Mammalogy: the study of the evolution, ecology, physiology, and anatomy of members of the Class Mammalia (Chordata, Vertebrata).

Mammalogy has been of practical interest to humans since our ancestors evolved in Africa, as some mammal species were hunted by our ancestors while other species hunted our ancestors.

1 Many mammals have been domesticated by humans.

Date Species Scienfic name (ybp) Locaon Dog Canis lupus familiaris 35,000 Eurasia Sheep Ovis orientalis aries 12,000 Southwest Asia Pig Sus scrofa domesca 11,000 Near East, China, Germany Goat Capra aegagrus hircus 10,000 Iran Cow Bos primigenius taurus 10,000 India, Middle East, and North Africa Guinea pig Cavia porcellus 7000 Peru Donkey Equus africanus asinus 7000 Egypt Water buffalo Bubalus bubalis 6000 India, China Horse Equus ferus caballus 6000 Eurasian Steppes Dromedary Camelus dromedarius 6000 Arabia Llama Lama glama 8000 Peru Reindeer Rangifer tarandus 5000 Russia Bactrian camel Camelus bactrianus 4500 Central Asia Yak Bos grunniens 4500 Tibet Alpaca Vicugna pacos 3500 Peru Ferret Mustela putorius furo 3500 Europe European Rabbit Oryctolagus cuniculus 600 Europe 2 Humans have long noticed the big mammals . . .

Cave painting of Lascaux (~16,000 ybp).

3 Humans have long noticed the big mammals . . .

. . . but the small ones are of great practical importance.

4 5 Binomial nomenclature: Introduced by Carolus Linnaeus, system of formal recognition of species that classifies each using the generic and specific epithet. The former is capitalized, as in:

Homo sapiens Myotis lucifugus Gorilla gorilla

Both are italicized, because we use Latin words in all languages.

Natural historians in the 17th and 18th centuries began to collect and document mammals from different regions.

Mammalogy begins to be recognizable as a science at some point after Darwin writes On the Origin of Species in 1859.

By the middle of the 20th century, Mammalogy courses were offered at a number of universities, many of which also curated collections of mammal species.

6 How do mammalogists study mammals?

• Observational studies – infanticide

• Mark-recapture – estimating census population size

• Tracking – understand the movement of mammals

• Field collections – trapping individuals to add to collection

• Physiological assays – understand hormone levels and stress indicators

7 Observational studies: Watching animals, either during the day or using infrared or night-vision goggles.

• Focal animal sampling tracks the behaviors of a specific individual for some specified period of time. • Scan sampling records the behavioral state of each animal in a group at predetermined intervals. • Observability is a key concept. Certain types of habitat make observation difficult, some animals are more difficult to observe.

8 Marking Methods: While natural polymorphism can sometimes be used to identify individuals, often they are marked in some way.

• Hair dyes. • Tags. Usually clipped on ears. • Leg bands. • Tattoos have also been used.

9 Monitoring Methods: Individuals can be tracked in various ways. These data are often used to address questions related to habitat use and biotic diversity.

• Radiotelemetry. • Passive Integrated Transponder (PIT). • GPS can also be used

10 Field Methods: Trapping is used to capture wild mammals. Great variety depending on target species.

• Stephenson box trap. Used to catch larger mammals such as deer.

11 Field Methods: Trapping is used to capture wild mammals. Great variety depending on target species.

• Stephenson box trap. • Sherman trap. Collapsible trap for small mammals such as ground squirrels

12 Field Methods: Trapping is used to capture wild mammals. Great variety depending on target species.

• Stephenson box trap. • Sherman trap. • Tomahawk trap. Slightly larger mammals, typically wire sides.

13 Field Methods: Trapping is used to capture wild mammals. Great variety depending on target species.

• Stephenson box trap. • Sherman trap. • Tomahawk trap. Slightly larger mammals, typically wire sides.

14 Field Methods: Trapping is used to capture wild mammals. Great variety depending on target species.

• Stephenson box trap. • Sherman trap. • Tomahawk trap. • Pitfall traps. • Leghold traps are not commonly used, and illegal in many parts of the world.

15 Field Methods: Trapping is used to capture wild mammals. Great variety depending on target species.

• Stephenson box trap. • Sherman trap. • Tomahawk trap. • Pitfall traps. • Leghold traps. • Mist nets. Used to catch flying or gliding mammals.

16 Field Methods: Trapping is used to capture wild mammals. Great variety depending on target species.

• Stephenson box trap. • Sherman trap. • Tomahawk trap. • Pitfall traps. • Leghold traps. • Mist nets. Used to catch flying or gliding mammals.

17 Field Methods: Trapping is used to capture wild mammals. Great variety depending on target species.

• Stephenson box trap. • Sherman trap. • Tomahawk trap. • Pitfall traps. • Leghold traps. • Mist nets.

• Shooting. Guns use to collect, usually with tranquilizer darts.

18 Physiological measures: Mammalogists focus on nutrition, energy metabolism, growth, locomotion, water balance and disease.

• Nutritional studies investigate the diet of focal species. Conducted via observational, measurement of scat or stomach contents. PCR can be used to amplified barcoding genes to identify prey species.

• Nutritional condition also assessed by measuring body fat, body mass and by using bioelectric impudence analysis.

• Metabolism. Measured using basal metabolic rate (BMR) in resting mammals and field metabolic rate (FMR) in active mammals.

• Radioimmunoassay (RIA) measure hormones and reproductive status.

19 Physiological measures: Mammalogists focus on nutrition, energy metabolism, growth, locomotion, water balance and disease.

20 Nutritional studies investigate the diet of focal species. Conducted via observational, measurement of scat or stomach contents. PCR can be used to amplified barcoding genes to identify prey species.

21 Genetic and molecular techniques: Genetic data have increased dramatically in the last decades.

• Karyotypes resulted from staining and fixing chromosomes. Can measure the number and size of chromosomes and also identify regions that contain a number of genes.

• Protein electrophoresis is used to separate protein molecules based on their charge, and provides a quick assay of genetic diversity.

22 Genetic and molecular techniques: Genetic data have increased dramatically in the last decades.

• Polymerase chain reaction (PCR) based methods. Gene sequences can be amplified and sequenced using primers and PCR reactions.

• Sequence markers such as Cytochrome b or the Recom- bination Activation Group genes provide useful data for systematics and phylogeography.

• Microsatellites have high mutation rates and are useful for landscape and population genetic studies.

23 24 What are phylogenies?

• history of organismal lineages through time • record of descent with modification • record of cladogenesis (formation of two lineages from an ancestral lineage)

Vocabulary:

1. clade 2. monophyletic 3. paraphyletic 4. sister taxa 5. node 6. synapomorphy 7. lineage 8. terminal taxa

25 Phylogenies

Self Quiz: Identify the following on the phylogeny to the right

Any clade

A monophyletic group containing monkeys

A paraphyletic group

The sister taxa to primates

A node containing elephants

The branch where the placenta evolved

A lineage that includes anteaters

26

Patterns of evolutionary change – clarification of monophyly, paraphyly, and polyphyly

27 Museum collections: Essential to mammalogy (and Biological Sciences in general). Serve as an archive of material, a source of data, and a location to train the next generation of mammalogists.

• Skins. Dried skins provide morphological data for systematic studies. • Skeletal materials are cleaned and stored. These provide a source of morphological data for systematic investigations. • Tissues. Soft tissues are preserved to act as a source of DNA for future genetic investigations.

28 Systematic investigations: Mammalogists are interested in variation (polymorphism) within and between species, as well as other types of variation include sexual dimorphism

• Morphometric. Studies quantify measurements among a series of landmarks on skulls and other bones.

29 Ventral view Dorsal view

Proximal end of humerus

Distal end of Lateral view humerus

30 Systematic investigations: Mammalogists are interested in variation (polymorphism) within and between species, as well as other types of variation include sexual dimorphism

• Morphometric. • Biomechanical. Investigate the forces involved with activities such as biting and running.

31 Systematic investigations: Mammalogists are interested in variation (polymorphism) within and between species, as well as other types of variation include sexual dimorphism

• Morphometric. • Biomechanical. • Phylogeography. Investigate the geographic pattern of genetic diversity.

32 Systematic investigations: Mammalogists are interested in variation (polymorphism) within and between species, as well as other types of variation include sexual dimorphism

• Morphometric. • Biomechanical. • Phylogeography. • Phylogenetic. Estimate the evolutionary relationships with some group.

33 Systematic investigations: Mammalogists are interested in variation (polymorphism) within and between species, as well as other types of variation include sexual dimorphism

• Morphometric. • Biomechanical. • Phylogeography. • Phylogenetic. • Species boundaries.

34 Genetic (genomic) data: Mammalogists have an unprecedented amount of resources to acquire genetic data

Polymerase Chain Reaction

PCR – small amounts of WGA are amplified using primers of known sequence and polymerase

35 Genetic (genomic) data: Mammalogists have an unprecedented amount of resources to acquire genetic data

Polymerase Chain Reaction Microsatellite

PCR is used to amplify regions that contain highly repetitive DNA elements (used for landscape genetics, parentage analysis, etc.).

36 Genetic (genomic) data: Mammalogists have an unprecedented amount of resources to acquire genetic data

Polymerase Chain Reaction Microsatellite DNA Sequencing – Sanger (terminal dye labeling)

PCR is used to amplify single gene regions. Regions are targeted on the basis of their mutational variability, for either shallow or deep evolutionary investigations. Mitochondrial DNA is often used.

37 Genetic (genomic) data: Mammalogists have an unprecedented amount of resources to acquire genetic data

Polymerase Chain Reaction Microsatellite DNA Sequencing – Sanger (terminal dye labeling) DNA Sequencing – Next generation methods

Solution based hybridization probes or restriction enzymes are used to reduce the representation of the genome in the library. Individual samples are then tagged with a barcode (unique sequence of DNA bases) and sequenced in parallel on machines that can generate 200 million sequence reads of ~100 bp or so each. Bioinformatic approaches are then used to assemble and edit the sequences and identify single nucleotide polymorphisms (SNPs).

38 Ornithorhynchus anatinus, Platypus (2007) Monodelphis domestica, Gray Short-tailed Opossum (2007) Sarcophilus harrisii, Tasmanian devil () Macropus eugenii, Tammar wallaby (2011) Phascolarctos cinereus, Koala (2013 draft) Erinaceus europaeus, Western European Hedgehog () Megaderma lyra, Greater false vampire bat (2013) Pteronotus parnellii, Parnell's mustached bat (2013) Pteropus vampyrus, Fruit Bat (2012) Eidolon helvum, Old World Fruit Bat (2013) Rhinolophus ferrumequinum. Greater horseshoe bat (2013) Myotis lucifugus, Little Brown Bat (2010) Otolemur garnettii, Small-eared Galago, or Bushbaby (2012) Macaca mulatta, Rhesus Macaque (2007) Pongo pygmaeus/Pongo abelii, Orangutan (Borneo/Sumatra) (2011) Gorilla gorilla, Western Gorilla (2012) Homo sapiens, Modern Human (Draft 2001 Complete 2006) Homo neanderthalensis, Neanderthal (Draft 2010) Pan troglodytes, Chimpanzee (2005) Pan paniscus, Bonobo (2012) Callithrix jacchus, Marmoset (2010) Felis silvestris catus, Cat (2007) Panthera leo, African Lion (2013) Panthera leo krugeri, White Lion (2013) Panthera tigris altaica, Siberian Tiger (2013) Panthera tigris tigris, Bengal Tiger (2013 Panthera uncia, Snow Leopard (2013) Canis lupus familiaris, Dog (2005) Ailuropoda melanoleuca, Giant panda (2010) Tursiops truncatus, Bottlenosed dolphin (2012) Loxodonta africana, African Elephant (2009) Equus ferus caballus, Horse (2009) Sus scrofa, Pig (2012) Bos grunniens, Yak (2012) Bos primigenius indicus, Zebu (2012) Bos primigenius taurus, Cow (2009) Mus musculus, Mouse (2002) Rattus norvegicus, Rat (2004) 39 Oryctolagus cuniculus, European Rabbit (2010)