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

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1 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

2 Many mammals have been domesticated by humans. Species Dog Sheep Pig Goat Cow Guinea pig Donkey Water buffalo Horse Dromedary Llama Reindeer Bactrian camel Yak Alpaca Ferret European Rabbit Scien)fic name Canis lupus familiaris Ovis orientalis aries Sus scrofa domes5ca Capra aegagrus hircus Bos primigenius taurus Cavia porcellus Equus africanus asinus Bubalus bubalis Equus ferus caballus Camelus dromedarius Lama glama Rangifer tarandus Camelus bactrianus Bos grunniens Vicugna pacos Mustela putorius furo Oryctolagus cuniculus Date (ybp) Loca)on 35,000 Eurasia 12,000 Southwest Asia 11,000 Near East, China, Germany 10,000 Iran 10,000 India, Middle East, and North Africa 7000 Peru 7000 Egypt 6000 India, China 6000 Eurasian Steppes 6000 Arabia 8000 Peru 5000 Russia 4500 Central Asia 4500 Tibet 3500 Peru 3500 Europe 600 Europe 2

3 Humans have long noticed the big mammals... Cave painting of Lascaux (~16,000 ybp). 3

4 Humans have long noticed the big mammals but the small ones are of great practical importance. 4

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6 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 17 th and 18 th 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 By the middle of the 20 th century, Mammalogy courses were offered at a number of universities, many of which also curated collections of mammal species. 6

7 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

8 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

9 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

10 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

11 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

12 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

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. 13

14 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

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 are not commonly used, and illegal in many parts of the world. 15

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. 16

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. Used to catch flying or gliding mammals. 17

18 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

19 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

20 Physiological measures: Mammalogists focus on nutrition, energy metabolism, growth, locomotion, water balance and disease. 20

21 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

22 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

23 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 Recombination 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

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25 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

26 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

27 Patterns of evolutionary change clarification of monophyly, paraphyly, and polyphyly 27

28 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

29 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

30 Ventral view Dorsal view Proximal end of humerus Distal end of humerus Lateral view 30

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. Investigate the forces involved with activities such as biting and running. 31

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. Investigate the geographic pattern of genetic diversity. 32

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. Estimate the evolutionary relationships with some group. 33

34 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

35 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

36 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

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) 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

38 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

39 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) Oryctolagus cuniculus, European Rabbit (2010) 39