A.T. Bowling - The Genetics of the Horse - 2000.pdf

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Systematics and Phylogeny
of the Horse
C.P. Groves 1 and O.A. Ryder 2
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Systematics and Phylogeny
C.P. Groves and O.A. Ryder
Department of Biological Anthropology, Australian National
University, Canberra, ACT 0200, Australia; 2 Center for Reproduction
of Endangered Species, Zoological Society of San Diego, PO Box 551,
San Diego, CA 92112–0551, USA
The Order Perissodactyla
1
The Family Equidae
2
Genetics of the Equidae
4
Generic Limits
5
Early History of the Genus Equus
6
The species question
7
The subspecies question
8
Nomenclature of Domestic Animals
9
A Taxonomy of the Genus Equus
9
Subgenus Equus : horses
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Subgenus Asinus : ass, onager and kiang
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Subgenus Hippotigris : zebras
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References
22
The Order Perissodactyla
The order Perissodactyla, known as odd-toed hoofed mammals, are character-
ized by the relative enlargement of digit III on each extremity. Other charac-
teristics include, in the skull, the persistence of the tuber maxillare, and, in the
dentition, the basic p -shape of the occlusal pattern of the maxillary molars
(modified in living Equidae, but extremely useful for recognizing primitive
fossil perissodactyls).
The order contains three living groups, the horses, tapirs and rhinos,
and two major extinct groups, the brontotheres (or titanotheres) and the
ancylopods (or chalicotheres). The brontotheres arose in the Early Eocene and
survived into the Oligocene but no longer; the ancyclopods arose in the late
Eocene and survived into the Pleistocene. Tapirs and rhinos differentiated in
the Late Eocene.
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©CAB International 2000. The Genetics of the Horse (eds A.T. Bowling and A. Ruvinsky)
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C.P. Groves and O.A. Ryder
The following outline classification of the Perissodactyla is based on
Prothero and Schoch (1989), but excludes the hyraxes which (contrary to the
classification of Prothero and Schoch) are not perissodactyls but are related to
the elephants and sirenians.
Order Perissodactyla
Suborder Titanotheriomorpha – brontotheres
Suborder Hippomorpha
Superfamily Pachynolophoidea
Superfamily Equioidea
Family Palaeotheriidae
Family Equidae
Suborder Moropomorpha
Parvorder Ancylopoda – chalicotheres
Parvorder Ceratomorpha – tapirs and rhinos
The Pachynolophoidea, restricted to the Eocene, were small perissodactyls
with simple teeth, but with some development of the complexity of the cheek
teeth which characterizes equids; in particular, the premolars were somewhat
molarized (meaning that they had come to resemble the molars to some
degree). The Palaeotheriidae, from the Late Eocene and Early Oligocene, were
larger (some of them tapir-sized) and longer necked, but still extremely primi-
tive; they include Palaeotherium , which was described by Georges Cuvier in
1804, and was one of the very first fossil mammals to be discovered.
The Family Equidae
The Equidae are known from the earliest Eocene. The famous Hyracotherium ,
described by Richard Owen in 1841, is very primitive, and the various species
which have been included within it, and which differ only very slightly from
each other, are now regarded as probable ancestors to the Pachynolophoidea,
the Palaeotheriidae and probably the Moropomorpha as well as the Equidae,
so many authors now place them on cladistic grounds into different genera.
The species described by Owen, Hipparion leporinum , is thought by Hooker
(1984) to be the ancestor of the Palaeotheriidae. The ancestor of the Equidae,
according to Hooker, is the species formerly known as Hyracotherium
cuniculum , which he places in a new genus Cymbalophus .
The general outline of the evolution of the Equidae is summarized by
Evander (1989). After Cymbalophus of the earliest Eocene (54 million years
ago (mya)) of Europe, the line moves to North America, and goes more or less
straight through a series of genera which (except for the last two, which do
overlap) simply mark points on the tree which are represented by good
fossil material: Orohippus (Early Eocene, 50–47 mya), Epihippus (Middle and
Late Eocene, 47–40 mya), Mesohippus (Late Eocene and Early Oligocene,
40–30 mya), and Miohippus (Latest Eocene and Oligocene, 37–25 mya). The
line leading to modern horses had thus gone through more than half of its
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Systematics and Phylogeny
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evolutionary history with hardly any branching until the latest stages. The
narrow basicranium so characteristic of modern horses was absent in the
primitive stages but had been developed by Mesohippus , and the dentition of
each is advanced over its predecessor(s): more complex, with more cusp
development, but still without any uniting of the cusps into ridges.
The line then, at the beginning of the Oligocene some 25 mya branched
into the Anchitheriinae and the Equinae. Both these lines were advanced
in having molar ridges, unlike their predecessors; the Anchitheriinae, which
lasted until about 12 mya in North America and 7 mya in Asia, lost some
features of the molars and the foot skeleton which the Equinae retained, while
the Equinae developed a close-packed foot skeleton suitable for running in
open grasslands.
The line of the Equinae continued through to the Middle Miocene (15
mya) via Kalobatippus, Archaeohippus and Parahippus , with increasingly
complex molars. From Archaeohippus on, the skull developed a post-orbital
bar, a complete strut of bone behind the orbit, separating it from the temporal
fossa. From the later species of Parahippus on, the crowns of the molar and
premolars had become high, covered with cementum, and suitable for shear-
ing silica-rich grasses, and the radius and ulna had become fused. The line
then, about 15 mya, split into three branches: the Protohippini, Hipparionini
and Equini, though Hulbert (1989) considers that the Protohippini are actually
a composite, made up of stem forms of the other two tribes and of their
common ancestors, and includes Protohippus itself in the Equini; all these
late groups are difficult to work out, and there was a good deal of parallel
evolution in such features as large size, development of a pre-orbital fossa and
retraction of the nasal notch. However, the Equini were the only horses to
reduce their toes to one on each foot (with the laterals, represented by
metapodials II and IV, retained as ‘splint bones’), whereas the Hipparionini
developed their lateral toes into support digits, perhaps for marshy country.
The Hipparionini, the last of the three-toed horses, lived in North America until
the beginning of the Pliocene, 5 mya, but survived in the Old World until
about 1 mya, disappearing last from Africa.
Evander’s (1989) classification of the family is (abbreviated and slightly
modified) as follows:
Family Equidae
Cymbalophus
Orohippus
Epihippus
Mesohippus
Miohippus
Subfamily Anchitheriinae
Subfamily Equinae
Kalobatippus
Archaeohippus
Parahippus
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C.P. Groves and O.A. Ryder
Tribe Protohippini
Tribe Hipparionini
Tribe Equini
Dinohippus
Hippidion
Onohippidion
Astrohippus
Pliohippus
Equus
In this classification, the five unranked genera coordinate with the two
subfamilies, and the three coordinate with the three tribes of Equinae, are
given the status of Plesion: a category which means that they are of limited
diversity (one or a few species in each), and primitive for that group (and very
likely ancestral to the remainder).
The genus Dinohippus , which lived in North America between about 8
and 5 mya, is the stem genus of Equus , and Hulbert (1989) even includes it in
Equus . It emerged gradually from Pliohippus , which lived in North America
from about 14.5 to 6 mya; Astrohippus lived in the same region from about 6 to
4.5 mya. Hippidion and Onohippidion were large single-toed horses that lived
in South America from the Early Pliocene until the end of the Pleistocene; their
earliest species lived in North America about 5 mya.
Genetics of the Equidae
Studies of chromosomes and DNA have provided a rich source of information
for interpretation of morphological and palaeontological data (George and
Ryder, 1986; Ryder et al ., 1978; Oakenfull et al ., unpublished observations).
The phylogenetic analysis of DNA sequence data sheds new light on the
systematics and taxonomy of Equus and is highly relevant for conservation
action plans for equid taxa (Oakenfull, equid action plan).
The first DNA-based studies of Equus involved the analysis of mitochon-
drial DNA restriction maps and required purification of mitochondrial DNA
(George and Ryder, 1986). With the advent of the polymerase chain reaction
(PCR), DNA sequence data have become the accepted standard in studies of
molecular evolution; PCR also allows a wide variety of samples previously
unusable for genetic analysis to be utilized in genetic studies. The complete
16,660 nucleotide sequence of a domestic horse mitochondrial DNA has been
published (Xu and Arnason, 1994).
The first extinct organism to have its DNA cloned was the quagga, Equus
( burchelli ) quagga , an event of technical wizardry made even more remark-
able for its accomplishment before PCR was invented (Higuchi et al .,
1984). Samples of dried tissue, a residue of a roughshod taxidermy, provided
sufficient DNA for the construction of a library that included quagga DNA
sequences.
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Systematics and Phylogeny
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Today, bone and tissue fragments, dried blood and dung samples provide
routine sources of DNA for comparative genetic studies. Despite these
advances, it is still the case that DNA sequence data are lacking for some equid
populations and named taxa that confound the assembly of a clear picture of
the systematic relationships of extant and recently extinct taxa. The Somali
wild ass, Syrian, Indian and Mongolian wild asses, and the kiang have yet to be
the subject of reports utilizing molecular methods on wild populations.
Although most equid taxa have been the subject of at least preliminary DNA
sequencing studies, the amount of data is still rather small, may not include
nuclear loci and may incorporate limited sampling of the potential variability
within extant wild populations. The investigation of molecular genetics of
captive and wild equids is an area of great current interest. Thus, we can
anticipate that new findings will soon become available (Oakenfull et al .,
unpublished observations) and that as more intensive analysis incorporating
additional loci and more extensive sampling of extant populations is carried
out, a more refined picture of evolutionary relationships and the resultant
taxonomy will emerge.
The most definitive genetic data pertinent to equid evolution collected
to date involve sequence analysis of mitochondrial DNA. The region of the
circular mitochondrial DNA at which strand displacement for the initiation of
DNA replication takes place (the d-loop) is thought to be the most rapidly
evolving portion of the approximately 16,500 bp molecule. Accordingly, this
region can identify recent divergences due to mutations. Other portions of the
mitochondrial DNA, such as the 12S region and the cytochrome b gene,
accumulate mutations at a slower rate and there is a proportionally smaller
chance that the same sequence of nucleotides is present as a result of two
mutations (a ‘forward’ mutation and a ‘back’ mutation). For this reason,
evidence of the divergence of lineages at the base of the phylogenetic tree
may be derived less ambiguously from more slowly evolving sequences.
Generic Limits
While most specialists have been content to include all living equids in a single
genus, Equus , from time to time different authors have proposed to set aside
one or more species into separate genera, on the general grounds that they
were ‘different enough’. Part of the philosophy was no doubt that horses,
asses, onagers and zebras are all the living species that we have in the family
Equidae, and there is sufficient ‘taxonomic room’ for several genera. The wish
to divide up the genus in this way persists in the modern era: Trumler (1961),
Groves and Mazák (1967) and Bennett (1980) are examples of this. A different
philosophy is behind Quinn’s (1957) multigeneric scheme: that author – incor-
rectly, as most specialists now concur – saw the different modern groups as
the end points of lineages which could be traced back deep into the Miocene,
and had even achieved monodactyly independently.
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