KW

Midterm Study Guide RNR 3018

Most Important topics

Evolutionary relationships (phylogeny- be able to draw a tree, not the old-school diagram from the beginning of each lecture)

  • A phylogenetic tree is a diagram that represents evolutionary relationships among organisms. Phylogenetic trees are hypotheses, not definitive facts.

  • The pattern of branching in a phylogenetic tree reflects how species or other groups evolved from a series of common ancestors.

  • In trees, two species are more related if they have a more recent common ancestor and less related if they have a less recent common ancestor.

  • Phylogenetic trees can be drawn in various equivalent styles. Rotating a tree about its branch points doesn't change the information it carries.

  • Each branch point (also called an internal node) represents a divergence event, or splitting apart of a single group into two descendant groups.

  • At each branch point lies the most recent common ancestor of all the groups descended from that branch point.

Key evolutionary innovations and where they can be placed on the phylogeny

Amphibians

Amphibians, which evolved about 365 million years ago from a lobe-finned fish ancestor, have undergone several key evolutionary innovations:

Development of Limbs: Amphibians were the first group of vertebrates to develop limbs, enabling them to leave the water and conquer the land.

Lungs: The sarcopterygian ancestor of amphibians possessed lungs, which provide the ability to breathe air. This trait appeared in bony fishes well before the fish-tetrapod transition.

Metamorphosis: Amphibians typically start out as aquatic larvae with gills known as tadpoles. The young generally undergo metamorphosis from larva with gills to an adult air-breathing form with lungs.

Skin Respiration: Amphibians use their skin as a secondary respiratory surface and some small terrestrial salamanders and frogs lack lungs and rely entirely on their skin.

In terms of phylogeny, amphibians are a paraphyletic group encompassing all tetrapods, excluding the amniotes (tetrapods with an amniotic membrane, such as modern reptiles, birds, and mammals). All extant (living) amphibians belong to the monophyletic subclass Lissamphibia, with three living orders: Anura (frogs), Urodela (salamanders), and Gymnophiona (caecilians). The earliest amphibians evolved in the Devonian period from sarcopterygian fish with lungs and bony-limbed fins, features that were helpful in adapting to dry land. They diversified and became ecologically dominant during the Carboniferous and Permian periods, but were later displaced in terrestrial environments by early reptiles and basal synapsids (mammal predecessors). The origin of modern amphibians belonging to Lissamphibia, which first appeared during the Early Triassic, around 250 million years ago, has long been contentious. However, the emerging consensus is that they likely originated from temnospondyls, the most diverse group of prehistoric amphibians, during the Permian period.

Reptiles

Reptiles, which first arose about 320 million years ago during the Carboniferous period, have undergone several key evolutionary innovations:

Development of Lungs and Legs: These are the main transitional steps towards reptiles.

Hard-Shelled External Eggs: The development of hard-shelled external eggs replacing the amphibious water-bound eggs is the defining feature of the class Reptilia and is what allowed these amphibians to fully leave water.

Scales or Scutes: Reptiles are defined as animals that have scales or scutes.

Ectothermic Metabolisms: Reptiles possess ectothermic metabolisms.

The evolution of these features did not occur in a single major evolutionary event, but rather through many small bursts of morphological changes over a period of 50 million years.

In terms of phylogeny, reptiles are a paraphyletic group comprising all non-avian and non-mammalian amniotes. The two largest lineages of reptiles, Archosauromorpha (crocodilians, birds, and kin) and Lepidosauromorpha (lizards, and kin), diverged near the end of the Permian period. The earliest known proto-reptiles originated around 312 million years ago during the Carboniferous period5. The earliest known eureptile (“true reptile”) was Hylonomus.

Mammals

Mammals, which first appeared during the late Carboniferous period, have undergone several key evolutionary innovations:

Differentiated Teeth: Mammals developed differentiated teeth with precise occlusion, which was crucial for capturing arthropods and crushing their exoskeletons.

Hard Palate: The development of a hard roof of the mouth created a dedicated airway to the lungs, allowing mammal ancestors to eat and breathe at the same time.

Spine Structure: The change from a spine that bends from left to right to one that enables bending up and down ultimately allowed mammals to take in more oxygen as they moved, helping them run faster.

Variety of Tooth Shapes: The variety of tooth shapes — incisors, canines, premolars, and molars — made it possible for mammals to eat many kinds of food.

Milk Production, Warm-Bloodedness, Hair: These are very familiar mammalian characteristics.

Jaw Joint: A joint in the jaw that makes chewing possible was a major evolutionary turning point.

Middle Ear Bones: The transformation of two bones in the reptile jaw, which migrated to the middle ear to become two members of a famous trio, the hammer and anvil.

In terms of phylogeny, mammals are a part of the synapsid lineage, which became distinct from the sauropsid lineage in the late Carboniferous period, between 320 and 315 million years ago. The only living synapsids are mammals. The lineage leading to today’s mammals split up in the Jurassic; synapsids from this period include Dryolestes, more closely related to extant placentals and marsupials than to monotremes, as well as Ambondro, more closely related to monotremes. Later on, the eutherian and metatherian lineages separated; the metatherians are the animals more closely related to the marsupials, while the eutherians are those more closely related to the placentals. Since Juramaia, the earliest known eutherian, lived 160 million years ago in the Jurassic, this divergence must have occurred in the same period.

Take home messages-

3 old clades:

  • monotremes

  • marsupials

  • eutherians

Major eutherian clades

  • present by late

  • Cretaceous

Eutherian diversification

  • after K-Pg extinctions

Birds

Birds, which evolved from theropod dinosaurs about 150 million years ago during the Jurassic period, have undergone several key evolutionary innovations:

Feathers: The evolution of feathers is a key innovation in birds. They provide insulation, enable flight, and are used in display and camouflage.

Beak: The bird beak is a key evolutionary innovation that allowed birds to diversify into a range of ecological niches.

Powered Flight: The ability for powered flight is a major evolutionary innovation in birds.

Respiratory System: Birds have a unique respiratory system that is highly efficient and adapted for flight.

In terms of phylogeny, birds are the only living descendants of dinosaurs. They evolved from a group called the theropod dinosaurs that included bipedal carnivores such as Tyrannosaurus rex and Velociraptor. Birds are deeply nested within the theropod phylogeny. The earliest bird known is Archaeopteryx, which had features of both birds and reptiles. Modern phylogenies place birds in the dinosaur clade Theropoda. According to the current consensus, Aves and a sister group, the order Crocodilia, together are the sole living members of an unranked reptile clade, the Archosauria. Four distinct lineages of bird survived the Cretaceous–Paleogene extinction event 66 million years ago, giving rise to ostriches and relatives (Palaeognathae), waterfowl (Anseriformes), ground-living fowl (Galliformes), and “modern birds” (Neoaves).

Skeletal features, particularly skulls

Amphibians

Salamander skeleton

  • Short neck (1 vertebra)

  • Short ribs along entire trunk

  • Little modification for attachment of pelvis to vertebral column

Frog skeleton

  • Adult frog skeleton modified from the amphibian plan-

    • Much reduced trunk

    • No tail

    • Modified pelvis and hindlimb

Reptiles

The jaws of reptiles are equipped with various adaptations, such as the movable quadrate bone in snakes and the kinetic skull of lizards.

Some reptiles, like turtles, have a unique bony shell that encases both the skull and the rest of the body.

Order Crocodylia- Crocodilians

  • Primitive trait:

    • no cranial kinesis (or is this secondary?)

  • Derived trait:

  • skull openings for muscle attachment

  • teeth in deep bony sockets

  • Discreet neck (as in all reptiles)

  • Ribs only on the thorax

  • Vertebral column not modified for pelvis

Order Testudines- Turtles

  • Primitive traits:

    • no skull openings for jaw muscle attachment

    • no cranial kinesis

  • Derived trait:

    • teeth lost

Tuatara, lizards, and snakes

  • Derived trait in tuatara

    • skull openings for jaw muscles

  • Derived trait in squamates

    • kinetic quadrate

  • Additional derived trait in snakes

    • kinetic upper jaw

Snakes have long neck and rib bones unlike amphibians

Definitions

  • Cranial kinesis refers to the ability of an animal’s skull to move relative to its braincase or other skull components.

    • Unlike humans, whose skulls are relatively rigid, animals with cranial kinesis exhibit flexibility and mobility in their skull structures.

Birds

Modern bird skeleton shows reptilian features and unique avian features -The avian features are modifications for flight.

  • No teeth - saves weight

  • Dinosaur skull

  • Modified hand and wrist

  • Giant sternum for attachment of flight muscles

  • Reduced tail- saves weight

  • Dinosaur pelvis

  • Bird bones are also hollow to save weight

Mammals

The path from reptiles to mammals- about 250 mybp.

This animal is in Therapsida, a clade that includes mammals.

  • Reptilian vertebral column and ribs

  • Mammalian limb orientation- under the trunk

  • Mammalian and reptilian skull characteristics

Mammalian skull characteristics:

  • Zygomatic arch

  • Coronoid process of dentary

  • Heterodont dentition

Reptilian skull characteristic:

  • Jaw articulation at the rear of the jaw on the articular

Evolution of the mammalian jaw

  • Appearance of heterodont teeth, some with multiple roots

  • Loss of jaw bones (articular moves to the middle ear, only dentary remains)

  • Enlargement of coronoid process

Names of the important families (amphibians, reptiles, rodents) and orders (mammals, birds) in Louisiana

Amphibians

Order: Caudata (salamanders)

Families:

  • Ambystomatidae (mole salamanders; mostly subterranian)

  • Amphiumidae (amphiumas; aquatic, large)

  • Plethodontidae (lungless salamanders; nasolabial groove)

  • Proteidae (mudpuppies & waterdogs; aquatic)

  • Salamandridae (newts)

  • Sirenidae (sirens)

Order: Anura (frogs & toads)

Families:

  • Bufonidae (toads)

  • Hylidae (treefrogs & allies)

  • Eleutherodactylidae (tropical frogs; no tadpole stage)

  • Microhylidae (narrow-mouthed toads & allies)

  • Ranidae (true frogs)

  • Scaphiopodidae (spadefoots)

Reptiles

Order: Crocodylia (crocodiles and alligators)

Family: Alligatoridae (alligators & caimans; short, wide heads)

Order: Testudines (turtles)

Families:

  • Cheloniidae (sea turtles)

  • Chelyridae (snapping turtles)

  • Dermochelyidae (leatherback)

  • Kinosternidae (musk and mud turtles)

  • Emydidae (box and water turtles)

  • Testudididae (tortoises)

  • Trionychidae (softshells)

Order: Squamata (lizards & snakes)

Families:

  • Anguidae (glass lizards)

  • Dactyloidae (anoles)

  • Gekkonidae (geckos)

  • Phrynosomatidae (horned lizards, Prarie Lizard and allies)

  • Scincidae (skinks)

  • Sphenomorphidae (forest skinks)

  • Teiidae (whiptails)

  • Colubridae (colubrid snakes)

  • Dipsadidae (rear-fanged snakes)

  • Elapidae (coral snakes & many other venomous allies)

  • Natricidae (harmless live-bearing snakes)

  • Typhlopidae (blind snakes)

  • Viperidae (vipers)

Birds

Orders:

  • Anseriformes (Waterfowl)

  • Galliformes (Game birds)

  • Gaviiformes (Loons)

  • Podicipediformes (Grebes)

  • Procellariformes (Seabirds)

  • Ciconiiformes (Wood Stork)

  • Suliformes (Cormorants, boobies, anhinga)

  • Pelecaniformes (Pelicans, herons, ibis)

  • Accipitriformes (Vultures, hawks, Osprey)

  • Gruiformes (Cranes & rails)

  • Charadriiformes (Shorebirds & gulls)

  • Columbiformes (Doves & pigeons)

  • Cuculiformes (Cuckoos, roadrunner, ani)

  • Strigiformes (Owls)

  • Caprimulgiformes (Poor-wills & nightjars)

  • Apodiformes (Swifts & hummingbirds)

  • Coraciformes (Kingfishers)

  • Piciformes (Woodpeckers)

  • Psittaciformes (Parrots)

  • Falconiformes (Falcons and caracara)

  • Passeriformes (Perching birds)

Mammals

Orders:

  • Didelphimorphia (opossums)

  • Cingulata (armadillos)

  • Sirenia (manatees, dugongs)

  • Artiodactyla (even-toad ungulates, whales)

  • Chiroptera (bats)

  • Eulipotyphla (shrews and moles)

  • Carnivora (carnivores)

    • Canidae (dogs)

    • Felidae (cats)

    • Mephitidae (skunks)

    • Mustelidae (weasels, otters)

    • Procyonidae (raccoons, coatis)

    • Ursidae (bears)

  • Rodentia (rodents)

    • Castoridae (beaver)

    • Geomyidae (pocket gophers)

    • Heteromyidae (pocket mice)

    • Cricetidae (New World rats and mice)

    • Muridae (Old World rodents)

    • Echimyidae (nutria and spiny rats)

    • Sciuridae (squirrels, chipmunks)

  • Lagomorpha (rabbits, hares, pikas)

  • Primates (monkeys, apes)

Recognition of classification levels (e.g. knowing how orders and families are written)

See Correct use of taxonomy and lists

Basic biology of the different groups, depending on what was emphasized in lecture

General characteristics of amphibians

  • Glandular skin produce toxins and mucous (highly variable among species)

  • True middle ear with columella (transmits vibrations for hearing- also in reptiles and birds)

  • One neck vertebra (no neck vertebrae in fish, multiple in amniotes)

  • No dermal bone (a fish trait- fish scales are dermal bone)

  • No claws (an amniote trait)

  • Eggs cannot resist desiccation

  • Highly variable respiration- lungs, gills, skin

General characteristics of reptiles

  • Specialized neck vertebrae

  • All breathe with lungs

  • Keratinized epidermal scales and claws

  • Internal fertilization

  • Amniote egg (or live birth)

  • Strong olfaction

  • Some return to marine life (no amphibians are marine)

  • Some with temperature dependent sex determination

American Alligator - biology is typical of crocodilians

  • Endemic to SE US

  • May reach >5 m and live >50 years (!)

  • Apex predators

  • Nest on mounds in marsh vegetation

  • Winter in deep holes dug laterally into banks

  • Nest temperature determines sex (warmer -> males)

  • Females guard nests

  • Communicate vocally

Turtle Biology

  • Lay eggs on land

  • Usually no parental care

  • Unusual life history with high adult survival and very low survival before adulthood

  • Bony shell usually covered with keratinized epidermal scutes that are periodically shed (except softshells and leatherback)

  • Bony shell plates fused to ribs and vertebrae

  • Eat plant and animal material

Lizard Biology

  • External ears (lacking in snakes), but rarely communicate vocally

  • No LA lizards are aquatic

  • Most lizards (all LA lizards) lay eggs, either one at a time (anoles) or clutches of up to 50

  • Some lizards (e.g. skinks) show parental care of eggs, others (e.g. anoles) do not

  • All LA lizards eat animal prey

Snake Biology

  • Highly modified jaws and skull

  • Diverged from lizards ~100mya (?)

  • Some with vestigial pelvis

  • Live bearing or egg laying

  • Eat animals only

Bird Stuff

  • 4 chambered heart- separates blood with oxygen from blood without oxygen

  • Endothermy (warm-blooded)-

    • allows fast metabolism at any environmental temperature

  • Oviparity- lay eggs one at a time

  • No urinary bladder

  • Muscular gizzard- replaces teeth to grind food

  • Short gut

  • Large brain

  • Excellent vision

These are traits related to:

  • high mobility

  • high energy requirements

  • diurnal activity

Characteristics of mammals

  • Uniquely modified skull (jaw, ear, zygomatic arch)

  • Heterodont dentition

  • Specialized skeleton, especially feet

  • Hair (another type of keratinized epidermis)

  • Dermal muscles

  • Mammary glands (and other skin glands)

  • Endothermy

Skin glands unique to mammals

  • Mammary glands – provide nourishment for young during postnatal growth (milk stimulated by endocrine system)

  • Sweat glands – promotes evaporative cooling and eliminates waste – typically restricted in location

  • Sebaceous glands – secretions lubricate hair and skin

Hair (also called pelage)

  • Keratin-based product of epidermis

  • Critical for endothermy

  • Pelage patterns important for communication or crypsis

  • Hair oriented by dermal muscles

Endothermy- Circulatory system

  • Complete separation of systemic and pulmonary circulation (4 chambered heart, 2 chambers receive blood and 2 pump blood)

  • Many mammals can alter heart rate

    • Hibernation

    • Carnivore lethargy, alarm bradycardia (‘freezing’)

    • Bats – resting and active heart rates differ by 500 beats per minute, and change within 1 second

  • Only in endotherms, with high oxygen demand, is it critical always to separate oxygenated blood (coming from the lung) from deoxygenated blood (coming from the body’s capillary beds)

Endothermy- Fat and energy storage

  • Not unique to mammals, but important for energy storage, source of heat and water, and insulation

  • Temperate mammals typically have localized fat storage

  • Boreal and aquatic species store fat subcutaneously over the body

Endothermy- Respiratory system

  • Diaphragm – unique to mammals

  • Heart and particularly lungs are large relative to body surface- required for endothermy

  • Exchange of gases occurs via alveoli, where oxygen enters bloodstream

  • Lung surface- humans have 70 m2 of lung surface, about 40 times the surface area of the body

Biology of venomous snakes in Louisiana

Family Viperidae

  • ~250 species worldwide except Australia

  • Derived venom-injecting through elongated hollow fangs

  • Hemotoxic venom – local tissue damage

  • Loreal pits detect heat to 0.2 degrees C

  • Vertically elliptical pupils in North American viperids

  • Triangular head

Biology of the annual cycle in birds

Annual cycle - Most birds exhibit an annual reproductive cycle, which includes stages such as breeding, nestling/fledgling, molt, migration (for migratory species), and non-breeding (refractoriness).

  • breeding

  • molt

  • migration

  • molt

  • migration

Regulation of cycle

  • Photoperiod

    • Photoperiod refers to the duration of daylight or the length of time that a bird is exposed to natural light during a 24-hour period. It plays a crucial role in regulating various physiological processes in birds, particularly their reproductive cycles.

  • What about ducks?

    • Long distance migrants have relatively fixed timing of migration

    • Short distance migrants (like ducks, or robins) may show variation within the migration period due to local conditions- but they still respond to photoperiod

Timing of breeding

  • latitudinal variation

  • variation among species

  • Timing of breeding is an evolved response to match food availability to energy needs of reproduction

  • Breeding duration is more narrow at higher latitudes and higher elevations

  • Variation among species is greatest in the tropics, least at high latitudes

Migration - predictable seasonal movements (most migrants)

Nomadism - unpredictable aseasonal movements (rare in temperate zone)

Facultative migration - a combination (American Robins, ducks)

Evolution of migration

  • Migration route reflects evolutionary history of the species

  • Migration can evolve rapidly or disappear

  • Timing is changing with global climate change

  • The sexes within a species often differ in winter distribution or timing of migration

Physiology

  • Hyperphagy - migratory fattening - innate

    • varies with distance to travel and barriers to cross

    • stopover sites can be critically important

  • Zugunruhe - nocturnal restlessness - innate

    • varies with distance to travel

  • Speeds- 25-50 km/hour, plus tailwinds

  • Range- up to 9 days straight (usually >12 h for Gulf crossing)

Daily timing of migration

  • Hawks, swallows, swifts - by day

  • Cuckoos, hummingbirds, most songbirds - by night

  • Shorebirds and waterfowl - day or night

Why these differences?

  • Different bird species occupy distinct ecological niches and habitats. Their feeding preferences, nesting requirements, and foraging strategies vary significantly.

  • Food availability

  • Photoperiod and Circadian Rhythms

  • Evolutionary History and Genetics

Navigation - How do they know where they’re going?

  • homing vs migration

    • Homing is the ability of certain animals to return to a specific place when displaced from it, often over great distances. This behavior can occur in any compass direction and at any season. Homing is usually associated with shorter distances and shorter periods of time, often daily, and typically involves a return to a home base after a journey in search of food or mates.

    • Migration, is the regular, repeated mass movement of animals for breeding or avoidance of climatic extremes. It usually involves longer distances and longer periods of time.

  • Visual landmarks - important for local movements

  • Celestial navigation - sun, stars

    • Sun compass - use position of the sun for direction (requires an internal clock)

    • Geomagnetism (magnetic fields)

  • Olfaction - mostly used for local movements

  • learning

Birds have well defined annual cycles

All birds:

  • Breeding

    • territory establishment (singing)

    • courtship

    • nest construction

    • egg laying and incubation

    • care of nestlings and fledglings

  • Molt

Migratory birds:

  • Migration to wintering grounds

  • Molt (usually just body feathers)

  • Migration to breeding grounds

Describing dentition in mammals (dental formula)

Dentition and dental formulas

I = incisor

C = canine

P = premolar

M = molar

(U = upper, L = lower)

The numbers are read as how many of either incisors, canines, premolars, or molars. It is read in that order as well.

For example,

U 5 1 3 4 26 ← This is the upper row. It is saying that there are 5 incisors, 1 canine, 3 premolars and 4 molars on each side of the mouth, so there is 26 in maxillary.

L 4 1 3 4 24 ← This is the lower row. It is saying that there are 4 incisors, 1 canine, 3 premolars, and 4 molars, and there is 24 in the mandibular totaling 50 in all Didelphis (opossums)

(Fun fact! The term, "maxillary", is given to teeth in the upper jaw and "mandibular" to those in the lower jaw.)

Inferring diet and taxonomy from dentition in mammals

In Canidae, the carnassial tooth in canids is a premolar on the maxillary and a molar on the mandible.

Ungulates are highly specialized for plant diet:

  • Often lose upper incisors

  • Usually lose canines

  • Long, flat molars and premolars with irregular surfaces

Armadillo skull- bizarre (As are all Xenarthra skulls- anteaters, sloths)

Armadillo have peg-like teeth. These peg-like, single-rooted teeth are often not classified as incisors etc:

U 0 0 { 8 } 16

L 0 0 { 8 } 16 = 32 Dasypus

Hispid Cotton Rat skull- typical rodent

Highly derived- loss of lots of teeth

  • Elongated incisors

  • No canines or premolars

  • Few broad molars

U 1 0 0 3

L 1 0 0 3

Key aspects of the Earth’s history relevant to modern patterns of diversity

Moderately important topics:

LA vs worldwide diversity, particularly amphibians, reptiles, and mammals

Bird orders in bold

Broad geographic patterns of breeding periods in birds

Evolution and extreme examples of migration in birds

Mammal legs and feet

Diversity of reproductive physiology in mammals

Less important topics:

Turtle families

Biology of individual species from the mammals lecture (except to illustrate general traits)

Characters useful for id but not evolutionarily meaningful (e.g. illustrations of scale patterns)

Family or order names and details for taxa with few LA species unless they were emphasized (e.g. Crocodylia is important, Sirenidae is not)

Mechanics of flight

ID of birds based on feet or bills

Navigation cues