Methods for
CHAPTER 2 Studying
Mammals
Field Methods Like most fields of biology, mammalogy relies on a diverse array of
Trapping and Marking research methods that cross disciplinary boundaries. No single chapter
Monitoring could describe them all, so we present a selection of techniques that are
Observational Methods widely used by researchers in different branches of mammalogy. For
convenience, we divide this chapter into three major sections: field
Laboratory and Museum methods, laboratory and museum methods, and systematic methods.
Methods These categories are not disciplinary—a single research project might
Physiological Measures employ methods from each. For example, a phylogenetic study of a
Stable Isotope Analysis particular group of mammals might begin with field work in which
Genet ics and Molecular Techniques specimens are collected, proceed to museum work in which t hose speci-
Analyses of Museum Specimens mens are prepared and examined, and culminate with a reconstructed
phylogeny, proposed classification, and estimated divergence times for
Systematic Methods major groups.
Intraspecific Variation An overview such as we provide h ere w
ill inevitably omit many
Intraspecific Phylogeography important topics and lack detail on those that are discussed. Indeed,
Species Boundaries some of the techniques we describe are complex and scarcely amenable
Phylogenet ic Inference to cursory treatment. Our goal is to present t hese methods in the con-
Classification text of the research questions they w ere developed to address. We in-
Estimating Divergence Times clude extensive references to more thorough and advanced descriptions
of each. Of course, no textbook treatment can replace hands-on expe-
rience and we strongly encourage mammalogy students to take advan-
tage of any field, laboratory, or data-analysis opportunities associated
with their course.
We cannot overemphasize the importance of mathematics and sta-
tistics in modern biology. Any student aspiring to a career in mam-
malogy must obtain sufficient training in modeling, probability the-
ory, statistical inference, experimental design, and computing. These
topics are too extensive for us to cover here, but readers may consult
any number of helpful texts at introductory or advanced levels (e.g.,
Quinn and Keogh 2002; Morisson et al. 2008; Motulsky 2014; Zar
2010; Gotelli and Ellison 2013; Hector 2015).
16
, Chapter 2 Methods for Studying Mammals 17
Field Methods in East Africa, and enclosures have been used to trap groups
of ungulates (Kichenside 1998) and primates (Rawlins et al.
1984). Pitfall traps, consisting of a can or bucket buried in
Mammalogists often ask such questions as: How many squir- the ground, are used to capture very small mammals, such
rels live in a particular forest or woodlot? What are the sizes as mice and shrews (Umetsu et al. 2006; Santos-Filho et al.
and shapes of their home ranges? Does their socio-spatial 2015). Pitfall traps are most frequently employed as kill
system include dominance hierarchies or territories? When traps, but may function as live traps if checked frequently.
are the squirrels most active? Answering questions like these Padded leghold traps can be used for medium-large species
usually entails identifying and monitoring individual ani- (Luengos Vidal et al. 2016). Mist nets are often the method
mals in the field. But most mammals are difficult to observe of choice to catch bats, particularly when the bats follow a
directly in the wild b ecause they spend at least part of their regular flight path to and from their roost (Trevelin et al.
time in inaccessible places, are active at night, or are simply 2017). Larger nets, fired by guns, have been used to cap-
too small to see easily in their natural habitat. For these rea- ture ungulates such as bighorn sheep (Ovis canadensis;
sons, researchers have developed a set of indirect methods DeCesare and Pletscher 2006). Kill (“snap”) traps used
for studying mammals in the field. with small mammals include Museum Special, Victor, and
McGill types (Stanley et al. 2014). Traps for capturing bur-
rowing mammals include the “harpoon mole,” cinch, and
TRAPPING AND MARKING Macabee-type gopher traps. Descriptions of these and
other special-purpose traps and trapping methods are pro-
Trapping vided by Martin and colleagues (2001).
Guns that fire tranquilizer darts are often used to im-
Methods for capturing wild mammals include a variety of mobilize larger mammals (Kreeger 2012). This technique
trapping and netting techniques (Wilson et al. 1996; is helpful when animals are held for only a brief period,
Christman 2010; Hoffman et al. 2010). W hether mammals after which they may be given an antagonist drug to reverse
are live-trapped or killed depends on the nature of the the anesthetic. For example, Lowe and Alderman (2014)
study and the reason for their capture. Although many anesthetized female moose (Alces alces) with darts shot from
studies now employ livetrapping, kill-trapping is often nec- a helicopter to study the effects of population monitoring
essary and justified. For instance, museum collections on fecundity and recruitment. Auer and coworkers (2010)
maintain reference specimens for taxonomic studies and immobilized red deer (Cervus elaphus) with shots from a
biotic surveys, but the skin, skeleton, or tissue materials re- dart gun to study the effects of different anesthetics during
quired for such analyses cannot be obtained from live ani- surgery. Dart guns can also be used to catch animals for
mals. If trapped animals are to be used for a museum col- translocation or captive study ( Jessup et al. 2014).
lection, it is necessary to ensure that the specimen is not The care of animals captured in the wild and held in
damaged by the capture procedure. Trapping to remove captivity has been important since the advent of zoologi-
animals, such as pest species, from an area can best be ac- cal parks and the use of mammals as laboratory subjects.
complished with kill traps, guns, or poison. Mammal
trapping of any sort usually requires permits issued by
government conservation authorities and procedures ap-
proved by an institutional animal care and use commit-
tee (IACUC). Mammalogists must follow standard, le-
gally mandated practices for safe and humane h andling of
trapped animals, such as t hose published by the American
Society of Mammalogists (Sikes et al. 2011).
Live traps come in several types and sizes (Powell and
Proulx 2003). For small rodents, the most widely used are
sophisticated Longworth traps, simpler Sherman or Elliott
traps made of sheet metal, wire-mesh Tomahawk traps, and
newer plastic BioEcoSS TubeTraps (Lambert et al. 2005).
For species of intermediate size, such as raccoons (Procyon
lotor), larger Tomahawk or Havahart traps with wire mesh
sides are available (Baldwin et al. 2004). Box traps (Fig-
ure 2.1) are constructed for capturing large mammals
such as ungulates or carnivorans (Grassman et al. 2005). Figure 2.1 Stephenson box trap. Large box traps of the
The dimensions and operations of such traps are adapted type shown here are used to capture larger mammals, such as
white-tailed deer (Odocoileus virginianus). Animals captured in
to the subject species. Box traps can also be used to cap- this manner can be measured, tagged, dyed for individual
ture groups of smaller animals. Rood (1975) used large box identification, or fitted with collars for tracking by
traps to capture banded mongoose (Mungos mungo) groups radiotelemetry.
, 18 Part 1 Introduction
In a landmark volume, Crandall (1964) spelled out many MONITORING
of the procedures to be followed in caring for captive mam-
mals. This topic has become increasingly significant as Methods for monitoring the movements of wild mammals
zoos and wildlife parks expand their mission to include may be divided into t hose that involve tracking physical
conservation as well as exhibition. Working with captive signs of animals and t hose that involve radio tagging. Both
mammals has enabled us to get a better understanding of are widely used, and the choice of method is dictated by the
their physiology and behavior, information that is critical nature of the species studied, the research question, and the
for management of captive populations (Flacke et al. 2016). cost of conducting the research. Researchers must also en-
Kleiman and colleagues (2010) provide an updated com- sure that the monitoring procedure does not alter the be
pendium of procedures to care for captive mammals. havior or survivorship of the animals being studied.
Powder tracking (Lemen and Freeman 1985) involves
coating a small mammal with a fluorescent dust; its move-
Marking ments after release can then be traced at night with an ul-
traviolet light. This technique has been used to study space
Appropriate marking techniques vary with the species be- use (Kraft and Stapp 2013), habitat selection (Long et al.
ing studied and w hether individuals are free-ranging, held 2013), food hoarding (White and Geluso 2012), and disper-
in zoos, or are laboratory stocks (Silvy et al. 2012). For sal (Kuykendall and Keller 2011). Bait marking can also be
techniques used with zoo and laboratory animals, see Kalk used to assess spatial relations. When small plastic pellets
and Rice (2010) and Lane-Petter (1978), respectively. H ere are ingested with bait food, the locations of feces contain-
we are concerned only with free-ranging mammals and ing pellets mark areas visited by individuals (Kilshaw et al.
t hose maintained in semi-natural conditions. 2009). Fecal pellet surveys have been used to monitor wild
In some instances, physical features of individual mam- populations of ungulates (McShea et al. 2001), snowshoe
mals can be used for identification. Individuals of large- hares (Lewis et al. 2011), and rodents (Whisson et al. 2015),
bodied species (e.g., ungulates, primates) can be identified while tracking tubes (or tunnels) have been used with
by a profile of observable characteristics such as size, color- smaller mammals (Wilkinson et al. 2012; Stolen et al. 2014).
ation, scars or other marks of injury, and behavior patterns. Activity patterns and habitat use in species with low popu-
Vibrissae spot patterns have been used to identify individ- lation density, secretive habits, or nocturnal activity may
ual polar bears (Anderson et al. 2010). This approach is well- be monitored with camera traps (Franco et al. 2011;
developed in studies of cetaceans, many of which show natu O’Connor et al. 2017). Aquatic species pose special prob
ral color or shape variations on their tail flukes and dorsal lems for field monitoring; Churchfield and colleagues
fins (Elwen et al. 2014). Such markings can be photographed (2000) used baited tubes to survey water shrews (Neomys
and the images archived for a permanently accessible record fodiens). Field monitoring of wild populations has been rev-
of individual identification (Mizroch et al. 2004). Photo- olutionized by DNA markers (see “Genet ics and Molecu-
graphic identification has been enhanced by computerized lar Techniques” later in this chapter) associated with scat,
matching techniques (Torres et al. 2017). Cunningham hair, or other biological residues (Ma et al. 2016).
(2009) used a computer matching system to estimate the The use of passive integrated transponder (PIT) tags
size of a harbor seal (Phoca vitulina) population. began as a means of identifying individuals in the field
In species with more cryptic habits and appearances, (Neubaum et al. 2005), but has developed into an effective
artificial marking devices are used to identify individuals monitoring technique for mammals and other vertebrates
that have been captured and released. The most common (Smyth and Nebel 2013). PIT tags are small (1 cm), glass-
devices are coded metal or plastic ear tags (Tettamanti encased, electronic devices implanted beneath the skin.
et al. 2015) or dyes (Michener 2004). Researchers en- Each PIT tag contains an integrated circuit with a digital
gaged in long-term field studies may give animals per- identification code and an antenna that transmits the code
manent brands or tattoos. McGregor and Jones (2016) when it is activated by the electric field of a transceiver. If
argued that use of electronic tattoo pens is a minimally an animal is close enough to a transceiver for its PIT to be
invasive technique for marking medium-sized Austra- activated, the tag transmits its code to a data-logging sys-
lian marsupials. Freeze-branding with liquid nitrogen tem that identifies the individual. PIT tags are inexpensive
results in permanent white hairs or unpigmented skin and long-lasting; they require no internal battery and can
where the liquid was applied; this is a common technique persist safely after implantation for many years. O’Shea and
for large mammals such as cattle or horses (Turner et al. coworkers (2010) fitted nearly 3,000 big brown bats (Eptesi-
2007). Clipping fur patterns and using depilatories to re- cus fuscus) with PIT tags for a study of population recruit-
move patches of hair have been used as marking tech- ment patterns in Colorado. Soanes and colleagues (2015)
niques in several species (Glennon et al. 2002), as have used PIT tags and cameras to monitor the use of road-
toe clips (Borremans et al. 2015) and ear notching (Ngene crossing structures by arboreal marsupials in Australia.
et al. 2011). The latter marks may be visible from a dis- Radiotelemetry has been used extensively in wildlife
tance in larger mammals, particularly with the use of tracking since the 1950s (Bensen 2010). A radiotelemetry
binoculars. system includes a battery-powered radio transmitter at-
CHAPTER 2 Studying
Mammals
Field Methods Like most fields of biology, mammalogy relies on a diverse array of
Trapping and Marking research methods that cross disciplinary boundaries. No single chapter
Monitoring could describe them all, so we present a selection of techniques that are
Observational Methods widely used by researchers in different branches of mammalogy. For
convenience, we divide this chapter into three major sections: field
Laboratory and Museum methods, laboratory and museum methods, and systematic methods.
Methods These categories are not disciplinary—a single research project might
Physiological Measures employ methods from each. For example, a phylogenetic study of a
Stable Isotope Analysis particular group of mammals might begin with field work in which
Genet ics and Molecular Techniques specimens are collected, proceed to museum work in which t hose speci-
Analyses of Museum Specimens mens are prepared and examined, and culminate with a reconstructed
phylogeny, proposed classification, and estimated divergence times for
Systematic Methods major groups.
Intraspecific Variation An overview such as we provide h ere w
ill inevitably omit many
Intraspecific Phylogeography important topics and lack detail on those that are discussed. Indeed,
Species Boundaries some of the techniques we describe are complex and scarcely amenable
Phylogenet ic Inference to cursory treatment. Our goal is to present t hese methods in the con-
Classification text of the research questions they w ere developed to address. We in-
Estimating Divergence Times clude extensive references to more thorough and advanced descriptions
of each. Of course, no textbook treatment can replace hands-on expe-
rience and we strongly encourage mammalogy students to take advan-
tage of any field, laboratory, or data-analysis opportunities associated
with their course.
We cannot overemphasize the importance of mathematics and sta-
tistics in modern biology. Any student aspiring to a career in mam-
malogy must obtain sufficient training in modeling, probability the-
ory, statistical inference, experimental design, and computing. These
topics are too extensive for us to cover here, but readers may consult
any number of helpful texts at introductory or advanced levels (e.g.,
Quinn and Keogh 2002; Morisson et al. 2008; Motulsky 2014; Zar
2010; Gotelli and Ellison 2013; Hector 2015).
16
, Chapter 2 Methods for Studying Mammals 17
Field Methods in East Africa, and enclosures have been used to trap groups
of ungulates (Kichenside 1998) and primates (Rawlins et al.
1984). Pitfall traps, consisting of a can or bucket buried in
Mammalogists often ask such questions as: How many squir- the ground, are used to capture very small mammals, such
rels live in a particular forest or woodlot? What are the sizes as mice and shrews (Umetsu et al. 2006; Santos-Filho et al.
and shapes of their home ranges? Does their socio-spatial 2015). Pitfall traps are most frequently employed as kill
system include dominance hierarchies or territories? When traps, but may function as live traps if checked frequently.
are the squirrels most active? Answering questions like these Padded leghold traps can be used for medium-large species
usually entails identifying and monitoring individual ani- (Luengos Vidal et al. 2016). Mist nets are often the method
mals in the field. But most mammals are difficult to observe of choice to catch bats, particularly when the bats follow a
directly in the wild b ecause they spend at least part of their regular flight path to and from their roost (Trevelin et al.
time in inaccessible places, are active at night, or are simply 2017). Larger nets, fired by guns, have been used to cap-
too small to see easily in their natural habitat. For these rea- ture ungulates such as bighorn sheep (Ovis canadensis;
sons, researchers have developed a set of indirect methods DeCesare and Pletscher 2006). Kill (“snap”) traps used
for studying mammals in the field. with small mammals include Museum Special, Victor, and
McGill types (Stanley et al. 2014). Traps for capturing bur-
rowing mammals include the “harpoon mole,” cinch, and
TRAPPING AND MARKING Macabee-type gopher traps. Descriptions of these and
other special-purpose traps and trapping methods are pro-
Trapping vided by Martin and colleagues (2001).
Guns that fire tranquilizer darts are often used to im-
Methods for capturing wild mammals include a variety of mobilize larger mammals (Kreeger 2012). This technique
trapping and netting techniques (Wilson et al. 1996; is helpful when animals are held for only a brief period,
Christman 2010; Hoffman et al. 2010). W hether mammals after which they may be given an antagonist drug to reverse
are live-trapped or killed depends on the nature of the the anesthetic. For example, Lowe and Alderman (2014)
study and the reason for their capture. Although many anesthetized female moose (Alces alces) with darts shot from
studies now employ livetrapping, kill-trapping is often nec- a helicopter to study the effects of population monitoring
essary and justified. For instance, museum collections on fecundity and recruitment. Auer and coworkers (2010)
maintain reference specimens for taxonomic studies and immobilized red deer (Cervus elaphus) with shots from a
biotic surveys, but the skin, skeleton, or tissue materials re- dart gun to study the effects of different anesthetics during
quired for such analyses cannot be obtained from live ani- surgery. Dart guns can also be used to catch animals for
mals. If trapped animals are to be used for a museum col- translocation or captive study ( Jessup et al. 2014).
lection, it is necessary to ensure that the specimen is not The care of animals captured in the wild and held in
damaged by the capture procedure. Trapping to remove captivity has been important since the advent of zoologi-
animals, such as pest species, from an area can best be ac- cal parks and the use of mammals as laboratory subjects.
complished with kill traps, guns, or poison. Mammal
trapping of any sort usually requires permits issued by
government conservation authorities and procedures ap-
proved by an institutional animal care and use commit-
tee (IACUC). Mammalogists must follow standard, le-
gally mandated practices for safe and humane h andling of
trapped animals, such as t hose published by the American
Society of Mammalogists (Sikes et al. 2011).
Live traps come in several types and sizes (Powell and
Proulx 2003). For small rodents, the most widely used are
sophisticated Longworth traps, simpler Sherman or Elliott
traps made of sheet metal, wire-mesh Tomahawk traps, and
newer plastic BioEcoSS TubeTraps (Lambert et al. 2005).
For species of intermediate size, such as raccoons (Procyon
lotor), larger Tomahawk or Havahart traps with wire mesh
sides are available (Baldwin et al. 2004). Box traps (Fig-
ure 2.1) are constructed for capturing large mammals
such as ungulates or carnivorans (Grassman et al. 2005). Figure 2.1 Stephenson box trap. Large box traps of the
The dimensions and operations of such traps are adapted type shown here are used to capture larger mammals, such as
white-tailed deer (Odocoileus virginianus). Animals captured in
to the subject species. Box traps can also be used to cap- this manner can be measured, tagged, dyed for individual
ture groups of smaller animals. Rood (1975) used large box identification, or fitted with collars for tracking by
traps to capture banded mongoose (Mungos mungo) groups radiotelemetry.
, 18 Part 1 Introduction
In a landmark volume, Crandall (1964) spelled out many MONITORING
of the procedures to be followed in caring for captive mam-
mals. This topic has become increasingly significant as Methods for monitoring the movements of wild mammals
zoos and wildlife parks expand their mission to include may be divided into t hose that involve tracking physical
conservation as well as exhibition. Working with captive signs of animals and t hose that involve radio tagging. Both
mammals has enabled us to get a better understanding of are widely used, and the choice of method is dictated by the
their physiology and behavior, information that is critical nature of the species studied, the research question, and the
for management of captive populations (Flacke et al. 2016). cost of conducting the research. Researchers must also en-
Kleiman and colleagues (2010) provide an updated com- sure that the monitoring procedure does not alter the be
pendium of procedures to care for captive mammals. havior or survivorship of the animals being studied.
Powder tracking (Lemen and Freeman 1985) involves
coating a small mammal with a fluorescent dust; its move-
Marking ments after release can then be traced at night with an ul-
traviolet light. This technique has been used to study space
Appropriate marking techniques vary with the species be- use (Kraft and Stapp 2013), habitat selection (Long et al.
ing studied and w hether individuals are free-ranging, held 2013), food hoarding (White and Geluso 2012), and disper-
in zoos, or are laboratory stocks (Silvy et al. 2012). For sal (Kuykendall and Keller 2011). Bait marking can also be
techniques used with zoo and laboratory animals, see Kalk used to assess spatial relations. When small plastic pellets
and Rice (2010) and Lane-Petter (1978), respectively. H ere are ingested with bait food, the locations of feces contain-
we are concerned only with free-ranging mammals and ing pellets mark areas visited by individuals (Kilshaw et al.
t hose maintained in semi-natural conditions. 2009). Fecal pellet surveys have been used to monitor wild
In some instances, physical features of individual mam- populations of ungulates (McShea et al. 2001), snowshoe
mals can be used for identification. Individuals of large- hares (Lewis et al. 2011), and rodents (Whisson et al. 2015),
bodied species (e.g., ungulates, primates) can be identified while tracking tubes (or tunnels) have been used with
by a profile of observable characteristics such as size, color- smaller mammals (Wilkinson et al. 2012; Stolen et al. 2014).
ation, scars or other marks of injury, and behavior patterns. Activity patterns and habitat use in species with low popu-
Vibrissae spot patterns have been used to identify individ- lation density, secretive habits, or nocturnal activity may
ual polar bears (Anderson et al. 2010). This approach is well- be monitored with camera traps (Franco et al. 2011;
developed in studies of cetaceans, many of which show natu O’Connor et al. 2017). Aquatic species pose special prob
ral color or shape variations on their tail flukes and dorsal lems for field monitoring; Churchfield and colleagues
fins (Elwen et al. 2014). Such markings can be photographed (2000) used baited tubes to survey water shrews (Neomys
and the images archived for a permanently accessible record fodiens). Field monitoring of wild populations has been rev-
of individual identification (Mizroch et al. 2004). Photo- olutionized by DNA markers (see “Genet ics and Molecu-
graphic identification has been enhanced by computerized lar Techniques” later in this chapter) associated with scat,
matching techniques (Torres et al. 2017). Cunningham hair, or other biological residues (Ma et al. 2016).
(2009) used a computer matching system to estimate the The use of passive integrated transponder (PIT) tags
size of a harbor seal (Phoca vitulina) population. began as a means of identifying individuals in the field
In species with more cryptic habits and appearances, (Neubaum et al. 2005), but has developed into an effective
artificial marking devices are used to identify individuals monitoring technique for mammals and other vertebrates
that have been captured and released. The most common (Smyth and Nebel 2013). PIT tags are small (1 cm), glass-
devices are coded metal or plastic ear tags (Tettamanti encased, electronic devices implanted beneath the skin.
et al. 2015) or dyes (Michener 2004). Researchers en- Each PIT tag contains an integrated circuit with a digital
gaged in long-term field studies may give animals per- identification code and an antenna that transmits the code
manent brands or tattoos. McGregor and Jones (2016) when it is activated by the electric field of a transceiver. If
argued that use of electronic tattoo pens is a minimally an animal is close enough to a transceiver for its PIT to be
invasive technique for marking medium-sized Austra- activated, the tag transmits its code to a data-logging sys-
lian marsupials. Freeze-branding with liquid nitrogen tem that identifies the individual. PIT tags are inexpensive
results in permanent white hairs or unpigmented skin and long-lasting; they require no internal battery and can
where the liquid was applied; this is a common technique persist safely after implantation for many years. O’Shea and
for large mammals such as cattle or horses (Turner et al. coworkers (2010) fitted nearly 3,000 big brown bats (Eptesi-
2007). Clipping fur patterns and using depilatories to re- cus fuscus) with PIT tags for a study of population recruit-
move patches of hair have been used as marking tech- ment patterns in Colorado. Soanes and colleagues (2015)
niques in several species (Glennon et al. 2002), as have used PIT tags and cameras to monitor the use of road-
toe clips (Borremans et al. 2015) and ear notching (Ngene crossing structures by arboreal marsupials in Australia.
et al. 2011). The latter marks may be visible from a dis- Radiotelemetry has been used extensively in wildlife
tance in larger mammals, particularly with the use of tracking since the 1950s (Bensen 2010). A radiotelemetry
binoculars. system includes a battery-powered radio transmitter at-
