversity through the ages, Biological Reviews of the Cambridge Philosophical Society, Vol 64 (1989), p279.

18. A. Azzaroli, Ascent and decline of monodactyl equids: a case for prehistoric overkill, Ann. Zool. Fennici 28:151-163 (1992), p151.

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