MBIO162 Vertebrate Diversity

11 February 2025: Chordates I

• Phylum Chordata

  • Main clades: 

    • Cephalochordata

    • Urochordata

    • Vertebrata

• Chordate body plan

  • Four defining features of the Chordata

    • Notochord (seen in common ancestor)

    • Dorsal, hollow nerve cord

    • Muscular, post-anal tail

    • Pharygenal slits or clefts

• Evolution of vertebrates

  • Earliest chordates

    • Cephalochordata (Lancelets)

      • 28 species in shallow seas.

      • Filter feed using a mucus net

      • Show the four defining features of chordates very clearly, both as larvae and adults.

    • Urochordata (Tunicates)

      • Marine filter feeders

      • 410 species

      • Planktonic larva is clearly a chordate

      • Adults are sessile and benthic

  • 2R hypothesis

    • Where cephalochordates and tunicates have a single gene, vertebrates often have two to four equivalent genes

    • Result of two whole-genome duplication events between 540 and 485 mya

    • May explain the diversity of vertebrates

      • Gene duplication is one of the most important evolutionary forces.

        • Genome duplication is the process by which additional copies of the entire genome are generated, due to nondisjunction during meiosis

          • The resulting cells and organisms are polyploid – they contain more than two homologous sets of chromosomes.

  • Vertebrata (Vertebrates)

    • About 64,240 species

    • Recent discoveries of early vertebrates from lower Cambrian (530 mya)

    • Similar to cephalochordates, but with:

      • Large brain

      • Skull

      • Eyes

      • “Teeth”

  • Timeline

    • Silurian (440 mya)

      • Radiation of agnathans

        • First jawed fish

    • Ordovician (500 mya)

      • First agnathans (jawless fish)

    • Cambrian (550 mya)

      • All major phyla present

      • First vertebrates

• Jawless vertebrates

  • Myxini (Hagfish)

    • 92 species, all marine scavengers.

    • Agnathans

      • “Without jaws”

    • Feed by knotting and using teeth-like processes on tongue

    • Cartilaginous skeleton

    • Well developed notochord

    • Probably Cambrian origin

    • Slime!

  • Petromyzontida (Lampreys)

    • 48 species, marine and freshwater

    • Agnathans 

      • “Without jaws”

    • Larvae filter feeders, adults parasitic or do not feed

    • Notochord and simple vertebral column

• Evolution of jaws

  • Jaws allow efficient feeding and a wider range of food items

  • Jaws well represented in early Silurian

  • Probably evolved in Ordovician (500-440 mya)

  • 4 clades:

    • Chondrichthyes

    • Placoderms†

    • Acanthodians†

    • Osteichthyes

• Sharks

  • Chondrichthyes (sharks, rays, etc)

    • 1,280 species (Elasmobranchii)

      • Sharks, skates, rays

    • 56 species (Holocephali)

      • Chimeras (aka spook fish)

    • Almost exclusively marine

      • Some (ex. Bull shark and Amazonian stingrays) can live in freshwater

    • Cartilaginous skeleton reinforced with small bone plates

    • Well-developed jaws and paired fins

    • Well-developed sense of smell and lateral line system

    • No swim bladder

    • All carnivores*

    • All have internal fertilisation

      • Males have modified pelvic fins to transfer sperm to female

    • Development ranges from ovipary (ex. dogfish) to vivipary (ex. bronze whaler shark)

    • Few offspring

• Bony fish

  • Actinopterygii (Fin fish)

    • 41 species (Chondrostei)

      • Sturgeon, paddlefish, birchir

    • 8 species (Holostei)

      • Gars and bowfin

    • 34,196 species (Teleostei)

      • Ray-finned fish

    • Global distribution and very abundant in all aquatic systems

    • Ossified endoskeleton (i.e. bones)

    • Skin covered in scales and mucus.

    • Swim bladder

    • Teleosts

    • Fins supported by rays

    • Jaw modifications

    • Most have external fertilisation and pelagic larvae hatch from the eggs.

      • Therefore, produce huge numbers of eggs

    • Some species do show parental care

    • A few are ovoviviparous (ex. guppy) or viviparous (ex. Surf perch)

  • Actinistia (Coelacanths)

    • 2 living species

      • Latimeria menadoensis 

        • West Indian Ocean

      • Latimeria chalumnae

        • Indonesia

    • “Discovered” in 1938 after an 80-million-year absence

    • Fleshy fins

    • Hinged skull

    • Ovoviviparous

  • Dipnoi (Lungfish)

    • 6 species, southern hemisphere

    • Live in swamps and shallow pools

    • Gulp air into lungs

    • Evolved in lower Devonian

    • Closest living relatives to the tetrapods*

      • Osteichthyes

        • Characterized by jaws and mineralized skeletons

13 February 2025: Chordates II

• Evolution of tetrapods

  • First amphibians (e.g. Acanthostega) date from the late Devonian (375 mya)

    • Common by Carboniferous

  • Limbs evolved from the fins of lobe-finned fish

    • ​​Lungfish are the closest living relatives of the tetrapods

  • Timeline

    • Tertiary (65 mya)

      • Radiation of mammals and birds

    • Cretaceous (135 mya)

      • Dinosaurs dominant 

    • Jurassic (192 mya)

      • Dinosaurs abundant, first birds

    • Triassic (230 mya)

      • First dinosaurs and mammals

    • Permian (290 mya)

      • Reptiles radiate, amphibians decline

    • Carboniferous (350 mya)

      • Amphibians dominant, first reptiles

    • Devionian (410 mya)

      • Diverse fish, first amphibians 

• Amphibia

  • Worldwide distribution, but most diverse in the humid tropics

    • 830 species (Urodela)

      • Newts and salamanders

    • 7,772 species (Anura)

      • Frogs and toads

    • 225 species (Apoda)

      • Caecillians

  • Characteristics of amphibians

    • Thin skin with limited keratinisation

    • Skin permeable to oxygen and water

    • Most restricted to damp environments

    • Fertilization generally external

    • Eggs have no shell

      • Prone to desiccation and need physical support

    • Larvae fish-like with gills and lateral line system

      • Lack legs or lungs

      • Usually aquatic herbivores

    • Adults usually terrestrial carnivores with lungs and four legs

    • Amphi bios – “double life”

• Amniotes

  • The amniotic egg

    • Four specialised membranes 

      • Protect from desiccation, allow gas exchange, store food and waste

    • Allows amniotes to be truly terrestrial

    • Evolved in the Carboniferous

  • Origins of amniotes

    • Hylonomus is the oldest known amniote 

      • Carboniferous period, 312 mya

    • Westlothiana (338 mya) and Casineria (340 mya) may be amniotes

    • Two main clades: reptilia and mammalia

  • Reptiles

    • Testudines (Turtles)

      • 366 species in 14 families

        • Terrestrial, freshwater and marine

      • Shells and skeleton unique to clade.

      • Show many ancient reptilian characters:

        • Skull morphology

        • Scales (β-keratin)

        • Internal fertilisation but lay eggs

        • Ectothermic

      • The origin of the turtle body plan is one of most intriguing mysteries in evolutionary morphology, but we are starting to piece it together

    • Crocodilia (Crocodilles and alligators)

      • 27 species in 3 families

        • All semi-aquatic predators; most tropical

      • Have changed little since the Triassic

      • Secondary palate

      • Heart with septum, like bird

    • Aves (Birds)

      • Origin of birds

        • Archaeopteryx – the first bird

          • Jurassic Period

            • 150 mya

        • Mixture of reptilian and avian characters

      • 11,276 species in 254 families (Gill et al. 2024)

      • Barrowclough et al. (2016) used molecular and morphological data and estimated that there were over 18,000!

        • Very controversial

      • Global distribution in most habitats

      • Characteristics of birds

        • Feathers (β-keratin)

        • Large, keeled sternum

        • Fore-limbs modified for flight

        • Hind-limbs for bipedal walking

        • Internal fertilisation and hard-shelled amniotic eggs

        • Endothermic

    • Sphenodontia (Tuatara)

      • One species of lizard-like, carnivorous reptile found on islands off the coast of New Zealand

      • Once a diverse group, but most went extinct 65 mya

      • Skull differs from that of lizards

      • Retains ancestral features

    • Squamata (Snakes and lizards)

      • 11,869 species in 68 families.

        • Mainly tropical, terrestrial carnivores

      • Lizards retained ancestral body plan and characters.

      • Snakes highly specialised

        • Limbless

        • Elongate

        • Modified jaws and skull.

  • Mammalia (Mammals)

    • Origins of mammals

      • Hadrocodium wui

      • Early Jurassic (195 mya) 

        • Mammal with a relatively large brain and a malleus and incus in the inner ear as in modern mammals

    • 6,615 species in 167 families

    • Taxonomy being revised constantly

    • Worldwide distribution in almost all ecosystems

    • Characteristics of mammals

      • Hair (α-keratin)

      • Specialised teeth (heterodont)

      • Articulation of jaw between dentary and squamosal bones

      • Endothermic

      • Internal fertilisation

      • Amniotic eggs

      • Mammary gland

        • Live birth (most of the time)

14 February 2025: Birds are dinosaurs 

• Linnean classification

  • Linnaeus (1758) introduced hierarchical structure and binomial nomenclature

    • Linnaean system underlies all non-phylogenetic systems of taxonomy

      • Kingdom, Phylum, Class, Order, Family, Genus, Species

        • Ex. Calypte anna (hummingbird)

          • Kingdom: Anamalia

          • Phylum: Chordata

          • Class: Aves

          • Order: Apodiformes

          • Family: Trochilidae

          • Genus: Calypte

          • Species: Calypte anna

      • Until recently, evolutionary theory had little impact on systems of classification

• Characteristics of birds

  • Feathers (β -keratin)

  • Large, keeled sternum

  • Fore-limbs modified for flight

  • Hind-limbs for bipedal walking

  • Internal fertilisation

  • Hard-shelled amniotic eggs

  • Endothermic

• Fossil birds

  • Fossil record of birds is not extensive.

    • Although recent finds in China are changing this

  • Continual debate over the classification and date of fossils

  • Oldest known bird is Archaeopteryx

    • Without its feathers, Archaeopteryx looks exactly like a small coelurosaur

    • Jurassic, 150 mya

    • Transitional fossil, with a mixture of reptilian and avian characters

      • Transitional fossils = any fossilized remains of a life form that exhibits traits common to both an ancestral group and its derived descendant group

    • Found in 1861, two years after “On the Origin of Species” was published

    • Not considered to be the ancestor of all living birds

• Phylogenetic classification

  • Phylogeny

    • The evolutionary history of an organism or group of organisms.

  • Cladistics 

    • Method of classification using hypothesised evolutionary relationships among organisms

      • Assumes is that members of a taxonomic group (clade) share unique features (synapomorphies) which were not present in distant ancestors.

      • Members of a clade are more closely related to members of the same clade than to other organisms.

    • Provides explicit and testable hypotheses of organismal relationships

  • Cladograms

    • Testable evolutionary hypotheses

    •  Number of trees increases factorially with the number of species.

      •  Three species = 3 trees

      •  22 species =

        • Need a computer

    • The “best” tree requires the fewest evolutionary changes – parsimony

    • B is best supported by the data

    • Hypothesised to reflect the true branching pattern.

      • Can’t be proven to be correct

    • Pierolapithecus catalaunicus

      • 13 MYBP

      • The ancestor of all great apes?

• Birds and theropod dinosaurs

  • Molecular evidence shows that Tyrannosaurus rex is a close relative of the birds

    • Collagen from T. rex bones is more similar to bird collagen than to collagen from other animals 

      • But what are Dromaeosaurs?

  • Key similarities:

    • Elongate, mobile S-shaped neck

    • Tridactyl foot with digitgrade posture

    • Intertarsal ankle joint

    • Hollow, pneumatised bones

  • Key differences:

    • Feathers

    • Endothermy

  • Examples:

    • Microraptor gui

      • A four-winged dinosaur from China

      • 124-128 mya

    • Probably a Tyranossaurid or Composgnathid

      • 99 mya

• Dinosaurs with feathers

  • Types of feathers in modern birds (that were all shared with tsister taxon the Dromaeosaurs

    • Wing

    • Down

    • Tail

    • Contour

    • Semiplume

    • Bristle

    • Filoplume

  • Feathered pterosaurs

    • Yang et al. (2019) suggest that pterosaurs also had feathers

    • Feathers may have evolved 70 million years earlier than previously thought, in the early Triassic (250 mya)

      • Kongonaphon, a small archosaur from the Middle Triassic, may have been fuzzy

        • Hu et al. (2018) described a Jurassic dinosaur (Caihong juji) with iridescent feathers

  • Colored eggs

    • Birds are the only living amniotes with coloured eggs.

      • But egg colour pigments have a single evolutionary origin in nonavian theropod dinosaurs.

  • Behaviour

    • Jaculinykus yaruui, a dinosaur that lived 72 MYA, slept like a bird

  • Calls in non avian dinosaurs

    • Pinacosaurus granger, an ankylosaur, had a larynx very similar to that of a bird

  • What really defines the birds?

• Why did birds survive the K-T extinction?

  • Cretaceous–Paleogene (K–Pg) extinction event (also known as the Cretaceous–Tertiary (K–T) extinction)

    • A sudden mass extinction of three-quarters of the plant and animal species on Earth, approximately 66 million years ago

  • The cerebral hemispheres - where higher cognitive functions such as speech, thought and emotion occur in humans - are much bigger in living birds than in Ichthyornis (early birds)

    • That pattern suggests that these functions could be connected to surviving the mass extinction

17 February 2025: Amphibian life-history strategies

• Body size is not a fixed attribute of a clade

  • Non-avian dinosaurs went extinct 66 mya

  • Brontotheres (ancient mammals related to horses, rhinos and tapirs) radiated to fill the niches left by herbivorous dinosaurs

  • Mass increased 1,000 times in just 16 million years

    • Largest species about 5,000 kg

      • Twice the size of a white rhino

• What are life-history strategies?

  • Life-history strategies are patterns of resource acquisition and allocation exhibited by organisms during their lives

  • Life-history strategies have evolved through natural selection to maximise individual fitness

  • Components of life-history

    • Growth

    • Development

    • Maintenance

    • Survival

    • Reproduction

      • Mode of reproduction

        • Asexual and sexual reproduction

        • Separate sexes, simultaneous hermaphrodites and sequential hermaphrodites

        • Reproductive maturation time

        • Semelparous and iteroparous

          • Semelparous

            • Sockeye Salmon reproduce once and then die

          • Iteroparous

            • Atlantic Salmon reproduce many times

        • Number of offspring

          • Offspring size versus number

            • In any one breeding attempt, there is a trade-off between quality and quantity

              • Ocean sunfish produce millions of tiny eggs.

              • Lemon sharks give birth to a few live young

    • Factors that influence fitness

  • Allocation and trade-off

    • Allocation

      • Resources (energy, nutrients, time) must be allocated to growth, maintenance and reproduction

    • So why not maximise everything?

    • Trade-off 

      • Energy is limited, so energy allocated to one function                                                      is not available for another

• Amphibian life-history

  • Most lay eggs which are externally fertilised in water and then hatch into aquatic larvae; these metamorphose into terrestrial adults

    • But, amphibians display a remarkable diversity of modes of reproduction and parental care

• Reproductive strategies of:

  • Caecilians

    • All caecilians have internal fertilisation

      • Males have an intromittent organ, the phallodeum, which is inserted into the female’s cloaca

    • Some species lay eggs which the female may protect until they hatch

    • About 75% of species are viviparous

      • At birth caecillians are 30-60% of their mother’s body length

      • Initial growth supported by yolk

      • Embryos feed by scraping the oviduct walls with specialised embryonic teeth

        • The epithelium of the oviduct produces a creamy substance

      • Large energetic investment from female

    • Diversity of species

      • Rhinatrematidae

        • Terrestrial with aquatic larvae (13 species)

      • Ichthyophidae

        • Terrestrial with aquatic larvae (57 species)

      • Chikilidae

        • Terrestrial, lay eggs but have no larval stage (4 species)

      • Scolecomorphidae

        • Terrestrial and  viviparous (6 species)

      • Caeciliidae

        • Terrestrial & aquatic with oviparous and viviparous species (44 species)

  • Urodeles (Salamanders)

    • Most have internal fertilisation

      • Salamanders do not have an intromittent organ

    • Male lays spermatophores and has to entice the female, during a mating dance, to collect them directly into her cloaca

    • 10% retain external fertilisation

    • Courtship patterns important for species recognition

      • Salamanders show elaborate secondary sexual characters and species-specific pheromones

    • Kleptogenesis in Ambystoma (mole salamanders)

      • Klepton

        • A species that requires input from another biological taxon (normally from a species which is closely related to the kleptonic species) to complete their reproductive cycle

      • Hybrid all-female populations

      • No males for 5 million years!

      • Females use sperm from a related species to fertilize their eggs

      • Sperm genome usually discarded, and eggs develop asexually

      • Occasionally incorporate the sperm’s DNA, resulting in hybrid offspring

        • Genome from up to five species

    • Most lay eggs in water

      • Gilled aquatic larvae transform into terrestrial adults

    • Some species, like Salamandra salamandra, are ovoviviparous; giving birth to small larvae that fed on their own egg yolk

    • Salamandra atra shows aplacental viviparity, giving birth to two live young (one from each uterus)

      • Nourished first by egg yolk, then by the other eggs in the uterus, and finally by uterine secretions absorbed though their gills

  • Anurans (Frogs)

    • Fertilisation is usually external.

    • Internal fertilisation in a few species

      • May be widespread in species which mate on land

    • Only 6 species of frogs are viviparous and have internal fertilisation

    • 20% have no tadpole stage

    • Parental care

      • Large yolky eggs to nourish larvae.

      • 1 to 20,000 eggs laid

      • Many arboreal frogs lay their eggs on leaves or in foam nests.

        • Adults may guard eggs

      • Dart poison frogs

        • Adults guard the eggs and transport the tadpoles

        • Females provide food for the tadpoles by laying unfertilised eggs

      • Pygmy marsupial frog

        • Female broods eggs under skin on back

        • Tadpoles deposited in water

18 February 2025: Vertebrate flight

• Physics of flight

  • Four forces

    • Drag

    • Lift

    • Thrust

    • Weight

  • Lift and weight

    • Air flowing around the wing creates low pressure on the upper surface

    • This "sucks" the wing upwards, generating lift

  • Drag and thrust

    • Drag

      • Force exerted on an object moving through a fluid; always oriented in the direction of relative fluid flow

        • Drag is minimised by streamlining

    • Thrust 

      • Force induced in the direction of flight, opposing the drag force

        • Thrust is produced by wing flapping, hence the need for large flight muscles

• Evolution of flight

  • Flight has evolved only four times:

    • Insects, pterosaurs, birds and bats

  • Convergent evolution

    • The evolution of the same functional trait in unrelated lineages

    • Wings of insects, pterosaurs, birds and bats are analogous structures

  • Macroevolution

    • Once powered flight is attained, flying lineages radiate quickly

  • How did flight evolve?

    • Ground up scenario: 

      • Given a bipedal cursorial (running) ancestor of a flying lineage, flight must have proceeded from the ground into the air

    • Trees down scenario: 

      • Given an arboreal ancestor of a flying lineage, flight must have proceeded from the trees into the air.

  • Why did flight evolve?

    • Escape from predators

    • Catching flying prey

    • Movement from place to place

    • Access to new niches

    • Hind legs used as weapons

    • The high diversity of insects, bats and birds suggests that flight is highly advantageous

• Pterosaurs, birds and bats

  • Pterosauria 

    • Derived from bipedal, terrestrial archosaur 

      • “Ground up” scenario

    • Late Triassic to end of Cretaceous (200-65 mya)

    • Wing supported by elongated 4th digit

    • Keeled sternum

    • Pteroid bone

    • Endothermic?

    • Pteranodon longiceps

      • 6 m wingspan, but only 12 kg

      • Comparatively small body

      • Wing bones thick but hollow

      • Flew by soaring

      • Large brains and optic nerves

      • Large crested head

      • Beak used for scooping up fish

      • Modern analogue – pelican

  • Aves (birds)

    • Derived from bipedal, terrestrial coelosaurs 

      • “Ground-up” scenario

    • Similarities with pterosaurs: 

      • Hollow bones; keeled sternum; stout humerus

    • Differences:

      • Bird wing supported by radius, ulna, and modified wrist bones.

    • Feathers

      • Modified scales

      • Flight feathers – stiff, light and interlinked by barbules to form an efficient aerofoil

      • Streamlining

      • Renewable

      • Allow for a lot of variation in wing morphology 

    • Avian skeleton

      • ​​Keeled sternum

      • Pneumatised bones

      • Uncinate processes on ribs

      • Bones of the pelvis fused

      • Limbs moved by muscles near the center of the body

      • Beak and gizzard

      • Tail vertebrae reduced

  • Chiroptera (bats)

    • Bat fossils are uncommon

      • Oldest are from the Eocene (55 mya)

    • Bats are related to the Dermoptera (flying lemurs) and have close affinity with the primates

      • “Trees down” scenario

    • Membranous wing supported by the arm and digits 2-5

    • Keeled sternum; fused clavicles, scapula and sternum

    • New bone, the calcar, supports the uropatagium from the heel

    • Bat wings have high camber (to generate lift) and low wing loading (mass/area) giving a low stall speed and high manoeuvrability.

      • As in birds, limbs moved by muscles near centre of body

    • Most species only 5-10 g

• Disadvantages of flight

  • Energetically very costly

    • Constrains body size and morphology

  • Flight lost in Struthiformes (ostrich, emu, etc), penguins, and many oceanic island species (ex. rails)

• Convergent evolution

  • Pterosaurs, birds and bats are only distantly related but have independently evolved flight

  • Convergence

    • Aerofoil

    • Light body weight

    • Keeled sternum

    • Reduction and fusion of bones

  • Ambopteryx

    • A dinosaur with bat wings

      • Great example of convergent evolution and homology

• Homology

  • The wings of bats are homologous to your arms

  • The pentadactyl limb structure is inherited from the common ancestor of all tetrapods, but it has evolved different functional morphologies

  • Homology versus analogy

    • Homology is the existence of shared ancestry between a pair of structures in different taxa.

      • A common example is the forelimbs of vertebrates, where the wings of bats, the arms of primates, the front flippers of whales and the forelegs of dogs and horses are all derived from the same ancestral tetrapod limb

    • Analogous organs do similar jobs in two taxa, that were not present in their last common ancestor but rather evolved separately

      • For example, the wings of insects and birds evolved independently in widely separated groups, and converged functionally to support powered flight, so they are analogous

    • A structure can be homologous at one level and analogous at another

      • Pterosaur, bird and bat wings are analogous as wings (having evolved in different ways in the three groups), but homologous as forelimbs (as they are all derived from the same ancestral tetrapod limb)