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Evolution, phylogeny, ecology and conservation of the Clade Glires:
Lagomorpha and Rodentia
15
Volume 6 of the Handbook of the Mammals of the World presents a thorough synthesis of the mam-
malian clade Glires, consisting of the orders Lagomorpha and Rodentia. The number of species
in each of these two orders is in constant ux as new species are described, recognized forms are
split into multiple previously cryptic species, and previously recognized species are lumped into
one. There are currently 92 species of lagomorphs treated in this volume. The number of species
of rodents will only be fully dened when Volume 7 is completed; it is likely to be close to 2400
species, or about 40% of all living mammals. Given the extremely large number of species, the or-
der Rodentia will be treated partially in this volume and completed in Volume 7. This volume will
cover two of the three major groupings of rodents, based upon skull morphology: sciuromorphs
(squirrel-like skull morphology) and hystricomorphs (porcupine-like skull morphology). Volume
7 will cover the remainder of the rodents in the suborder Myomorpha, or rodents with mouse-like
skull morphology, including the superfamilies Dipodoidea and Muroidea. Those two superfami-
lies account for two-thirds of all rodent species. This introductory chapter will summarize the fossil
record and early evolutionary history of lagomorphs and rodents, the phylogenetic relations of
families of rodents and lagomorphs in their respective orders, and morphological characteristics
that help to dene their higher-level relationships. It also addresses the diverse array of adaptations
in lagomorphs and rodents, their important ecological roles, aspects of their social behavior, and
their conservation.
We discuss how the study of phylogenies has evolved over the years, using techniques as var-
ied as morphological comparisons, chromosomal structures, protein isozymes and electrophore-
sis, and most recently, a battery of increasing complex and data intensive molecular approaches.
Much of the evolution in techniques has directly affected rodent phylogenetic research, largely
driven by the search to better understand the relationships among species in this incredibly diverse
group, which is often composed of cryptic species complexes that require detailed and integrative
study to untangle. Understanding the development of phylogenies is an important contribution to
understanding the presentation of species in these next two volumes. Phylogenies form the basis
for most of the species presentations when sufcient data are available, and the sections on family-
level systematics discuss important recent changes in our understanding of evolutionary history
based upon the results of new molecular approaches and associated informatics.
Lagomorphs and Rodents in the Context of the Mammalian Radiations
Hares, rabbits, pikas, and rodents are a diverse group of mammals with an exceptional variability of
body forms and sizes, morphological and physiological adaptations, and ecological roles and func-
tions. Rabbits, hares, and pikas are in the order Lagomorpha and are absent as native species only
on a number of continental and oceanic islands and Antarctica and Australia, although they have
been introduced to Australia, causing signicant ecological impacts. Rodents are classied in the
order Rodentia and are present on all continents except Antarctica and are natively absent from
New Zealand and a number of oceanic islands. Although these two orders have long-divergent
histories of independent evolution, they are sister taxa in a clade of mammals referred to as Glires.
Mammals are grouped into a number of higher-level clades that reect their diversication in rela-
tion to the early separation of the supercontinent Pangea into the northern continent of Laurasia
and the southern continent of Gondwana.
The southern continents gave rise to egg-laying monotremes (represented now by the four
species of echidna, Tachyglossidae, and the duck-billed Platypus, Ornithorhynchus anatinus) and
the marsupial radiation that persists today with a diversity of more than 350 species living in South
America and Australia. The group of true placental mammals, or Eutheria, has major clades that
Evolution, Phylogeny, Ecology, and
Conservation of the Clade Glires:
Lagomorpha and Rodentia
ThomasE. Lacher, Jr., WilliamJ. Murphy, Jordan Rogan, AndrewT. Smith, and NathanS. Upham
0
60 40 20 0
5
10
15
20
25
Paleogene
Cenozoic
Lagomorpha
100%
Neogene
Genera sampled in bin
(Approximate)
0
60 40 20 0
50
100
150
200
250
Paleogene
Cenozoic
Rodentia
100%
Neogene
Genera sampled in bin
(Approximate)
Evolution, phylogeny, ecology and conservation of the Clade Glires:
Lagomorpha and Rodentia
16
speciated and diversied in both the northern and southern continental landmasses. Current evi-
dence suggests that the superorders Afrotheria (elephants, hyraxes, manatees and dugongs, the
aardvark, elephant shrews, and insectivorous taxa like golden moles and tenrecs) and Xenarthra
(armadillos, sloths, and anteaters) had a Gondwanan origin and diversication. Which of these
groups diverged earliest from other eutherians is actively debated, with some studies suggesting
that Afrotheria diverged rst and others arguing for Xenarthra as the basal-most group. Some
studies nd that Afrotheria and Xenarthra are monophyletic, a superordinal group referred to as
Atlantogenata.
The northern continental landmasses are considered the region for the evolution and radia-
tion of two other superorders: Laurasiatheria and Euarchontoglires. Often these two superorders
are grouped under the magnorder Boreoeutheria, or the “northern eutherians.” Laurasiatheria
contains shrews, moles, hedgehogs, and the unusual shrew-like solenodon; whales, dolphins, por-
poises, and narwhals; even-toed ungulates like antelopes and deer; bats; odd-toed ungulate group of
horses, rhinoceroses, and tapirs; pangolins; and all the varied forms of carnivores like felids, canids,
mongooses, and other taxa. Euarchontoglires contains the clade Euarchonta, which is the primates,
colugos, and tree-shrews, and their sister clade Glires, which is the clade of interest to us in volumes
6 and 7 of the Handbook of the Mammals of the World, and contains Lagomorpha and Rodentia.
Fossil Record and Early Evolutionary History of Lagomorphs and Rodents
Lagomorphs and rodents rst appear in the late Paleocene to early Eocene of Eurasia and North
America, between about 55 and 57 million years ago. Recent work suggests that there were two
major sister clades: the Duplicidentata, containing Lagomorphs plus stem fossil groups, most likely
genera like Mimotona and Mimolagus derived from the Anagaloidea; and the Simplicidentata, with
the sister family Eurymylidae grouped with Rodentia. The fossil record shows a rise and several
peaks and declines in diversity of both lagomorphs and rodents during their evolutionary history
(Figures 1 and 2).
The family Leporidae (hares and rabbits) likely originated in Asia during the Eocene and di-
versied into North America and Asia during the Oligocene and Miocene. Some early Eurasian
leporid genera include Shamolagus, Lushilagus, Dituberolagus, and Strenulagus. Early North Amer-
ican leporids were Mytonolagus, Megalagus, and Tachylagus. Leporids remained restricted to the
Northern Hemisphere until the Miocene–Pliocene transition, when they expanded their distribu-
tion to South America and Africa. Their largest radiation in the late Miocene was similar to that
experienced by the family Ochotonidae and may have been associated with the expansion of open
grassland habitats during the Miocene. The largest known leporid, the giant Nuralagus rex weigh-
ing 12kg (Figure 3) was present on the island of Minorca (Balearic Islands) in the Mediterranean
until the late Pliocene. In the absence of predators, it probably walked and could not hop. The
extant genera of leporids began to appear in the early Miocene, with the two most diverse genera,
Lepus and Sylvilagus, rst observed in the fossil record 8·6 and 7·2 million years ago, respectively.
Diversication of species and ecologies within these genera then followed.
The family Ochotonidae (pikas) is apparently slightly more recent, observed rst in Asia in the
late Eocene, radiating into North America and Europe in the Oligocene. Two early genera from
Europe were Amphilagus and Piezodus; about the same time, the genera Bohlinotona and Sinolagomys
were present in Asia. The rst observed members of the current genus Ochotona are present in the
late Miocene. The genus Prolagus of the now extinct family Prolagidae was abundant during the
Pliocene and Pleistocene in the Mediterranean region; one species (P.sardus) persisted until re-
cent times, at least until two thousand years ago. It is interesting to note that the Ochotonidae once
encompassed a much larger geographical distribution and disparity of forms, with up to 18 genera
extant during the Miocene extending into Africa. They declined to their current diversity of 29
species in the single genus Ochotona, with two species living in the mountains of western North
America and a broader distribution of the remaining species in Europe and Asia.
Why did both of these groups show dramatic declines in diversity after the Miocene (Figure 1)?
Many paleontologists speculate that lagomorphs are essentially small “ungulates” dependent upon
grazing, and they were outcompeted by the diversication of the group Artiodactyla, the even-toed
ungulates. The scarcity of lagomorphs in Africa, the site of the most diverse radiation of artiodac-
tyls, lends some support to this idea.
For Rodentia, their exceptional diversity of modern and fossil forms renders their evolution-
ary history complex and thus often disputed, especially in the untangling of how modern families
originated. There were two earlier radiations of now extinct groups that mirrored the morphology
of the modern rodentiform skull with well-developed incisors and no canines; the presence of a
diastema, or gap between the incisors and cheekteeth; and cheekteeth with often complex multi-
ple cusp patterns. The rst group was part of the mammal-like reptile radiation, the Tritylodonts
(Figure 4). They rst appeared in the late Triassic and were succeeded by the early mammaliform
group, Multituberculata (Figure 5) in the mid-Jurassic. Multituberculates were an amazingly suc-
cessful group and persisted for 100 million years, overlapping with early eutherian mammals for
70 million years. The multituberculates were most likely replaced by the radiation of placental
rodents, but it is interesting that the particular rodentiform morphology has been part of multiple
successful radiations.
The oldest known fossils that represent the modern order Rodentia are from the late Paleocene
of North America represented by the families Paramyidae, Alagomyidae, and Ischyromyidae. Some
paleontologists view the family Alagomyidae as the most primitive of all rodents, and a sister taxon
to the remaining Rodentia radiation. The family Paramyidae and the representative genus Paramys
(Figure 6) have skulls that are similar in general morphology to rodents with a sciuromorph skull,
in particular the skull of the modern Mountain Beaver (Aplodontia rufa). These early rodents all
had a sciuromorph-like cranial structure, the protrogomorphous condition, which supported a
large temporalis muscle attached to the braincase and a reduced masseter muscle that originated
Figure 1. Trends in the number of genera of fossil lagomorphs over time.
Peak generic richness appeared during the Miocene. Data from the
Paleobiology Database website (https://paleobiodb.org/navigator/).
Figure 2. Trends in the number of genera of fossil rodents, showing
a similar peak in generic richness in the Miocene. Data from the
Paleobiology Database website (https://paleobiodb.org/navigator/).
Evolution, phylogeny, ecology and conservation of the Clade Glires:
Lagomorpha and Rodentia
17
on the zygomatic arch. The “porcupine-like” morphology, the hystricomorphous condition, rst
appeared in the Eocene in the Old World, originating in Asia then expanding into Africa and
eventually South America. One of the more primitive of the modern families, the Ctenodactylidae
or gundis, had an early to middle Eocene origin. The earliest recorded fossil with this skull mor-
phology from South America dates from the mid-Eocene in Peru, about 41 million years ago. This
suggests that the South American hystricomorph rodents, known as caviomorphs, dispersed from
Africa to South America across the widening southern Atlantic Ocean via rafting, a nding that
molecular evidence supports. Fossil and molecular data also remarkably support an African origin
and similarly timed oceanic dispersal to South America for Neotropical monkeys (Platyrrhini) and
burrowing blind snakes (Amphisbaenia).
The late Eocene to middle Oligocene was the time of explosive diversi cation of rodents. By
this time, all three major groupings of skull morphology were present, and rodents were in direct
competition with Multituberculates, which were declining in diversity. Modern rodent families
began to occur by the late Oligocene and with the novel spread of dry conditions in the Miocene
that favored the development of grasslands and deserts, many modern arid-adapted families like
Heteromyidae and Dipodidae rst appeared. By the late Miocene, the modern rodent families
were essentially all present.
Skull Morphology in Lagomorphs
There is relatively little variability in the morphology of the skull among lagomorphs, but all lago-
morphs possess several de ning features. Lagomorphs, like rodents, possess gnawing incisors, no
canines, and a diastema between the incisors and cheekteeth. Indeed, they super cially look very
much like rodents. A major difference is the presence of two pairs of upper incisors and one pair
of lower incisors; however, the second pair of upper incisors is reduced in size, lacks a cutting
edge, and is located posterior to the large pair (Figure 7). The upper and lower incisors grow-
ing continuously and develop chisel-like edges as in rodents. The family Leporidae—rabbits and
hares—has upper incisors with smooth-cutting edges whereas the Ochotonidae has a prominent
notch in the incisors. Lagomorphs generally have more teeth overall than rodents, with the typical
tooth formula being I2/1, C0/0, P3/2, M2–3/3 (×2) =26–28. The cheekteeth in lagomorphs
are somewhat offset, with the upper cheekteeth extending labially above the lower cheekteeth, so
that the teeth can occlude on only one side at a time. This results in a side-to-side chewing motion,
obvious to anyone who has observed a rabbit foraging. The pterygoideus muscles and the bite
from well-developed masseter muscles largely controlled this transverse movement. The cusp pat-
terns in lagomorphs are simpler than generally observed in rodents, with fewer transverse ridges.
Lagomorphs also possess a fenestrated rostrum, resembling a lattice of bone (Figure 7). This is
more prominent in leporids than in ochotonids, where the latticing is reduced.
Skull Morphology and the Major Groups of Modern Rodents
The single distinguishing characteristic of rodents is the presence of a pair of upper and lower
incisors that grow continuously and are covered only on the front surface by enamel. The incisors
develop into sharp chisels because the posteriors of the teeth, composed of softer dentine, wear
more quickly. Rodents have no canines and relatively few cheekteeth. Common tooth formulas
range from I1/1, C0/0, P0/0/, M3/3 (×2) =16 to I1/1, C0/0, P2/2, M3/3 (×2) =22. Almost
all rodents are herbivorous, and the occlusal surfaces of the cheekteeth usually have complex
rings, prisms, or ridges to effectively grind coarse material.
Much of the discussion of rodent evolution, diversity, and ecology refers to differences in the
morphology of the cranium, the mandible, and the associated musculature. As discussed under
the emergence of early mammals, the skull morphology of the genus Paramys (Figure 6) was an
early example of the sciuromorph condition. That condition in modern rodents is best repre-
sented in the family Aplodontiidae and the single species Mountain Beaver, Aplodontia rufa (Figure
8). This particular morphology is referred to as the protrogomorphous condition, present only
in the Mountain Beaver among modern rodents. The de ning character is the restricted origin
of the masseter muscle entirely on the zygomatic arch. The sciuromorphic condition is similar in
that there is the absence of an opening anterior to the orbit that allows for the passage of muscles
that attach on the rostrum and pass through this opening and insert on the mandible. There is,
however, a space for the attachment of the lateral masseter muscle on the rostrum and the anterior
surface of the zygomatic arch. This is clear on the skull of modern sciuromprhs like chipmunks
(Figure 9) and beavers (Figure 10). The super cial masseter also attaches to the rostrum, although
lower that the lateral masseter. This enables the jaw to move forward and backward and up and
down, allowing a grinding motion during mastication by the cheekteeth.
This condition is progressively more developed in myomorph and hystricomorph rodents. In
myomorphs, there is a small infraorbital foramen (Figure 11) that allows passage of the medial mas-
seter muscle; the super cial masseter and the lateral masseter have similar origins and insertions,
as in sciuromorphs (Figure 12). The infraorbital foramen is greatly enlarged in hystricomorphs,
as in the New World porcupines (Figure 13) and the springhare (Figure 14). A general summary
of the progressive change from the protrogomorphous condition, through the sciuromorphous
condition, to the hystricomorphous condition illustrates the shift of muscle attachments progres-
sively to the rostrum and an enlargement of the size and role of the medial masseter (Figure 15).
The functional morphology of this shift is associated with the use of the incisors versus the
cheekteeth: the former for gnawing and the latter for chewing and grinding. Rodents use incisors
to clip vegetation, gnaw at seeds and fruits, and dig, fossorial. Gnawing requires the tips of the
incisors to be in contact; however, in resting position, the lower incisors are posterior to the upper
incisors. Thus, the lower jaw needs to shift forward for gnawing. The gradual movement of the at-
Figure 3. Reconstruction of the giant fossil leporid Nuralagus rex (above),
alongside a modern European Rabbit (Oryctolagus cuniculus).
Figure 4. Skull of the
mammal-like reptile genus
Tritylodon, an advanced
therapsid of the early Jurassic
period, approximately 200
million years ago. The skull
morphology was an early
take on the pattern present in
modern rodents.
Figure 5. The skull of the
extinct mammal genus
Ptilodus, a member of
the Multituberculata.
Multituberculates were an
extremely successful group of
mammals, with skulls similar
to the modern mammalian
order Rodentia.
Figure 6. Skull of the extinct
rodent genus Paramys form
North America and Eurasia,
with a protogomorphous
skull morphology, similar to
the modern sciuromorphous
condition.
Evolution, phylogeny, ecology and conservation of the Clade Glires:
Lagomorpha and Rodentia
18
tachment of components of the masseter muscle to the rostrum allows the lower jaw to be pulled
forward during gnawing behavior, but this moves the cheekteeth out of alignment for grinding
and masticating food. Biting power is conferred to the cheekteeth by the super cial and lateral
masseters and the temporalis. These, in combination with the medial masseter, allow for a strong
bite, grinding power, and the ability to control movements of the jaw forward, backward, and later-
ally to effectively grind coarse plant material (for most rodents) or insects and occasionally small
vertebrates in a minority of species.
In addition to these differences in the cranium, there are also notable differences in the mandi-
bles among rodents; these differences are summarized as the sciurognathus and hystricognathous
conditions (Figure 16). In the sciurognathus condition, the angular process is in line with the ra-
mus of the dentary bone, the process projecting upward (dorsally) from the posterior base of the
mandible. The angular process in hystrognaths is located off the plane of the ramus, de ected off
to the sides, often with a ange-like appearance. The coronoid process also is reduced in hystrog-
naths compared with sciurognaths. Only hystricomorphous rodents are hystricognathus; all others
are sciurognathous but with signi cant variability across the suborders.
Phylogenetic Relationships of Modern Lagomorph and Rodent Families
Within-family evolutionary relationships of lagomorphs and rodents, where these are reasonably
understood, are discussed in the chapters herein (and will be in the next volume of Handbook of
the Mammals of the World). In this introductory section, the general consensus on phylogenetic
relationships among both families and genera within Lagomorpha and relations among families
within the order Rodentia are presented; however, the individual chapters may differ somewhat
from the relationships discussed here.
There is still debate concerning the phylogeny of genera within the Lagomorpha. Two recent
publications have presented a fairly consistent phylogeny, which is represented schematically
in Figure 17. There is only the genus Ochotona in the family Ochotonidae, but eleven genera of
Leporidae. Both publications have a consistent tree, except for the clade that contains the genera
Oryctolagus, Bunolagus, Caprolagus, and Pentalagus. Both publications show Oryctolagus and Bunola-
gus to be sister taxa, but one publication shows Caprolagus and Pentalagus to be sister in a separate
branch, rather than having Pentalagus as sister to the other three genera as shown in Figure 17.
The total number of families of rodents has changed over the last decade, but the general con-
sensus is that there are 34 living families (Table 1). The best current tree based on DNA evidence
for the ancestor-descendant relationships among these 34 families is presented in Figure 18. The
overall topology of Rodentia can be viewed at a broad scale as forming three principal divisions of
mouse-, squirrel-, and cavy-related clades. Each of these clades is strongly supported and recipro-
cally monophyletic from the other two, but there is considerable debate over which two clades are
most closely related to each other to the exclusion of the third. Most DNA analyses based on multi-
ple genes nd a sister relationship between the squirrel- and cavy-related clades (Figure 18), albeit
with uncertain support. In contrast, analyses based on rare genomic mutations sometimes nd the
squirrel-related clade to have diverged rst and the mouse- and cavy-related clades to be sisters.
The mouse-related clade supports the shared evolutionary history of three traditional rodent
suborders: the Castorimorpha consisting of beavers (Castoridae), kangaroo rats and pocket mice
(Heteromyidae), and pocket gophers (Geomyidae); the Anomaluromorpha consisting of scaly-
tailed squirrels (Anomaluridae) and springhares (Pedetidae); and the highly speciose Myomorpha
consisting of seven families and well over 300 genera. Cricetidae and Muridae each have more than
700 currently described species, are extremely diverse ecologically, and together are distributed in
most biomes across every continent except Antarctica. The squirrel-related clade encompasses the
suborder Sciuromorpha and includes the mountain beaver (Aplodontiidae) and dormice (Gliri-
dae) along with about 300 described species of ground, tree, and ying squirrels (Sciuridae).
Cavy-related rodents form the third clade, consisting of 17 families (with a few exceptions such
as Laonastes) that have both a hystricognathous mandible and hystricomorphous skull. The names
Ctenohystrica and Histricormorpha are both used to refer to this clade; many researchers replace
the older name of Hystricomorpha with Ctenohystrica in an effort to avoid confusion over members
of other clades (e.g. Anomalurus) that also display the hystricomorphous condition. Members of this
clade generally have larger bodies and longer generation times than rodents in the mouse- and squir-
rel-related clades. It includes a subclade called Hystricognathi, which groups together African and
Asian porcupines (Hystricidae) with the Phiomorpha of Africa and the Caviomorpha of the Ameri-
cas and Caribbean Islands. The phiomorphs comprise African mole-rats (Bathyergidae), the evolu-
tionarily distinct lineage of the Naked Mole-rat (Heterocephalus glaber, Heterocephalidae), the Noki
or Dassie Rat (Petromus typicus, Petromuridae), and cane rats (Thryonomyidae). Their sister group
on the other side of the Atlantic Ocean is the caviomorphs, which includes ten families that range
from burrowing tuco-tucos (Ctenomyidae) to arboreal spiny rats (Echimyidae), New World porcu-
pines (Erethizontidae), and the large semi-aquatic capybaras (Caviidae), among others. While the
morphological and ecological disparity of rodents in the cavy-related clade has inspired zoologists to
delimit more families here than in the two other main clades, these families are often depauperate,
with ve that are monotypic and about 300 species assigned to this clade. Note in the tree presented
that Capromyidae and Myocastoridae are often included within Echimyidae, as in this volume.
Constructing Phylogenies: A Brief History of Methods and Approaches
Mammals have traditionally been classi ed and organized into hierarchical groups based on infer-
ences derived from shared sets of morphological characteristics evident in the anatomy of living
and extinct species. This system of classi cation was useful for recognizing the major mammalian
lineages, de ning the majority of modern orders and families of mammals, and describing thou-
Figure 8. The modern species
Aplodontia rufa in the
family Aplodontiidae. The
skull morphology is similar
to Paramys. Aplodontia,
the Mountain Beaver, is
considered a living fossil,
perhaps the most primitive
living rodent.
Figure 9. The skull of the
Cliff Chipmunk (Tamias
dorsalis), Sciuridae,
showing the sciuromorphous
condition.
Figure 10. The skull of the
North American Beaver
(Castor canadensis),
Castoridae. This is
another example of the
sciuromorphous cranium.
Beavers are placed in
their own clade, the
Castorimorpha, along with
the families Heteromyidae
and Geomyidae.
Figure 11. An example of the
myomorphous condition,
with a small passage through
the infraorbital foramen, as
seen in Stephen’s Woodrat
(Neotoma stephensi),
Cricetidae.
Figure 7. Examples of the
skulls and fenestration in two
species of leporids, the Arctic
Hare Lepus arcticus (left)
and the Antelope Jackrabbit
L.alleni (right). Note also
the double upper incisors.
TemporalisLateral masseter
Lateral masseterSuperfi cial masseter
Medial masseter
Evolution, phylogeny, ecology and conservation of the Clade Glires:
Lagomorpha and Rodentia
19
sands of living species. Despite being useful for recognizing many natural groups of mammals,
morphological characteristics were often insuf cient to identify commonalities shared by multiple
groups of mammals (e.g. superorders or suborders), particularly when these groups radiated with-
in short periods of geological time. Furthermore, phylogenetic analysis of morphological data may
be problematic across divergent groups of mammals where morphological convergence may mani-
fest in disparate regions across the globe where organisms are subject to similar selective pressures.
The advent of molecular genetic technologies in the latter one-half of the 20th century revolu-
tionized systematics and taxonomy across the “Tree of Life.” Early applications included the elec-
trophoretic analysis of protein polymorphisms, which allowed examination of genetic variation
without directly sequencing DNA or protein. Similarly, DNA–DNA hybridization and restriction
fragment length polymorphisms (RFLPs) were methods applied directly to DNA samples that al-
lowed indirect estimates of molecular divergence between two individuals or species. While each of
these technologies was instructive for advancing knowledge of genetic variation within populations
and genetic distances between species, they masked the full extent of DNA sequence variation be-
tween taxa and lacked suf cient resolution to resolve phylogenetic relationships among distantly
related groups of mammals, or even the branches of recent, rapid radiations.
Two major advances in genetic technology altered the landscape of mammalian molecular sys-
tematics. The rst came in the late 1980s with the advent of the polymerase chain reaction (PCR).
The ability to amplify and directly sequence short stretches of orthologous DNA sequence loci in
many species or individuals quickly led to a revolution in molecular phylogenetics. Early applica-
tions of PCR primarily targeted mitochondrial DNA (mtDNA) based on its higher copy number
per cell (and hence ease of ampli cation) and the more rapid rate of sequence evolution, which
provided ample variation within only several hundred base pairs of sequence. Limitations of the
eld at this time were that many studies often relied on sequence data from a single mitochondrial
gene fragment or suffered from biased taxonomic sampling because of cost constraints that lim-
ited the amount of sequence data that could be feasibly generated per species or taxon.
During the ensuing two decades, as sequencing technology and costs improved, there was a
substantial increase in the identi cation of cryptic species, and a considerable reorganization of
higher-level mammalian phylogeny as a result of PCR-based mtDNA sequencing. Recognizing the
limitations of taxonomic inference from a single, maternally inherited genetic marker, a concerted
effort ensued to increase the application of nuclear DNA (nDNA) sequence variation to mammali-
an phylogenetics. This revolution was facilitated by PCR primers designed from emerging databases
of human and mouse protein coding sequences that preceded the rst whole genome sequences of
both species. The dawn of the era of mammalian comparative genomics in the rst decade of the
21st century further accelerated taxonomic and phylogenetic discoveries, accompanied by the emer-
Higher level Classifi cation Families Genera Species Typical Species
Suborder Castorimorpha Family Castoridae 1 2 Beavers
Family Heteromyidae 566 Pocket Mice, Kangaroo Mice and Kangaroo Rats
Family Geomyidae 741 Pocket Gophers
Suborder Myomorpha
Superfamily Dipodoidea Family Sicistidae 114 Birch Mice
Family Zapodidae 3 5 Jumping Mice
Family Dipodidae 12 33 Jerboas
Superfamily Muroidea Family Platacanthomyidae 2 2 Tree Mice
Family Spalacidae 726 Muroid Mole-rats
Family Calomyscidae 1 8 Brush-tailed Mice
Family Nesomyidae 21 67 Pouched Rats, Climbing Mice and Fat Mice
Family Cricetidae 14 4 748 True Hamsters, Voles, Lemmings and New World Rats and Mice
Family Muridae 159 834 True Mice and Rats, Gerbils and relatives
Suborder Anomaluromorpha Family Anomaluridae 3 7 Anomalures
Family Pedetidae 1 2 Springhares
Suborder Hystricomorpha
Infraorder Ctenodactylomorphi Family Ctenodactylidae 4 5 Gundis
Family Diatomyidae 1 1 Khan-you
Infraorder Hystricognathi Family Hystricidae 311 Old World Porcupines
Family Thryonomyidae 1 2 Cane Rats
Family Petromuridae 1 1 Noki
Family Heterocephalidae 1 1 Naked Mole-rat
Family Bathyergidae 516 African Mole-rats
Family Erethizontidae 317 New World Porcupines
Family Cuniculidae 1 2 Pacas
Family Caviidae 620 Cavies, Capybaras and Maras
Family Dasyproctidae 215 Agoutis and Acouchys
Family Chinchillidae 3 6 Viscachas and Chinchillas
Family Dinomyidae 112 Pacarana
Family Abrocomidae 210 Chinchilla Rats and Inca Rats
Family Ctenomyidae 169 Tuco-tucos
Family Octodontidae 814 Viscacha Rats, Degus, Rock Rats and Coruro
Family Echyimyidae 27 99 Hutias, South American Spiny-rats and Coypu
Suborder Sciuromorpha Family Aplodontiidae 1 1 Mountain Beaver
Family Sciuridae 60 292 Tree, Flying and Ground Squirrels, Chipmunks, Marmots and Praire Dogs
Family Gliridae 929 Dormice
Figure 12. An illustration
of the muscle attachments
for the temporalis and the
various segments of the
masseter in a myomorphous
rodent, the Hispid Cotton
Rat (Sigmodon hispidus),
Cricetidae. Note the passage
of the medial masseter
through the infraorbital
foramen.
Figure 13. The large
infraorbital foramen present
in a hystricomorphous
rodent, the North American
Porcupine (Erethizon
dorsatum), Erethizontidae.
Table 1. Summary of the
classi cation of Rodentia
used in these volumes, with
the current estimates of the
number of genera, species,
and the associated common
names of the most typical
species for each family. The
numbers of genera and
species are in constant ux
due to ongoing taxonomic
revisions.
Infraorbital foramen
Temporalis
Lateral masseterSuperfi cial masseter
(Pseudotomus, Paramyidae)
TemporalisLateral masseter
Lateral masseterSuperfi cial masseter
Albert’s Squirrel
(Sciurus aberti, Sciuridae)
TemporalisMedial masseter
Lateral masseterSuperfi cial masseter
North American Porcupine
(Erethizon dorsatum, Erethizontidae)
Medial masseter
Porcupine
Evolution, phylogeny, ecology and conservation of the Clade Glires:
Lagomorpha and Rodentia
20
gence of the eld of bioinformatics. Genomics facilitated the generation of large DNA sequence su-
permatrices, containing tens of thousands of base pairs of aligned nucleotides, and both revolution-
ized and brought consensus to many parts of the mammalian phylogeny. Advances in computing
power and development of more sophisticated probabilistic-based phylogenetic algorithms rapidly
increased the amount of nDNA and mtDNA data that could be analyzed per species. The net result
was greater accuracy in phylogenetic reconstruction and estimations of divergence times.
The second major breakthrough in understanding mammalian phylogenetics and evolution
happened more recently with the development of next-generation sequencing (NGS) technolo-
gies. The NGS technologies lowered the cost and massively increased the amount of DNA that
could be collected per species, on the scale of the entire genome. NGS was accompanied by the de-
velopment of new methods to sample much larger, less-biased phylogenetic datasets in a far more
cost-effective and ef cient manner. The RAD sequencing approaches (RADseq) allow re-sequenc-
ing of tens of thousands of nuclear loci in multiple individuals or closely related species. DNA
capture hybridization allowed sequencing of hundreds to thousands of selected target loci using
pre-speci ed DNA or RNA “baits” that could be exploited to capture orthologous loci in divergent
relatives. NGS and capture hybridization were particularly important in the expansion and revolu-
tion of the eld of “ancient DNA,” allowing for retrieval of small amounts of target DNA within a
milieu of contaminating DNA. Complete mitochondrial genomes also could be easily generated
from a relatively small amount of genomic sequence data given their high copy number per cell.
Despite the recent wealth of approaches for sequencing large amounts of nDNA, mitochondrial
phylogenies have and still dominate the mammalian systematic literature. While many of the earli-
er revolutionary phylogenetic ndings based on mtDNA were eventually con rmed by nDNA, the
strictly maternal inheritance and unique properties of the mitochondrial environment introduce
potential sources of con ict in mammalian phylogenetic inference and taxonomy. The mtDNA
phylogenies differ from nuclear-based phylogenies for several reasons, including differences in nu-
cleotide composition, saturation of substitutions across deeper timescales, and the overwhelming
tendency toward male-biased dispersal in mammals. Because of the latter fact, maternally transmit-
ted mtDNA will not accurately re ect nuclear gene ow and hence may not reliably track species
boundaries. This latter aspect demands caution in the application of mtDNA barcodes to identify
unknown species or for taxonomic purposes.
Our current ability to sequence large, genome-wide phylogenetic datasets comes with many ad-
ditional challenges for the future of the elds of mammalian systematics and taxonomy. These in-
clude accurately aligning whole genomes across divergent groups of mammals and partitioning and
analyzing genome datasets to account for local “gene tree” histories to address impacts of hybridi-
zation versus incomplete lineage sorting on phylogenetic accuracy. How much of the mammalian
phylogeny is reticulated versus truly bifurcating? Are all nuclear markers equal, and do difference
facets of genome organization, such as gene density, recombination and guanine-cytosine content
(GC-content) in uence phylogenetic signal? How many species of mammals really exist? Can we
use genetic data to improve our understanding of the process of reproductive isolation and hence
improve our concept of de ning new mammalian species? While many new challenges and ques-
tions will emerge in the genomics era, it is undoubtedly an exciting time to know that full resolution
of the mammalian “Tree of Life” and, with it, an improved understanding of the genetic basis of
the vast mammalian phenotypic diversity are nally within reach. Applications of these approaches
will contribute signi cantly to the resolution of rodent systematics and help to discover and identify
relationships among many groups of morphologically similar and highly cryptic rodents.
Ecological Roles of Rodents and Lagomorphs
The orders Rodentia and Lagomorpha comprise nearly one-half of all species of mammals. There
is little wonder that rodents, with about 2400 total species, have developed diverse morphologi-
cal adaptations and behaviors that have allowed them to survive, thrive, and disperse throughout
ecosystems all around the globe and, in turn, have had an enormous in uence on these environ-
ments. Rodents inhabit every continent on Earth except Antarctica, throughout a wide variety of
habitats from deserts to tropical rainforests and human modi ed landscapes such as urban areas;
there are few places these mammals are not found. Although occurring in more modest numbers
and diversity than Rodentia, with less than 4% the richness, species of Lagomorpha are compa-
rably ubiquitous throughout the world and share many similar morphological traits with their
close rodent relatives. They are native or introduced (e.g. Australia) to just as many continents
and habitats as their rodent counterparts. Compared with other orders of mammals, lagomorphs
and rodents have been some of the most successfully colonizing mammals, and they have complex
histories of interactions with humans.
The enormous success of these two mammalian groups can be attributed to a number of unique
adaptations through time. Their global presence and frequent high abundance have resulted in
the diversi cation of rodents and lagomorphs into myriad ecological roles, the majority of which
have important impacts on the functioning of the ecosystems where they occur. The extent of the
in uence that rodents and lagomorphs have on these ecosystems, and their impact on humans
makes them some of the most important organisms in existence. Whether they are having a posi-
tive in uence, through seed dispersal, or a more negative in uence through their contribution to
crop losses or as disease vectors, there is no denying the unparalleled impact these species have on
every region they inhabit.
Adaptations and Life History Strategies of Lagomorpha and Rodentia
It is unlikely that rodents or lagomorphs would have been such successful colonizers without the
development of particular adaptations throughout evolutionary time. Most rodents and lago-
Figure 15. A comparison
of the attachment of the
masseter muscles in the
protogomorphous condition
(Pseudotomus), the
sciuromorphous condition
(Sciurus), and the
hystricomorphous condition
(Erethizon).
Figure 14. Another example
of the hystricomorphous
condition in the Southern
African Springhare (Pedetes
capensis), Pedetidae.
Springhares are in the rodent
clade Anomaluromorpha.
Angular processAngular process
A B
Lagomorpha
OchotonidaeLeporidae
Ochotona
Nesolagus
Pronolagus
Poelagus
Caprolagus
Bunolagus
Oryctolagus
Pentalagus
Sylvilagus
Brachylagus
Romerolagus
Lepus
Evolution, phylogeny, ecology and conservation of the Clade Glires:
Lagomorpha and Rodentia
21
morphs are relatively small and physically adapted for quick or surreptitious movements to avoid
predators. Lagomorphs, such as rabbits or pikas, are adapted to sprint for short distances until
they reach the safety of cover, while hares are adapted to run long distances to tire their predators,
running at up to 80km/h when sprinting with the ability to run up to 50km/h for several hours
if necessary. Rodents have a broader litany of life-history adaptations. Primarily due to the fact
that there is a greater number of rodent species than lagomorph species, rodents, more so than
lagomorphs, possess different physical adaptations facilitating a variety of species-speci c habitat
preferences. Such adaptations include burrowing capabilities for fossorial species such as the Na-
ked Mole-rat, other necessary physical modi cations needed for arboreal species like claws and
long tails, or the thick, waterproof fur and a waterproo ng castor oil gland found in semi-aquatic
species, such as beavers.
A few physical adaptations are similar or identical between the two orders, speci cally those
related to aspects of tooth morphology. During a period of about 60 million years, rodents have
undergone signi cant modi cations of their teeth and jaws that have allowed exploitation of the
much greater diversity of food resources that they encounter in different vegetation types. This
shift allowed for a more generalist feeding pattern, which in turn resulted in successful coloni-
zation of the diversity of habitats and environments that have made rodents perhaps the most
successful mammalian radiation to date. The tooth morphology of rodents evolved over time to
include complex heterodont dentition, in particular complex cusp patterns and generally higher
crowned molars and premolars. Speci c adaptations of the cheekteeth vary among species. Murid
rodents, such as the Old World mice and rats, are some of the most successful colonizers in the
world, and they most notably possess a chevron cusp pattern on their teeth—a pattern that repre-
sents one of the most derived mammalian occlusal surface patterns. All rodents possess a few den-
tal characteristics that are consistent across the entire order, including a single pair of continuously
growing, deep-rooted incisor teeth. The function of these teeth in rodents plays a crucial role in
their evolutionary success as it allows them to continuously and ef ciently eat brous plant mate-
rial and gnaw through tough, inedible materials. The thick enamel coating on only the anterior
surfaces of these teeth is an additional adaptation to aid in the gnawing process. Rodents grind
their incisors against one another while chewing. This process acts as a sort of self-sharpening
system, wearing down the dentine layer of the posterior one-half of the tooth and creating an
especially sharp enamel-edged cutting surface.
Rodent jaws are also extensively modi ed to maximize gnawing capabilities, which are largely
driven by a set powerful jaw muscles—the masseter complex and the pterygoideus—that allow con-
tinuous forward and backward motion of the jaw. Rodents have four distinctive cranial adaptations
that allow the differential placement of these muscles in the skull; the Protogomorphous, Hystri-
comorphous, Sciuromorphous, and Myomorphous conditions. While these adaptations appear
to have evolved independently of one another, there is some evidence that three of them—the
Hystricomorphous, Sciuromorphous, and Myomorphous modi cations—developed in tandem
with the rise of specialized feeding patterns in modern rodents. Speci cally, sciuromorphs, like
squirrels, have the Sciuromorphous condition for ef cient gnawing, hystricomorphs such as cavies
have the Hystricomorphous condition for enhanced grinding and chewing, and myomorphs have
the Myomorphous condition resulting in their exceptional success among all rodents as highly
adaptable generalist feeders.
Lagomorphs also possess a pair of continuously growing incisors, but they are distinguished
from rodents in that the enamel of the incisors covers the entire tooth rather than just the anterior
side. Both lagomorphs and rodents lack canine teeth and instead possess a large diastema between
their incisors and their cheekteeth. The diastema is also related to the gnawing capabilities of
both groups; it provides space for the skin of the cheeks to shield the mouth and the throat from
damage that might be in icted by biting through inedible materials such as wood, which can then
be safely discarded from the mouth. While these two groups possess striking similarities in aspects
of their cranial anatomy and morphology, there are several distinguishing traits between the two.
Lagomorphs possess an additional small pair of peg-like incisors in the upper jaw, directly behind
the sharp rst pair—a trait that rodents are lacking. The chewing motion of lagomorphs is also
quite distinct from that of rodents in that lagomorphs chew by moving their jaws from side to side
or in a transverse motion, while rodents use a proal, or forward and backward, chewing motion.
Lagomorphs also possess some unique cranial characteristics such as the extensive fenestration on
part of the maxilla bone to reduce the weight of their skull and allow faster motion and maneuver-
ability through landscapes. This fenestration is greatly reduced in the non-hopping pikas.
Rodents and lagomorphs have other similar life history strategies that have facilitated their
success as nearly ubiquitous mammals. They have high rates of fecundity and reproduce often;
this is particularly true of muroid rodents that will be covered in the next volume. This allows for
high rates of population growth when conditions are favorable, resulting in ease of dispersal and
colonization and high survivability despite extensive predation and hunting pressures. While some
features of reproduction can differ among families in both orders, most are characterized by large
litter sizes and relatively short gestation periods, all of which promote high growth rates and high
potential tness despite changing environmental conditions. The common commensal female
Brown Rat (Rattus norvegicus) can reproduce up to 15 times per year, and her offspring reach sex-
ual maturity, and reproduce themselves, at 3–4 months old. One female breeding year-round can
be responsible for more than 2000 descendants each year. The observed adaptability of rodents is
most certainly facilitated by their exceptional reproductive capacity.
Role in Ecosystems and Ecosystem Services
As some of the most abundant and widely distributed animals on the Earth, it is no surprise that
rodents and lagomorphs have unique and often disproportionate roles and impacts in ecosystems.
While these roles may vary in extent and in uence, key roles include food for predators, dispersers
Figure 16. Differences in the position of the angular process in relation to
the ramus of the dentary in the (A) sciurognathus condition and the (B)
hystricognathus condition.
Figure 17. An example of the likely phylogeny of the genera of lagomorphs.
There is some variability among phylogenies in the organization of some
of the branches as explained in the text. All phylogenies are really scienti c
hypotheses.
0.05 expected substitutions / site
97
100
97
100
100
99
100 100
72
100
95
100
100
77
32
100
74
98
100
98
98
99
100
100
100
100
91
100
88
100
100
100
100
100
100
CASTORIMORPHA
ANOMALUROMORPHA
MYOMORPHA
SCIUROMORPHA
CTENOHYSTRICA
PHIOMORPHA
CAVIOMORPHA
HYSTRICOGNATHI
(= Hystricomorpha)
Lagomorpha
Rodentia
Mouse-related clade
Squirrel-related clade
Cavy-related clade
Oryctolagus cuniculus LEPORIDAE
Ochotona princeps OCHOTONIDAE
Ctenodactylus gundi CTENODACTYLIDAE
Laonastes aenigmamus DIATOMYIDAE
Hystrix brachyura HYSTRICIDAE
Heterocephalus glaber HETEROCEPHALIDAE
Fukomys damarensis BATHYERGIDAE
Thryonomys swinderianus THRYONOMYIDAE
Petromus typicus PETROMURIDAE
Chinchilla lanigera CHINCHILLIDAE
Dinomys branickii DINOMYIDAE
Abrocoma bennettii ABROCOMIDAE
Ctenomys boliviensis CTENOMYIDAE
Octodon degus OCTODONTIDAE
Capromys pilorides CAPROMYIDAE
Myocastor coypus MYOCASTORIDAE
Hoplomys gymnurus ECHIMYIDAE
Erethizon dorsatum ERETHIZONTIDAE
Cuniculus taczanowskii CUNICULIDAE
Dasyprocta punctata DASYPROCTIDAE
Cavia porcellus CAVIIDAE
Ictidomys tridecemlineatus SCIURIDAE
Aplodontia rufa APLODONTIIDAE
Graphiurus murinus GLIRIDAE
Castor canadensis CASTORIDAE
Cratogeomys castanops GEOMYIDAE
Dipodomys heermanni HETEROMYIDAE
Jaculus jaculus DIPODIDAE
Typhlomys cinereus PLATACANTHOMYIDAE
Rattus norvegicus MURIDAE
Cricetulus barabensis CRICETIDAE
Cricetomys gambianus NESOMYIDAE
Calomyscus bailwardi CALOMYSCIDAE
Spalax ehrenbergi SPALACIDAE
Pedetes capensis PEDETIDAE
Anomalurus beecrofti ANOMALURIDAE
Evolution, phylogeny, ecology and conservation of the Clade Glires:
Lagomorpha and Rodentia
22
of seeds and fungi, modiers and facilitators of vegetation change, and soil aerators. Some species
of rodents have even been recognized as keystone species or ecosystem engineers. These species,
such as beavers and prairie dogs, have such a disproportionate impact on the ecosystems in which
they inhabit that the functionality of these ecosystems would be dramatically altered or impaired if
these species were no longer to exist.
Food Sources: As primarily herbivores, rodents and lagomorphs comprise the second tier of the
ecological pyramid and are at the base of many predator-prey dynamics. As such, they are vital
foods for countless species in habitats all over the world, forming links between different species
at various trophic levels. The great abundance and small- to medium-size of most rodents and
lagomorphs makes them a particularly well-suited source of sustenance for many medium- to large-
Figure 18. Phylogenetic tree depicting the evolutionary relationships between
families of Rodentia and Lagomorpha based on a maximum-likelihood
(ML) analysis of 31 genes and 39,099 nucleotide base pairs. This
analysis was conducted in RAxML version 8.2.4 on a concatenated
data set partitioned by DNA type (mitochondrial coding, exon, or nuclear
non-coding) and codon position. Numbers at the nodes are ML bootstrap
support values based on 1000 replicates. This data set is unpublished
(N.Upham, J.Esselstyn, and W.Jetz).
Evolution, phylogeny, ecology and conservation of the Clade Glires:
Lagomorpha and Rodentia
23
bodied species higher on the ecological pyramid, such as wild cats, foxes, and raptors and often the
primary factor for determining the abundance such predator species. For example, in one particu-
lar study on the inuence of lagomorph species on higher trophic levels, researchers found that
population declines in the Black-tailed Jackrabbit (Lepus californicus) resulted in marked declines
in populations of Kit Foxes (Vulpes macrotis) in western Utah and Coyotes (Canis latrans) in north-
western and southern Idaho. Similarly, rodents and lagomorphs can have signicant inuences on
cycles of reproduction in higher trophic levels; for example, the uctuation in the proportion of
breeding tawny owls (Strix aluco) in England from as little as 0 to 80% depending on abundances
of voles or mice available for consumption. Were it not for the vital food source provided by ro-
dents and lagomorphs, the food web of most ecosystems would likely collapse, and many species
in higher trophic levels would decline and potentially be threatened with extinction. Rodents may
also be important in other trophic levels because they host a number of parasites such as ticks
and mites and frequently exist in very tight host-parasite relations. It is not uncommon to have a
single species of an ectoparasite found only on a single species of rodent, indicating a very tight
co-evolutionary history.
Seed Dispersal and Vegetation Facilitation: Many species of rodents and lagomorphs aid in the dis-
persal of plant seeds and, in turn, the growth and survivorship of those plants. These relationships
are observed in a several ways, but primarily through two processes: seed consumption and seed
caching. In the process of seed caching, rodents gather large quantities of seeds from various
locations and store them in a particular area. There they might later be accessed and consumed
in times when food sources are less plentiful. This process, however, often results in large quanti-
ties of seeds being forgotten, lost, or dropped by their “cachers” along the way, facilitating the
germination and growth of various plant species across vast areas of land. A study by N.E. West in
central Oregon found that about 15% of ponderosa pine (Pinus ponderosa, Pinaceae) and up to
50% of antelope bitterbrush (Purshia tridentata, Rosaceae) growth resulted from seed caches left
behind and spread by rodents. Consumption of these plant seeds has also been shown to be an ef-
fective method of dispersal by lagomorphs and rodents. As lagomorphs forage over wide ranges of
landscapes in various habitat types such as grasslands, shrublands, and woodlands, they often pick
up and transport seeds either by intentional consumption, such as the undigested seeds of eshy
plant fruits, or by chance, as in the process of foraging on foliage and unintentionally spreading
seeds of various neighboring forb and grass species that can attach to their fur. This process is
termed epizoochory.
While consumption and caching of seeds can often result in positive effects on plant growth,
it also has negative implications for some plant species. In California, meadow mice have been
found to reduce the seed dispersal of preferred food plants by an estimated 20% in some regions
due to their harvesting and storing activities. Consumption of wild barley (Hordeum leporinum) and
wild oat (Avena fatua, both Poaceae) seeds by meadow mice and House Mice (Mus musculus) also
markedly decreased their densities by 30% and 62%, which allowed for the increased success of
other plant species such as Italian ryegrass (Lolium multiorum) and brome grasses (Bromus mollis
and B.diandrus, all Poaceae).
Lagomorphs and rodents also signicantly alter vegetation in different habitats through direct
consumption of plants; they have been shown to alter plant composition, primary productivity,
reproduction, and decomposition of plant materials in several environments. While their impacts
have been negligible in some regions, in other regions, they might consume up to 60–80% of all
annual primary production. Grazing by some species can actually help to increase plant produc-
tion for some types of vegetation, as was found to be the case with voles (Microtus oeconomus and
M.middendorfi) that were shown to increase shoot growth of two plant species. Prairie dogs (Cy-
nomys spp.) create islands of habitat in the prairies of North America through a combination of
selective grazing and burrow construction. These effects occur at multiple levels; the small-scale
single burrow, the colony, and the landscape level complex of colonies found in these grasslands.
Their presence increases plant diversity, often increases the presence of high-quality forbs for larg-
er herbivores like American Bison (Bos bison), aerate the soil, increase soil nitrogen content, and
provide food for predators like Coyotes (Canis latrans). The changes in patterns of vegetation as-
sociated with colony complexes can enhance the diversity of other organisms like grassland birds.
As far as altering plant species composition and distribution, some researchers argue that rodents
and lagomorphs have signicantly contributed to range destruction in some regions, while others
actually attribute the presence of these small mammals in these areas as byproducts of preexist-
ing conditions occurring naturally that aided their invasion. Regardless, cases of both positive
and negative impacts of rodents and lagomorphs on plant species composition and distribution
have been observed, as seen with Northern Pocket Gophers (Thomomys talpoides) decreasing the
number of perennial forbs in Colorado but increasing the amount of sedges and grasses in Utah.
Finally, rodents and lagomorphs have been found to be important players in the decomposition
of vegetation. Facilitation of decomposition is accomplished by several mechanisms that increase
the rates of decomposition, including the addition of feces and discarded green vegetation to the
leaf litter layer, making rodents and lagomorphs more efcient than even insects or ungulates at
mineralizing organic material.
Effects on Soil: Many species of rodents and lagomorphs also inuence the chemical composition
and structure of soil. Burrowing species like moles are responsible for extensive changes to soil
structure, as is the case with pocket gophers whose underground tunnels were found to lower bulk
densities and increase aeration of soils in subalpine grasslands in Utah. This process was shown to
greatly change the water drainage and absorption process in these soils by promoting increased
ltration and absorption rates that can, in turn, decrease runoff and soil erosion. Such tunneling
activities are also known to help support a variety of other soil or burrow-dwelling species and
promote root growth by carrying oxygen through the soil via aeration. In a different landscape in
Utah, however, this same species was found to have actually caused soil to compact as result of their
Extinct (EX)
Extinct in the Wild (EW)
Critically Endangered (CR)
Endangered (EN)
Vulnerable (VU)
Near Threatened (NT)
Least Concern (LC)
Data Deficient (DD)
Not Evaluated (NE)
[Adequate data] [Threatened]
[Evaluated]
unknown
extinction
risk
increasing extinction risk
Evolution, phylogeny, ecology and conservation of the Clade Glires:
Lagomorpha and Rodentia
24
burrowing activities, causing a decreased rate of in ltration and level of moisture in these soils.
Perhaps more importantly, rodents and lagomorphs are known to alter the chemical composition
of soils and nutrient cycling in ecosystems. This is done through their large addition of nitrogen-
rich excrement and displacement of nutrients lower in the soil layer to layers closer to the surface
through their burrowing and digging activities.
Distribution of Fungi: Rodents in particular have also been identi ed as important dispersers of
fungi, many of which play critical roles in the ecosystems in which they exist. Several types of
hypogeous fungi, such as truf es, rely almost entirely on the dispersal of their spores by small
herbivorous mammals like rodents. This dispersal is primarily accomplished through the rodent’s
consumption of the fungi, also known as mycophagy, and the resulting excretion of the fungal
spores that can travel through the rodent digestion system undamaged. Voles and red squirrels
can spread other fungi, such as species of mushrooms that occur above the soil surface through
the process of caching. This allows for greater exposure of the fungal spores to environmental
conditions, ultimately allowing them to spread and grow. In forests in the western USA, rodents
have been recognized as key dispersal agents of mycorrhizal fungi and the accompanying nitrogen-
xing bacteria that provide numerous bene ts to the root systems of many plant species in these
areas. Mycorrhizal fungi and plant species have mutualistic relationships in which fungi provide
essential nutrients for plants to grow and thrive, such as orchids whose seeds will not germinate or
grow without the facilitation by a fungus, while the plant provides byproducts of its photosynthesis
to the fungus that can be used in metabolic processes. This process of distributing fungal spores
and facilitating fungal growth in ecosystems plays a crucial role in forest succession and the rees-
tablishment of forests following signi cant disturbance events such as res.
Human Interactions and Economic Importance
While members of Rodentia and Lagomorpha are often seen as pests, they are actually among the
most important animals on the planet. Humans have long exploited rodents and lagomorphs for
several purposes, including food, articles of clothing, and as pets. While lagomorphs and rodents
have economic importance, rodents are comparably more valuable because they are more widely
exploited for a greater number of purposes, while lagomorphs are primarily valued as game ani-
mals. Perhaps one of the more signi cant and controversial uses of rodents and some lagomorphs
is their extensive use in laboratory research, often for medical purposes, to better understand
diseases and conditions af icting human populations.
As Food Sources: Up to 89 species of rodents, primarily Hystricomorphs, and several species of
lagomorph have been recognized as regular sources of food for people around the world. Many
cultures have been known to consume rats, and domestic guinea pigs have been a recognized
delicacy since as far back as 2500 and were the main source of meat consumed by the Inca
Empire by 1500. In contemporary Peru, guinea pigs are often consumed in dishes such as “cuy
al horno” (roasted guinea pig) and as many as 64 million guinea pigs are raised for consump-
tion each year. In the USA, squirrels, Woodchucks (Marmota monax), muskrats, gophers, rats, and
North American Porcupines (Erethizon dorsatum) have been used as food sources through time. In
areas of Amazonia where larger game mammals are harder to encounter, agoutis and pacas were
found to make up about 40% of the game consumed by indigenous people each year. Lagomorphs
are also highly valued game animals, and they are extremely abundant, with millions being hunted
each year. Lagomorphs are primarily hunted for sport and meat.
Exploitation for Clothing: Lagomorphs have rather thin skin that is easily torn, and their pelts are
rarely used for clothing. An exception has been Snowshoe Hares (Lepus americanus) whose fur was
historically a desirable commodity. Historically, people have heavily exploited rodents for their
fur pelts, which were used to create various articles of clothing. In North America, species with
particularly thick or heavy fur pelts, such as North American Beavers (Castor canadensis), Common
Muskrats (Ondatra zibethicus), and the introduced Coypu or Nutria (Myocastor coypus), have been
frequently hunted, dating back to the North American fur trade when beavers were used to cre-
ate warm insulating clothing such as jackets and robes. Beaver pelts were popular during the late
1700s and early 1800s in the manufacture of hats and were adopted by the military for standard
use. The use of beaver pelts became so intense that they were almost extinct east of the Mississippi
River by 1880 and almost extinct throughout North America by 1930. Capybara (Hydrochoerus hy-
drochaeris) fur is highly favored in the production of ne gloves and other light leather products.
The incredibly soft fur of Chinchillas has also been extensively exploited for human use, so much
so that their wild populations have nearly been extirpated, although they are now extensively bred
in captivity due to their high economic value.
As Pets: Many rodents and lagomorphs are also very popular in the pet trade where rabbits, mice,
rats, guinea pigs, chinchillas, hamsters, gerbils, and several other species are regularly sold and
owned by individuals worldwide, making up a hugely successful industry. Maintaining these species
as pets requires special care, particularly with regard to diet.
For Laboratory Research: Perhaps the most important use of rodents and lagomorphs is their use
as model organisms for laboratory studies and medical testing. The House Mouse is generally
recognized as the most commonly used laboratory rodent, and rats and mice comprise 95% of all
laboratory animals. Historically, however, guinea pigs were widely used in laboratory studies until
the late 20th century. As many as 2·5 million guinea pigs were used each year in the 1960s for labo-
ratory studies in the USA, and their use played a signi cant role in the development of the germ
theory by L.Pasteur and other scientists in the late 1800s.
Figure 19. A summary graph of the Categories of the IUCN Red List of
Threatened Species.
Family CR EN VU DD Total DD % Threatened
%
Leporidae 1 7 5 5 62 8.1 21.0
Ochotonidae 1 3 0 3 30 10.0 13.3
Total 210 5 8 92 8.7 18.5
Family CR EN VU DD Total DD % Threatened
%
Abrocomidae 1 0 0 6 10 60 10
Anomaluridae 0 0 0 1 7 14.3 0.0
Aplodontiidae 0 0 0 0 1 0.0 0.0
Bathyergidae 0 0 1 1 15 6.7 6.7
Calomyscidae 0 0 0 2 8 25.0 0.0
Capromyidae 4 4 3 0 19 0.0 57.9
Castoridae 0 0 0 0 2 0.0 0.0
Caviidae 1 0 0 3 18 16.7 5.6
Chinchillidae 2 0 0 1 7 14.3 28.6
Cricetidae 21 31 44 85 698 12.2 13.8
Ctenodactylidae 0 0 0 2 5 40.0 0.0
Ctenomyidae 3 6 6 24 60 40.0 25.0
Cuniculidae 0 0 0 0 2 0.0 0.0
Dasyproctidae 1 1 1 3 13 23.1 23.1
Diatomyidae 0 1 0 0 1 0.0 100.0
Dinomyidae 0 0 1 0 1 0.0 100.0
Dipodidae 0 2 2 8 50 16.0 8.0
Echimyidae 2 7 4 25 89 28.1 14.6
Erethizontidae 0 0 1 6 18 33.3 5.6
Geomyidae 3 1 0 1 39 2.6 10.3
Gliridae 0 0 2 10 28 35.7 7. 1
Heteromyidae 3 6 5 1 62 1. 6 22.6
Hystricidae 0 0 1 0 11 0.0 9.1
Muridae 17 62 55 134 7 11 18.8 18.8
Myocastoridae 0 0 0 0 1 0.0 0.0
Nesomyidae 1 6 3 9 59 15.3 16.9
Octodontidae 3 0 2 2 13 15.4 38.5
Pedetidae 0 0 0 0 2 0.0 0.0
Petromuridae 0 0 0 0 1 0.0 0.0
Platacanthomyidae 0 0 1 0 2 0.0 50.0
Sciuridae 215 16 41 279 14.7 11. 8
Spalacidae 0 2 2 3 21 14.3 19.0
Thrynomyidae 0 0 0 0 2 0.0 0.0
64 144 150 368 2255 16.3 15.9
Evolution, phylogeny, ecology and conservation of the Clade Glires:
Lagomorpha and Rodentia
25
Today, mice and rats are preferred for reasons related to convenience because they are easily
housed and are relatively inexpensive to obtain. They are also favored for specic characteristics
that include their short gestations, high fertility levels, docile demeanor and ease of handling,
small size, and their susceptibility to many diseases and conditions that humans experience. As a
result, they are considered vitally important resources to better understand human health. There
are biological, behavioral, and genetic similarities between mice and humans that cause mice to
react to certain conditions or treatments in ways that closely resemble human responses. Rodents
also make effective models for studying human conditions and treatments because their anatomy
and physiology are extensively studied and very well understood, which allows researchers to more
easily track the causes of physiological changes to their normal condition. Rodents are used to
study many human ailments including HIV and AIDS, Parkinson’s disease, cancer, cystic brosis,
hypertension, diabetes, and obesity. Mice and other rodents are also often used in studies focused
on genetics, behavior, sensory information, physiology, and psychology and are used to test the
viability of certain drugs and treatments for particular ailments. Overall, the use of rodents in labo-
ratory studies, in particular those related to biomedicine, is a huge industry that is recognized by
many researchers as crucial to our understanding of human diseases and conditions and the ways
in which we can cure or treat them.
Rodents as Pests and Vectors of Disease
Rodents and lagomorphs are also recognized as pests for the negative impacts they can have on
certain aspects of ecosystems, and particularly on human health and livelihood. There are a few
negative impacts in particular that rodents are most often recognized as causing, including exten-
sive annual crop damage and spread of diseases.
Crop Losses: While rodents and lagomorphs can have some very positive effects on natural vegeta-
tion in landscapes, they are also known to cause considerable damage to grain stores and crops
worldwide each year. On average, rodents alone consume an estimated US$ 30 billion in cereal
grains and cash crops annually. While signicant crop losses occur due to consumption by rodents
each year, only a small number of species actually cause the greatest amounts of damage, primarily
species of mice and rats.
Crops and cereal grains that have most commonly been reported as experiencing signicant
losses due to consumption by rodents are rice, tubers, cacao, sorghum, groundnuts, sugar cane,
and various fruits and vegetables. The extent of crop losses differs across different regions of the
world, but it has been known to commonly occur in almost every continent including the USA,
South America, Africa, Asia, and Europe. In 2003, it was estimated that the amount of rice con-
sumed by mice and rats in Asia would have been enough to feed a staggering 200 million people.
In South America, crop losses to rodents can reach up to 90%, and in Tanzania and Indonesia,
they were found to be reduced by about 15% in particular years.
Lagomorphs, in particular species in the family Leporidae, have been known to cause exten-
sive crop damage, especially in regions where their population numbers can experience explosive
growth under ideal conditions. Damage to agricultural land by lagomorphs is reported as far back
as 63. Presently in North America, the greatest losses are typically damage to alpine trees by
snowshoe hares and pikas (Ochotonidae) and loss of crops to jackrabbits and cottontails. In the
western USA, in particular, jackrabbits have at times become so widespread that they have required
signicant control measures to reduce their impact on agricultural lands. In Asia, four species of
pika have been identied as pests for causing damage to trees and crops of local value. The intro-
duction of European Rabbits (Oryctolagus cuniculus) to several other regions of the world, however,
has arguably resulted in the greatest levels of agricultural damage and losses through establish-
ment of large populations that overgraze lands. The case study of European rabbits in Australia is
a classic example of the potential damage that results from the introduction of an exotic species
to a landscape without an understanding of the potential ecological impact. Twenty-four individu-
als were introduced as a game animal in 1859, and they almost immediately underwent explosive
growth resulting in overgrazing, increased erosion, and competition with domestic and native spe-
cies over access to forage. Some estimates placed the population size at ten billion by 1920, and the
population was an estimated 600 million in the early 1960s. The introduction of an infectious and
generally fatal viral disease in 1950 eventually reduced numbers to 100 million. Resistance to the
virus in the remaining population resulted in numbers increasing to 200–300 million. There has
been the introduction of a second biological control agent, rabbit hemorrhagic disease, to attempt
to reduce numbers. The Australian government also built an extensive “rabbit-proof fence” in the
early 1900s extending more than 3200km. The cost of rabbit impacts on Australian agriculture is
currently estimated at AU$ 113 million annually.
As Vectors of Disease: Throughout history, rodents have been known to be the vectors of agents
responsible for widespread epidemics. Perhaps the most well-known case is that of the bubonic
plague in the Middle Ages, which was spread by European rats carrying eas with the bacterium
Yersinia pestis that then spread to humans, resulting in the deaths of millions.
Rodents have also been identied as reservoir hosts and vectors for a number of infectious
diseases such as Lyme disease, listeriosis, rabies, murine typhus, Weil’s disease, trichinosis, hanta-
viruses, and toxoplasmosis among others. To curb the threat of the spread of disease by rodents,
humans have developed several mechanisms to control population numbers. Trapping and poi-
soning rodents were once the most commonly used methods to control their populations, but
because they were found to be dangerous and ineffective in many instances, a combination of new
mechanisms and integrated pest management strategies have been implemented in many areas.
Some of these include methods of biological control by predation and the use of pathogens, the
modication of habitats, and alterations of farming practices.
Table 3. Critically Endangered (CR), Endangered (EN), Vulnerable (VU),
and Data Decient species numbers of Lagomorpha by Family. Percent
DD and percent in the three Threatened categories also presented. Data
are from Schipper and colleagues in 2008 from the Global Mammal
Assessment of IUCN. Note that there have been multiple taxonomic
changes since the study.
Table 2. Critically Endangered (CR), Endangered (EN), Vulnerable
(VU), and Data Decient species numbers of Rodentia by Family. Percent
DD and percent in the three Threatened categories also presented. Data
are from Schipper and colleagues in 2008 from the Global Mammal
Assessment of IUCN. Note that there have been multiple taxonomic
changes since the study, including at the level of Family.
Evolution, phylogeny, ecology and conservation of the Clade Glires:
Lagomorpha and Rodentia
26
Conservation of Rodents and Lagomorphs
Rodents and lagomorphs, like many extant groups, face conservation challenges in the face of
global habitat loss and degradation. Unlike the more charismatic mammals, such as large preda-
tors, marine mammals, and primates, they are rarely an emphasis of global conservation efforts
and, at worst, completely overlooked. This should be a concern given their important role in many
ecosystem processes.
Risk of extinction at the global level is assessed by the International Union for the Conserva-
tion of Nature (IUCN) through its Global Species Program and the Species Survival Commis-
sion. IUCN uses a series of quantitative criteria launched in 2001 to place species in one of nine
categories related to their assessment status and risk of extinction (Figure 19). The document
outlining this process, “The 2001 IUCN Red List Categories and Criteria version 3.1,” is available
at The IUCN Red List web site (http://www.iucnredlist.org). The Global Mammal Assessment pub-
lished in 2008 in Science was the rst attempt to assess all mammalian species, eliminating the Not
Evaluated category. That study showed that 21% of terrestrial mammals were under one of IUCN’s
threatened categories: Vulnerable, Endangered, or Critically Endangered. An additional 14·7%
were considered Data Decient (DD), indicating that we simply do not have information on these
species regarding their population trends or decline in distributions to assess the quantitative tar-
gets in IUCN Criteria. Forty-four percent of species described since 1992 are DD, so we know very
little about the many species recently named. The concern is that they might be quite rare, so the
number of threatened species may in fact be much greater.
If 2008 IUCN data are parsed by families of rodents and lagomorphs, rodents as an order
have slightly higher percentages of DD species and somewhat lower percentages of threatened
species (Table 2). The percent DD is quite high for several poorly studied families like Ctenodac-
tylidae, Ctenomyidae, Echimyidae, Erethizontidae, and Gliridae. Other than several mono- and
bi-specic families, the highest percentages of threatened species are in the families Calomyscidae,
Chinchillidae, Ctenomyidae, Dasyproctidae, Heteromyidae, and Octodontidae. Lagomorphs, as
an order, are well studied (8·7% DD) but have a percentage of threatened species that is close to
the overall percentage for mammals, especially for Leporidae (Table 3). There are clearly some
high-priority families of rodents that merit more intensive study, especially in the eld, and several
additional families that are particularly threatened. It is worth highlighting families typical of the
high Andes: Chinchillidae and Octodontidae. Both are currently at high risk, and the 2008 assess-
ments did not consider the risks associated with climate change in montane systems. New assess-
ments that consider the long-term consequences of a warming climate might result in even higher
estimates of risk for these families.
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