BIOL112 (animal bio)

Sem 2 2025

What is a species-scape?

Diagram of groups of organisms ranked in size according to their biodiversity. Larger = more biodiverse.

How are animals classified (taxonomy)?

Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species.

(Do Keep Ponds Clean Or Frogs Get Sick)

What is bionominal nomenclature?

Genus and species name that’s unique to every species (hierarchal classification), e.g. Panthera pardus (leopard)

2 benefits of using binomial nomenclature to classify organisms

Unique names get around ambiguous terms (e.g. fish could be used to describe cod or silverfish, an insect), and help with language barriers.

Outline phylogenies

Evolutionary relationships among organisms (can use phylogenetic trees). Determined using DNA.

What is a described species?

Species that is formally identified, usually through a scientific paper (describing it and why different). Unique binomial name.

What is an undescribed species?

Informally identified or yet to be discovered.

Example of undescribed species

Hoplodactylus maculatus, aka Woodworthia maculata. Different species within this classification, given nicknames as not formally identified.

Outline the Catalogue of Life

Central archive of describe species, created in 2001. Numbers can increase of reduce depending on new discoveries or DNA testing to discover “separate” species are actually the same.

How many species are there?

Impossible to answer right now, maybe as many as 2 billion.

Orange piegraph = prediction of every single species.

What type of animal is the most dominant?

Insects (all of which are arthropoda)

Is there more phyla in the sea or on the land?

More in the sea, but more known species on land due to easier access.

What phyla has been most described?

Anthropoda

Outline the global distribution of species

Most species found around the equator/in the tropics (latitudinal species gradients).

List 5 hypotheses for latitudinal species gradients

Geographic area hypothesis, species energy hypothesis, climate stability hypothesis, historical glaciation hypothesis, evolutionary rates hypothesis

Outline the geographic area hypothesis of latitudinal species gradients

Hypothesis that there are more species in the tropics due to there being more area - can discount this as there appears to be more area closer to the North pole.

Outline the climate stability hypothesis of latitudinal species gradients

More species at the tropics due to a more stable climate around the equator

Outline the species energy hypothesis of latitudinal species gradients

Area around the equator receives more light/water/etc (more primary production/photosynthesis)

Outline the historical glaciation hypothesis of latitudinal species gradients

More glaciation happens at the poles (ice ages), which can wipe out species and restart the speciation process. Slate not getting wiped clean as often at the equator.

Outline biodiversity hotspots

Most hotspots occurs around the equator. “Hottest” hotspots total less than 1.5% of the Earth’s land but contain 1/3 of all plant, amphibian, reptile, and mammal species.

Give the textbook definition for an animal

Animals are multicellular, heterotrophic eukaryotes with tissues that develop from embryonic layers.

(note: some animals don’t have embryonic layers)

What do most (but not all) animals have/do?

Have nervous and muscle tissue, reproduce sexually and undergo a specific process of development.

Outline the importance of collagen

Integral protein in animal body (only produced by animals) - makes up 40% of their proteins, high in hair, nails, etc.

Outline hox genes

Homeotic genes - regulatory genes controlling body plans of all multicellular organisms.

Animal homeotic genes contain a homeobox sequence (conserved DNA sequence) - Hox genes.

Spread across diff numbers of chromosomes. Purple ones responsible for anterior body plan, orange ones for posterior.

How long is the homeobox sequence of homeotic genes (Hox genes)?

180bp

List the 9 phyla we learn about in this course

Porifera, Cnidaria, Echinodermata, Chordata, Platyhelminthes, Mollusca, Annelida, Nematoda, Arthropoda

Summarise the phylum Porifera

Sponges.

Simplest multicellular animals.

No organs or true tissues (no nervous system).

Sessile.

Body with pores.

Gelatinous matrix stiffened with minute spicules.

Asexual or sexual reproduction.

Outline the 3 main Porifera clades

Demosponges (spicules made of spongin), calcareous (spicules made of calcium carbonate), glass (spicules made of silica).

Outline the structure/cells of Porifera

No tissues, loose aggregation of cells and a water canal system.

Water sucked in through pores, choanocytes have flagellum that move the water, collar covered in mucus and captures food particles which are transported to cell body and phagocytised.

Amoebocytes are totipotent, can change cell types ot repair sponge or remodel sponge away from/towards a stimuli.

Outline choanoflagellates vs choanocytes + significance

Choanoflagellate (protist) structure is similar to choanocytes (which Porifera have) - why scientists think Porifera are most basal (earliest diverging) phylum in animal kingdom.

Some version of collar cells/choanocytes found throughout animal kingdom.

Genome of choanoflagellate more closely related to animal species than fungi or mould species (again, evidence for Porifera being most basal extant animal phylum)

2 types of symmetry

Radial and bilateral

Outline radial symmetry

Can be divided into similar halves through more than 2 planes through the longitudinal axis.

Equips animal to meet the enviro equally well from all sides.

Cnidaria + Echinodermata (as adults)

Outline bilateral symmetry

Can be divided into similar halves along a sagittal plane (one way).

Allows for cephalisation (concentration of sense organs, nervous control, etc at anterior end of body, head + brain), advantage when moving in one direction.

Platyhelminthes + Nematoda + Mollusca + Annelida + Echinodermata + Arthropoda + Chordata.

Outline building body plans

Division within cells before growth of embryo. Cleavage forms a blastula with a blastocoel, then a gastrula with a blastopore.

Outline the embryonic germ layers

Ectoderm (outer - e.g. skin epidermis, nervous/sensory systems, pituitary gland, adrenal medulla, jaws/teeth)

Mesoderm (middle - skeletal/muscular systems, circulatory/lymphatic systems, excretory/reproductive systems, skin dermis, adrenal cortex)

Endoderm (inner - lining of digestive tract + associated organs, lining of respiratory/excretory/reproductive tracts, thymus, thyroid, parathyroid glands)

Summarise the phylum Cnidaria

Jellies, hydra, anemones, etc.

Diploblastic (no mesoderm, only mesoglea).

Radial symmetry (early evolution)

Gastrovascular cavity (single opening).

Mostly 2 forms - polyp and medusa.

Carnivores (using nematocysts to capture prey).

Online the structure of Cnidaria

Diploblastic - 2 layers of cells (ectoderm and endoderm) separated by mesoglea.

Polyp forms mostly sessile, medusa highly motile.

Outline the gastrovascular cavity in Cnidaria

2-way gut, mouth and anus is the same hole. Food particles taken in, broken down by enzymes in cavity, nutrients absorbed.

Can also use cavity as a hydrostatic skeleton (can close off mouth, rudimentary muscles).

Outline how Cnidaria are carnivores

Capture prey using nematocysts rejected from cnidocytes. Triggered by stimuli, expel threads, eject venom through threads into prey.

Can penetrate human skin causing minor irritation-death.

Outline colonial Cnidarians

Lots of individuals (zooids) working together with different tasks, e.g. blue man-o-war.

Dactylozooid – fishing, Gastrozooid – feeding, Gonozooid – reproduction, Pneumatocyst – ‘sail’

List the 3 variations of body cavities/body plans (requires ecto, meso, and endoderm)

Compact, Hemocoel, Coelom

Does body plan reflect evolutionary history?

No - just a gradient of organisation (compact, hemocoel, ceolom)

Outline compact body plans + example of a phyla that has this

No body cavity. E.g. Platyhelminthes.

Outline the phylum Platyhelminthes

Flatworms.

Triploblastic, compact body plan.

True muscular system, no blood vascular system.

Bilateral symmetry, moderate cephalisation.

Organ-system organisation (most basal phyla to have this).

Body flattened dorsoventrally.

Gastrovascular cavity (mostly), polymorphic (some only diffuse, some 1-way gut).

How does having a compact body plan + being flattened dorsoventrally benefit Platyhelminthes?

Allows for diffusion for nutrient absorption and waste excretion (as no vascular system).

(this stuff like the diff classes/groups of each phylum isn’t important except for the clades of chordata) 3 major classes of Platyhelminthes

Turbellaria (free-living), cestoda (parasitic tapeworms), trematoda (flukes, mostly parasitic)

Outline hemocoel body plans + example of a phyla that has this

Fluid filled hollow (hemolymph) NOT completely lined by mesoderm. E.g. nematoda

Outline the phylum nematoda

Roundworms.

Triploblastic with bilateral symmetry.

Longitudinal muscles only.

Complete digestive tract (1-way, 2 openings)

Hemolymph circulatory system.

Tough, transparent non-living cuticle.

Sexual reproduction (some species have 3 sexes).

Found in nearly every enviro, parasitise every type of animal and plant, very abundant.

Outline coelom body plans + examples of phyla that have this

Fluid filled cavity completely surrounded by mesoderm. E.g. Annelida, Mollusca, Arthropoda, Echinodermata, Chordata.

What was the advent of the coelom a major step for?

Evolution of more complex animals

What is the coelom important for?

Cushioning and suspending internal organs, meaning they can grow independently of body wall without being restricted.

Outline the phylum Annelida

Segmented worms.

Metamerism (segmentation).

Well-developed coelom.

Closed circulatory system (true heart + blood vessels).

Chitinous satae (except leeches).

Complete digestive and nervou ssystems.

What do leeches do?

Produce anaesthetic and hirudin (so can’t feel them and stop blood from clotting), consume 10x body weight in blood.

List 2 modes of development

Protostome, deuterostome

Outline patterns of cleavage for protostomes vs deuterostomes

What does determinate vs indeterminate cells mean?

Determinate = fate of cells is set in early development (if separate into separate cells, cells fail to produce whole organism as already have a set development path).

Indeterminate = cells can adapt and divide into a range of cell types (if separate into separate cells, can product whole larvae).

Outline coelom formation for protostomes vs deuterostomes

Outline the fate of the blastopore for protostomes vs deuterostomes

Blastopore = the first opening

Mnemonic for deuterostomes

DRI Pocket Anus

Outline the phylum Mollusca

Snails, slugs, squid, etc.

Foot and visceral mass covered with mantle (foot in snails, excurrent siphon in octopus and squid, visceral mass has most organs, shell secreted from mantle).

Ciliated gill in mantle cavity.

Nerve ring around oesophagus.

Open circulatory system.

What is the radula in Mollusca?

Chainsaw-like structure of hooks by the mouth, can scrape rocks to get nutrition (most of the lesser molluscs have this).

Outline the colossal squid (phylum Mollusca)

Hook-like swivelling suckers, larger animal eye (40 cm), found at depths > 1000m, over 8 m long and more than 450 kgs.

Phylogenetic tree for Kingdom Animalia

Outline the phylum Arthropoda

Insects, crustaceans, spiders, barnacles, etc.

Coelomate (reduced coelom, only envelopes reproductive and some excretory organs, rest of body bathing in hemolymph via hemocoelom).

Protostomes.

Jointed limbs.

Segmented (head, thorax, abdomen - specialised segmented).

Hard exoskeleton.

Open circulatory system.

80% of all described animals.

90% of Arthropods are insects.

Have non-living cuticle that needs to be shed as they grow through ecdysis (Ecdysozoa).

Outline Arthropoda ecdysis

Shed non-living cuticle about 20 times in their life. Vulnerable during shedding, clear soft exoskeleton before hardens/oxidises, can’t move well as muscles can’t act against soft exoskeleton.

Shed for growth, sometimes regeneration and metamorphosis - Complete metamorphosis (adult form looks different from larvae), incomplete metamorphosis (larvae looks like smaller version of adults, molt and grow in stages).

Outline the phylum Echinodermata

Sea stars, urchins, sea cucumbers, etc.

All marine and slow moving.

(Penta)radial symmetry as adults (but are bilateria, as larvae have bilateral symmetry).

Endoskeleton.

Extensive coelom, forms water vascular system.

Tube feet.

Outline how the water vascular system in Echinodermata is used for locomotion

Water taken in via madreporite, forced around ring canal into radial canal in each limb, surrounded by ampulla with podiums coming off of these.

During locomotion, ampulla filled with water, contracts and forces it down into podium, end of podium expands and inreases surface area, attaches to substrate.

End of podium has cells that produce adhesive proteins/substances to attach to surface. De-adhesive proteins created to unstick podium.

(not important as are other clade things except for chordata clades) 5 common clades in Echinodermata

Outline the phylum Chordata

Mammals, fish, reptiles, birds, etc.

Notochord.

Dorsal hollow nerve cord.

Pharyngeal slits.

Muscular, post-anal tail.

Outline notochords in Chordata

Long flexible rod that supplies structural support. In most vertebrates, replaced with a jointed skeleton and only gelatinous disks between the vertebrae remain.

Outline the dorsal, hollow nerve cord in Chordata

Develops into the CNS - brain and spinal cord. Other phylum can have a nerve cord, but dorsal and hollowness characteristic of Chordata.

Outline the post-anal tail in Chordata

Tail that goes past the anus. Often lost during development, but when retained is used for propulsion in most species.

Outline pharyngeal slits or clefts in Chordata

Slits develop into gill slits or feeding devices in aquatic animals. In tetrapods, they develop into parts of the ear and other structures in the head.

List 2 subphylum of Chordata + groups within these

Urochordata, vertebrata (gnathostomata - tetrapoda - amphibia, reptilia, mammalia)

Outline Urochordata (subphylum of Chordata)

Aka Tunicates. The “invertebrate vertebrates”.

Behave luck a sponge, suck water in through siphon, filter water and expel it through excurrent siphon.

Larvae more obviously Chordata. Don’t have vertebrate, but have dorsal, hollow nerve cord, notochord, and post anal tail in larvae form.

Outline examples of Vertebrata (subphylum of Chordata)

Have vertebral column and a cranium.

Myxini (hagfishes): no jaw and no vertebrae (have cartilage protrusions coming off of notochord, produce proteins that absorb water and swell (slime) when scared, could use that property to stop bleeding in surgeries).

Petromyzontida (lampreys): no jaw but has vertebrae (cartilaginous rings around notochord)

Gnathostomata: vertebrae and jaws (Chondrichthyes, Actinopterygii, Amphibia, Reptilia & Mammalia).

List marine examples of Chordata - Vertebrata - Gnathostomata

Chondrichthyes (sharks, skates, rays)

Actinopterygii (ray-finned fishes)

Outline Chondrichthyes (Chordata - Vertebrata - Gnathostomata)

Sharks, skates, rays.

Cartilaginous skeleton.

5-7 gill slits.

No swim bladder (have to keep moving)

Some have a spiral valve.

Outline Actinopterygii (Chordata - Vertebrata - Gnathostomata)

Ray-finned fishes.

Largest and most diverse taxon of all vertebrates (half of Chordata phylum).

Single gill slit on each side covered by an operculum (flap of skin).

Ossified skeleton.

Swim bladder (maintain buoyancy).

List examples of Vertebrata - Gnathostomata - Tetrapoda

Amphibia, Reptilia, Reptilia (birds), Mammalia

Outline Amphibia (Vertebrata - Gnathostomata - Tetrapoda)

Salamanders, frogs, and caecilians.

Ectothermic (body temp depends on external surroundings).

Moist skin with mucous glands (can breath through skin and produce poisonous mucous for defence).

Development through larval stage.

No scales (dry out easily).

Outline Reptilia (Vertebrata - Gnathostomata - Tetrapoda)

Lizards, snakes, turtles, crocodiles, etc.

Amniotes - shelled eggs.

Ectothermic.

Dry skin with scales.

No larval stage.

Well-developed lungs.

Outline Reptilia - birds (Vertebrata - Gnathostomata - Tetrapoda)

Birds are within Reptilia class, but have own defining characteristics.

Amniotes - shelled eggs.

Endothermic.

Front limbs modified for flight (mostly).

Scales on feet.

Body covered with feathers.

Adaptations to be light - no bladder, mostly single ovary, lack teeth, honeycomb bone structure.

Outline Mammalia (Vertebrata - Gnathostomata - Terapoda)

Amniote (most don’t have shelled eggs, but have the amniotic embryonic membranes - amniotic sac).

Endothermic.

Mammary glands.

Body covered with hair (dense or fine).

Well developed cerebrum (learning).

Outline 3 main clades within Mammalia (Vertebrata - Gnathostomata - Tetrapoda)

Monotreams (egg-laying).

Marsupials (pouch).

Eutherians (placental, allows for more developed fetuses when born - what humans are).

Rank the 9 phyla from most to least species (exact numbers don’t matter)

Arthropoda (1,000,000)

Mollusca (100,000)

Chordata (60,000)

Nematoda (25,000)

Platyhelminthes (20,000)

Annelida (16,500)

Cnidaria (10,000)

Echinodermata (7,000)

Porifera (5,500)

What is anthropogenic evolution?

Evolution caused by humans changing the enviro, causing organisms to adapt and evolve to human changes.

Peppered moth example of anthropogenic evolution

Britain 1800 - 100% typica (tree camo, black and white).

Britain 1896 - 95% carbonaria (black colouring, blend in with soot).

Britain 2010 - 90% typica (pollution cleaned up).

Briefly outline stonefly lifecycle

Nymph 1-4 years in streams → adults 1-4 weeks.

Outline stonefly colour

Zelandoperla has brown and black (melanic) variations. Melanic has yellow patches on arms and white patches on shoulders. Melanic inds mimics colouration of Austroperla (poisonous, feeds on wood and converts to cyanide, warning colouration).

List 2 types of mimicry

Batesian mimicry and mullerian mimicry

Outline Batesian mimicry

When a nontoxic species mimics a toxic species to deter predators

Outline Mullerian mimicry

When two toxic species mimic each other, reinforcing to predators that they are toxic

What type of mimicry is melanic Zelandoperla doing + evidence

Batesian mimicry.

Tested how palatable the melanic morph is (instead of testing for hydrogen cyanide). Put starved spiders in containers with live stoneflies. For non-mimic Zel., consumed 90% of the body on average. For models (Austroperla) ate about 5% of their body (due to toxicity). Mimic Zel. identical results to non-mimic (90% of body consumed), suggesting mimics are not toxic.

Outline quantifying stonefly colour

Quantified how dark specific regions of non-mimic, mimic, and aposematic model bodies (warning colouration). Mimic tibia colouration (yellow) not as contrasted as model tibia, but much more contrasted than non-mimic.

Mimic wing colouration (white) not as contrasted as model, but more contrasted than non-mimic.

Melanisation index created for each ind (single value). Mimics must overlap with Austroperla melanisation values.

Outline genetic basis of mimicry in stoneflies

Sequenced genotype of 48 mimics vs 48 non-mimics. Generally no difference between them - makes sense, same species.

Then looked at differences regions of genome. Most of genome identical, but found 6 markers different between melanic and nonmelanic Zelandoperla, including ebony gene.

Sequenced ebony gene, found 7bp indel (deletion in one of the sequences, runs at different speeds in gel, results in different bands). Low banding/allele = mostly nonmicic, heterozygous = mostly nonmicic but more mimic, high allele = mostly mimic. Explains 70% of the variation in colour.

Outline the distribution of mimicry

Mimicry only found at some sites, mostly restricted to coastal forested regions (around Dunedin and further south). Austroperla common in forests (feed on wood), rare in deforested streams. Zelandoperla mimics have advantage in forests because of Aus., deters predators, not advantageous in deforested areas as no Aus., birds won’t recognise colouration = poisonous.

Outline deforestation in NZ and stoneflies

>80% of native forest lost. Expect there to be less mimic Zelandoperla due to there being less Austroperla in deforested areas.

Outline study of deforestation in NZ and stonefly colouration

Took stonefly eggs/nymphs from forested and deforested streams, had subclades with geographic basis (no difference in genomes within the subclades).

Whiskey (forested) and Stoney (deforested) subclades - Whiskey 53% melanic, Stoney 20% melanic.

Chloris (forested) 38% melanic, Gilfillan (deforested) 14% melanic.

Generally 3x less mimics in deforested areas compared to forested areas.

Why are Zelandoperla stoneflies not 100% mimics in forested areas if it’s an advantange?

If mimic number too high, predators won’t think they are poisonous (when birds eat a black stonefly, most likely to be nonpoisonous (less likely to be Austroperla).

Frequency-dependent selection.