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?
MYA | Feature(s) | Clade |
250 | Increased BMR, filamentous feathers, skeletal pneumatisation | Avemetatarsalia – Dinosaurs and pterosaurs |
247 | Bipedal locomotion | Dinosauria (terrible lizard) |
231 | Furcula (wish bone), cervical air sacs, radially branched feathers | Theropoda (beast feet) |
190 | Three-fingered hand, modified carpal bone in wrist | Maniraptora (hand / seizing, robber) |
184 | Symmetrical flight feathers, arm flapping capability, elongation of hand bones, reduction of tail vertebrae | Pennaraptora (feather, robber) |
170 | Powered flight, arm elongation, partial fusion of pelvic bones | Aviales (extinct and modern birds) |
95 | Pygostyle, horny beak, high BMR, short-development time | Aves (modern 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)