A3.2 Classifications and cladistics Flashcards
How can we classify organisms?
- morphology
- anatomy
- cell structure
- mode of nutrition
- habitat
- behaviour
- reproduction
- DNA
- RNA
- Genome
- Proteome
What is the binomial system of classification?
The current hierarchy of taxa includes main taxa:
1. Domain
2. Kingdom
3. Phylum
4. Class
5. Order
6. Family
7. Genus
( pl.genera)
8. Species
Acronym = Decide King Prawn Curry Of Fat Greasy Sausages
What is a Kingdom?
Kingdom = largest & most inclusive grouping, e.g. plants, animals, fungi, etc. Second highest taxonomic rank, below domain.
What is a phylum?
Phylum = organisms constructed on a similar plan
What is a class?
Class = grouping of orders within a phylum
What is an order?
Order = group of apparently related families
What is a family?
Family = group of apparently related genera
What is a genus?
Genus = group of similar & closely related species
What is a species?
Species = group of organisms capable of interbreeding to produce fertile offspring
What is an example of scientific classification (Dog Flea)?
Domain: Eukaryote
Kingdom: Animalia
Phylum: Arthropoda
Class: Insecta
Order: Siphonaptera
Family: Pulicidae
Genus: Ctenocephalides
Species: Canis
What is the binomial name of a species composed of?
Genus species
E.g. for Dog flea
Genus: Ctenocephalides
Species: canis
Ctenocephalides canis
What is a prokaryotae?
Prokaryotae = prokaryote kingdom, bacteria & cyanobacteria ( group of photosynthetic bacteria), predominately unicellular organisms.
What is a protoctista?
Protoctista = protoctistan kingdom (eukaryotes), predominately unicellular, & seen as resembling ancestors of fungi, plants & animals
What is fungi?
Fungi = plant kingdom (eukaryotes), predominately multicellular organisms, non-motile & with heterotrophic nutrition.
What is plantae?
Plantae = plant kingdom (eukaryotes), multicellular organisms, non-motile, with autotrophic nutrition.
What is animalia?
Animalia = animal kingdom (eukaryote), multicellular organisms, motile, with heterotrophic nutrition
What is a domain?
Domain = highest taxonomic rank in hierarchical biological classification system, above kingdom level. There are three domains of life: archaea, eubacteria & eukarya
How was the domain classification discovered?
When RNA sequencing became possible Carl Woese had an idea of using RNA to study how related all living organisms are. His work allowed clear separation of all living organisms into three domains. His findings showed that prokaryotes should be divided into two groups: Bacteria or Eubacteria & Archaea
What are the biochemical differences between the three domains (eubacteria, archaea, eukarya)
What is cladistics?
Cladistics = classification system used to construct evolutionary trees. Organisms are categorized based on shared derived characteristics that can be traced to a group’s most recent common ancestor & aren’t present in more distant ancestors. Characteristics can be anatomical, physiological, behavioural, or genetic & protein sequences.
What are the benefits of cladistics?
- Cladistics offer an alternative approach to classification
- Cladistics uses cladogram diagrams that show clades
- There is no hierarchy of clades
- Cladistics aims to follow evolution
- Cladograms show points where two pop of a species diverge & become 2 species
- DNA sequences, ribosomal RNA (rRNA) sequences & protein structure are often used as evidence
- This change in approach from hierarchical taxa to cladistics is an example of a paradigm shift
What is a clade?
Clade = group of organisms that have evolved from a common ancestor
What is a cladogram?
Cladogram = diagram used in cladistics that shows evolutionary relations among organisms
What are two important features of cladograms?
- Branch points in tree - these represent time at which one taxa divides into two
- The degree of divergence between branches - this represents differences that have developed between two taxa since they separated
In a cladogram how do you know which two organisms are more closely related?
In cladograms, closer two organisms are in evolutionary terms, more derived characteristics they share. This means their common ancestor is more recent.
What is a node?
Node = branching point from ancestral pop in a cladogram. It represents a speciation event.
What is a terminal branch?
Terminal branch = indicates both extinct & extant species in a cladogram, leading to a terminal node.
What is a terminal node?
Terminal node = represents hypothetical last common ancestral interbreeding pop of taxon labelled at a tip of a cladogram.
What is a root?
Root = central trunk of a cladogram, indicating common ancestor to all groups that branch from it.
What are figworts?
Figworts were considered to be 8th largest family of flowering plants (angiosperms), containing 275 diff genera. Biologists have been classifying plants using external features (morphology) for many yrs. If these features are similar assumption is that plants are closely related, & that they share many genes. Genotype actually does influence phenotype, so this makes logical sense.
What was the problem with classifying the figwort family only using morphology?
However, many of figwort plants were too dissimilar in morphology to function as a meaningful grouping. Taxonomists examined genes for chloroplasts in figworts & decided to split the figwort species into five diff clades.
Now less than half of species remain in figwort family – which is now 36th largest among angiosperms.
What has new method led to with the classification of the figwort family?
New methods of analysis are providing evidence for reclassification of figwort family. In this method, a few genes are sequenced & their base sequences are compared to those of similar organisms. This allows reclassification to happen as is case with figwort family.
What did rRNA base sequencing do to classification?
Classification of all organisms into three domains can use evidence from rRNA base sequences.
This reclassification adding the extra taxonomic level ‘domain’ above kingdoms was proposed in 1977 by Carl Woese.
What did Carl Woese use to classify in comparison to Carl Linneus?
Classification uses info available to group organisms together. In time of Carl Linneus often this evidence was taken from morphological features. This can align with evolutionary pathways if right features are used, but DNA sequences or amino acid sequences have improved evidence available & have supported development of cladistics. Carl Woese was one of 1st to use DNA sequences & this revolutionised the tree of life.
How are single celled organisms classified?
Single celled organisms have been classified into Eukaryotes (with a membrane bound nucleus) & Prokaryotic Cells (without a nucleus). For a long time shape of prokaryotes was used to classify them.
How did Woese use DNA sequencing to classify prokaryotes?
A prokaryote is a simple, single-celled (unicellular) organism that lacks an organized nucleus or any other membrane-bound organelle. Prokaryotic DNA is found in a central part of the cell: nucleoid. With today’s DNA sequencing technology it seems like a logical idea to try to use part of this DNA to make comparisons between diff species of bacteria. Carl Woese was working in 1970’s, 30 yrs before human genome project & development of rapid DNA sequencing techniques. He wanted to find a small gene which was present in all species, to achieve this task.
All prokaryote cells have ribosomes. Ribosomes are made of ribosomal RNA. RNA is a molecule known to exist in earliest evolution of life on Earth
What is the ribosome structure?
The prokaryotic small ribosomal subunit, or 30S subunit, is smaller subunit of 70S ribosome found in prokaryotes. It is a complex of 16S ribosomal RNA (rRNA) & 19 proteins. This complex is implicated in binding of transfer RNA to messenger RNA (mRNA). Small subunit is responsible for binding & reading of the mRNA during translation. Small subunit, both rRNA & its proteins, complexes with large 50S subunit to form 70S prokaryotic ribosome in prokaryotic cells. This 70S ribosome is then used to translate mRNA into proteins.
Why was 16S rRNA perfect for Woese’s classification?
Carl Woese decided to explore diff in gene which codes for this 16S rRNA molecule found in ribosome small-subunit. It was a good choice, as it is just right length. Long enough to show diff between groups, but short enough to be sequenced using early technology available.
What did Woese’s DNA and RNA help with classification?
Woese’s approach was revolutionary bc comparisons of physical features are insufficient to differentiate between prokaryotes that appear fairly similar in observations. Comparison of DNA & RNA sequences provided Woese with a sensitive tool that revealed extensive variability of prokaryotes. RNA, which is transcribed from DNA, varies between organisms. This allowed Woese to suggest a new classification using rRNA base sequences. Pioneering work of American microbiologist Carl Woese in early 1970s has shown, however, that life on Earth has evolved along three lineages, now
called domains—Bacteria, Archaea, & Eukarya. Woese defined Archaea as a new domain, & this resulted in a new taxonomic tree. Many organisms belonging to Archaea domain live under extreme conditions & are called extremophiles. To construct his tree, Woese used genetic relationships rather than similarities based on morphology (shape).
What is the three domain classification system?
Classification of all organisms into three domains used evidence from rRNA base sequences.
This reclassification adding the extra taxonomic level ‘domain’ above kingdoms was proposed in 1977.
What is classification?
A system of organising knowledge on all living things based upon their characteristics and more recently their DNA.
Why is classification important?
- It allows us to better organise and understand the world around us by grouping similar things or ideas.
- It allows for better communication by providing a common language to discuss or refer to certain groups of things.
- It allows us to be more efficient by being able to quickly and easily find and categorise things and information.
- It allows for further research and analysis to identify patterns and trends to better understand the things we have classified and the systems and phenomena that are a part of them
What is taxonomy?
The science of categorisation or classification.
What is taxa?
A group of one or more populations of an organism or organisms seen by taxonomists to form a unit.
How are organisms placed into taxa?
There are also many intermediate taxa, such as subfamilies & superorders, that have been added to account for complexities in relationships between diff groups. Shared characteristics used to place species into taxa were mostly morphological. In other words, organisms that looked most alike were most closely related
Why is the traditional hierarchy of taxa a problem?
Traditional hierarchy of taxa poses some problems, however. These taxa are arbitrary & don’t reflect complex evolution that has occurred over billions of years. Traditional way of grouping organisms doesn’t always correspond to patterns of divergence generated by evolution.
What did we shift our classification system from traditional hierarchy of taxa to?
We have shifted our perspective of the classification of life. From a system based on similarities in appearance and behaviour, to a more precise and detailed one. The latter is based on the use of genetic analysis to determine evolutionary relationships, specifically nucleic acid or amino acid sequences.
What are the advantages of classification corresponding evolutionary relationships?
- It reflects evolutionary relationships among diff organisms, providing a natural & biologically meaningful way to group them in clades based on common ancestry.
- It reflects process of evolution, such as branching patterns of speciation shown through cladistics & emergence of new features.
- It can be used to make predictions about characteristics of organisms, e.g. their biochemistry or ecology, based on their evolutionary relationships.
- It helps us to understand diversity of life on Earth by providing a context for evolution & distribution of diff organisms.
What is the ‘molecular clock’?
Genetic & molecular differences between organisms slowly increase over time as a result of evolution. The ‘molecular clock’ is name given to this technique of measuring the time since there was a common ancestor. Molecular clock can only provide estimates because mutation rates depend on a range of things. These include size of a population, selection pressures, genome size as well as a degree of randomness
What is a calibration point?
The need for a calibration point in molecular clock analysis is an essential component. A calibration point is a period of time in which the precise moment at which two species diverged is known. As an example, the oldest fossil of a specific species that is known to exist can be used as a calibration point. The molecular clock can be used to calculate the divergence times of other species in reference to a calibration point once it has been established
