5.3 Classification of Biodiversity

What is the potential problem with using local names for organisms?

* Using different names for the same thing can be confusing
* Science is an international discipline so universal names are needed

System of naming used by scientists around the world

Binomial nomenclature → consists of 2 parts (genus, species)

* Universal among biologists and has been agreed and developed at a series of congresses

Who originally developed the binomial system of nomenclature?

Carl Linnaeus

Genus

A group of species that share common characteristics but may not be able to interbreed *(starts with capital letter)*

Species

A group of organisms in the same genus that are able to interbreed to produce fertile offspring *(starts with lower case)*

The scientific names of two organisms are *Rosa palustris* and *Brassica palustris*.

Why can it not be said that these two organisms belong to the same species?

Even if two organisms have the same species name (in this case both *palustris*), if they are from different genera, they cannot be from the same species. Many species names are descriptive words and translate to things like "common" or a colour.

Example of a subspecies

Organisms placed in the same species and subspecies are able to interbreed to have fertile offspring

* There are two subspecies of the eastern grey kangaroo (*Macropus giganteus)* , the *Macropus giganteus giganteus* and the *Macropus giganteus tasmaniensis.*
* They are able to interbreed to have fertile young but do not in nature due to their geographical isolation
* Neither of *these* subspecies of Eastern grey kangaroo can interbreed with the red kangaroo because it is classified as a different species.

Taxonomy

The branch of science concerned with classification, especially of organisms

How does the taxa form a hierarchy?

Taxa form a hierarchy based on their degree of relatedness. Organisms in the same species are most closely related, followed by organisms in the same genus, family, order, class, phylum, and kingdom. The further down you go in the hierarchy, the diversity gets fewer. (*groups within groups)*

Binomial nomenclature

A scientist or group that discovers a new species have the right to suggest a binomial name for their discovery. This name has to be approved by one of a number of international bodies before being accepted. These bodies have their roots in the International Zoological Congresses of the late 19th century.

Three domains of classification

* Eukaryota → eukaryotes
* (Eu)bacteria *(“true bacteria”) → bacteria*
* Archaea *(“primitive bacteria”) → archaeans*

Features of Bacteria

* **Histones associated with DNA:** absent
* **Presence of introns: rare or absent** (b/c they are too small)
* **Structure of cell walls:** Made of peptidoglycan
* **Structure of cell membranes:** Glycerol-ester phospholipids

Features of Archaea

* **Histones associated with DNA:** Proteins similar to histones are bound to DNA
* **Presence of introns:** Present in some genes, if they are big enough
* **Structure of cell walls:** Not made of peptidoglycan
* **Structure of cell membranes:** Glycerol-ester phospholipids

Features of Eukaryota

* **Histones associated with DNA:** Present
* **Presence of introns:** Frequent
* **Structure of cell walls:** Not always present + Not made of peptidoglycan
* **Structure of cell membranes:** Glycerol-ester phospholipids
* Often considered pathogenic and disease-causing

What did Carl Woese discover?

In 1977, while using DNA sequencing information to group organisms, an evolutionary microbiologist called Carl Woese discovered that organisms grouped together into prokaryotes actually had two separate ancestors. Thus he recognized that **Archaea** have a separate line of evolutionary descent from bacteria This disproved the belief that prokaryotes and eukaryotes were the only two lines of living.

What molecule gave scientists the idea that there are two distinct groups of prokaryotes?

The base sequence of rRNA was quite different in Archaea compared to Eubacteria

Where are Archaeans found?

In a broad range of extreme habitats:

* Deep ocean sediment
* Oil deposits
* Water with high salt levels
* High concentrations and temperatures

Examples of Archaeans

**Methanogens**: Methanobacterium, Methanococcus

**Extremophiles**: Thermococcus, Halobacterium

The Phylogenetic Tree

A tree showing evolutionary relationships and ancestry

Why are viruses not classified in any of the 3 domains?

Viruses have too few of the characteristics of life to be classified as living organisms: no metabolism and can only produce inside living host cell.

Eubacteria features

* Cell walls have peptidoglycan
* One cell present
* **Autotrophic** or **heterotrophic** nutrition
* Examples: *E. coli* , *Streptococcus*

Archaebacteria features

* No peptidoglycan in cell walls
* One cell present
* **Autotrophic** or **heterotrophic** nutrition
* Examples: *Halophiles*

Animalia Features

* Multicellular
* No cell walls
* Mitochondria present
* **Heterotrophic** nutrition (gain organic compounds by eating other living things)
* Carbohydrates stored as glycogen
* Examples: *Mammals, Fish, Insects, Worms*

Plantae Features

* Multicellular
* Cell walls made of cellulose
* Mitochondria present
* **Autotrophic** nutrition (contain chloroplasts to carry out photosynthesis)
* Carbohydrates stored as starch
* Examples: *Flowering plants, ferns*

Fungi Features

* Unicellular or multicellular
* Cell walls made of chitin
* Mitochondria present
* **Saprotrophic** nutrition (gain organic compounds by externally digesting dead organisms and absorbing products)
* Carbohydrates stored as glycogen
* Examples: *Yeasts, mushrooms*

Protoctista features

* Unicellular (usually)
* Cell walls may/may not be present
* Mitochondria present
* Various modes of nutrition (may or may not contain chloroplasts for photosynthesis)
* Carbohydrates stored as starch or glycogen
* Examples: *Giant kelp, amoeba*

Eight taxonomic levels

Domain

Kingdom

Phylum

Class

Order

Family

Genus

Species

__Panda__ binomial classification

**Domain**: Eukaryote

**Kingdom**: Animalia

**Phylum**: Chordata *(spine containing)*

**Class**: Mammalia

**Order**: Carnivora

**Family**: Urisdae

**Genus**: Ailuropoda

**Species**: melanoleuca

__Wolf__ binomial classification

**Domain**: Eukaryote

**Kingdom**: Animalia

**Phylum**: Chordata

**Class**: Mammalia

**Order**: Carnivora

**Family**: Canidae

**Genus**: Canis

**Species**: lupus

__Hibiscus Plant__ binomial classification

Domain: Eukaryote

Kingdom: Plantae

Phylum: Angiospermae

Class: Dicotyledonae

Order: Malvales

Family: Malvaceae

Genus: Hibiscus

Species: rosa-sinensis

Artificial classification

A method of grouping organisms based on superficial similarities rather than evolutionary relationships. It's a subjective approach that can lead to misclassification. As technology has improved and we have gained further knowledge of organisms and their relationships, artificial classification has become outdated 

Natural classification

A system of grouping organisms based on their evolutionary relationships and shared characteristics. It reflects the true relationships between species and helps to understand their evolutionary history. This allows for predictions of characteristics shared by species within a group

* A genus and it’s accompanying higher taxa, consist of all the species that have evolved from one common ancestral species.

Why would grouping animals that can fly like birds, bats and insects together not be appropriate?

Flight evolved separately in these groups, they do not share a common ancestor and differ in many ways. (This would be called artificial classification)

Plants and fungi were at one time classified together.  Why do you think scientists did this, and how do we now know that it was incorrect?

They share many features: both have cell walls, no nervous system, don’t move around etc.

But molecular research shows their cell walls evolved separately, and they differ in many other ways

Convergent evolution

Convergent evolution refers to the process by which different organisms evolve similar traits or characteristics in response to similar environmental pressures, despite not having a common ancestor. This often leads to the development of analogous structures that serve similar functions, but have different evolutionary origins.

→ can make distantly related organisms appear superficially similar (dolphins vs sharks)

Adaptive radiation

The process by which a single ancestral species evolves into a variety of different forms that are adapted to specific environments and niches. (common ancestor, different features)

→ can make closely related organisms appear different (dolphin vs dog)

How would classification be reviewed if new evidence showed that members of a group do not share common ancestors?

The group would be split into 2 or more different taxa

How would classification be reviewed if species classified in different taxa were found to be closely related?

2 or more taxa would be united into one OR a species would be moved from 1 genus to another (or between a higher taxa)

How does natural classification benefit the identification of species?

It makes it easier, because they can be assigned to taxa based on characteristics

How does natural classification benefit the predication of shared characteristics?

A common ancestor implies similar characteristics among species, thus is a new species is discovered, we can make prediction about characteristics (physical and behavioural) based on their ancestor.

Why is nucleic comparison the best indicator for relatedness between species?

Today, the ancestry can also be confirmed by DNA and protein analysis, making the grouping of certain organisms much more reliable - this is phylogenetic classification.

* Analysing nucleic acids is better than proteins because some mutations at the DNA level do not cause a change in the protein structure. These changes in nucleic acids could indicate that two organisms may not be as related as when one compares the protein structures

Radial Symmetry

Body parts arranged in a wheel

Bilateral symmetry

Right and left sides are symmetrical

Dichotomous Key

A series of paired opposing statements which guide the user to the identity (or allows the classification) of an item or organism using its visible features.

* Each time you are given a choice of two features, but you should always follow the one that applies: each choice leads to another choice until the organism is narrowed down to its genus and finally to its species

Branching keys

Numbered keys

Vascular tissue

 Transports water and sugars throughout the plant.

Rhizoids

Small root-like structures that help bryophytes to attach to the soil.

Xylem

A type of vascular tissue composed of non-living cells that transport water.

Phloem

A type of vascular tissue that transports sugars throughout the plant.

Chordata

A large phylum of animals that includes the vertebrates together with tunicates (sea squirts) and lancelets. They are distinguished by the possession of a notochord (a long, rod-like midline structure) at some stage during their development

Vertebrates

Vertebrates are a subphylum of **chordata** and are subdivided into seven classes. Subphylum Vertebrata are characterised by having a vertebral column or backbone which supports the spinal cord.

Mammalia characteristics

* Skin covered in hair follicles
* Skin also has sweat glands
* Habitat on land and in water
* Endothermic (warm-blooded) → they maintain their body at a metabolically favourable temperature
* Have four-chambered hearts + four pentadactyl limbs
* Breathing through lungs
* Give brith to young (except five species of monotremes)
* Rely on internal fertilisation for reproduction
* Examples: *platypus, bears, cats and humans*

Aves (Birds)

* Skin covered in feathers made of keratin, which are waterproof and insulate the body
* Habitat on land
* Most species can fly and some can also swim
* Endothermic (helps them live in diverse habitats)
* Four chambered hearts + Four pentadactyl limbs (two wings + two legs)
* Breathing through lungs (well-developed lungs to help with air ventilation) → need a lot of oxygen as it takes a lot of energy to fly
* Internal fertilisation + lay eggs
* Parent their offspring by feeding them and building them nests
* Examples: *hawks, sparrows and flamingos* (10, 000 species)

Reptilia

* Skin is dry and has scales made up of keratin
* Habitat on land
* Ectothermic (cold-blooded) → they regulate their body temperature using external sources, such as basking in the sun
* Internal fertilisation + most species lay eggs (usually with soft shells
* Three-chambered hearts
* Breathing through lungs → makes them more terrestrial than fish and amphibians
* Homodont are sharp and cone-shaped
* Most do not parent their offspring (exceptions: *crocodiles*)
* Examples: *turtles, crocodiles, snakes and lizards*

Amphibia

* Skin is exposed and moist
* Found in a variety of habitats: terrestrial, arboreal (trees) or freshwater aquatic systems
* Ectothermic and can use their skin as a secondary respiratory surface
* Three chambered hearts + four limbs with digits
* Have rudimentary lung sacs that allow for gas exchanges; however, during their larval stage they use gills as they start off by living in the water
* Lay many eggs that are coated in a jelly like substance for protection
* External fertilisation for reproduction
* Most amphibians leave their offspring once they hatch (exceptions: *some species of poison dart frogs*)
* Examples: *frogs, newts, salamanders*

Fish

* Covered in slimy scales that protect the body
* Habitat in fresh or sea water, with fins and tails adapted to swimming and balancing
* Ectothermic
* Two chambered hearts
* Breathing through gills
* Most rely on external fertilisation for reproduction
* __Three main classes:__
* Jawless fish
* Cartilaginous fish: *have gill slits instead of an operculum + have no swim bladder*
* Bony ray-finned fish: *largest of the three + have fins supported by a spine, have gills that are covered by an operculum and show a gill slit, have a swim bladder*