IB DP Biology Classification and cladistics Study Notes

A3.2.1—Need for classification of organisms

Need for Classification of Organisms

*Growing Number of Species*:

  – Millions of species have been named and described, with new ones discovered daily.

  – Biologists have accumulated vast knowledge about these species.

*Challenge*:

  – Storing and retrieving large amounts of biological information is difficult.

*Role of Classification*:

  – Classification organizes organisms into groups based on traits or evolutionary origins.

  – It simplifies the identification of organisms and the retrieval of relevant information.

*Hierarchical System of Classification*:

  – Developed over the last 300 years.

  – Organisms are classified into broad groups, with **domains** being the largest category.

  – These groups are further subdivided down to the **species** level, the most specific category.

*Importance of Classification*:

  – Without this system, identifying unknown species would be challenging.

*Example of Classification Process*:

1. *Domain*: Eukaryotic (based on cell structure)
2. *Kingdom*: Animal (based on general characteristics)
3. *Class*: Mammal (due to hair and mammary glands)
4. *Order*: Carnivora (based on dietary and other traits)
5. *Family*: Mustelidae (a group of carnivorous mammals)
6. *Genus*: *Pekania*
7. *Species*: *Pekania pennanti* (Fisher)

A3.2.2 Diffculties classifying organisms into the traditional hierarchy of taxa

*Taxon and Taxa*:

 – A *taxon* is a classification group (e.g., “phylum”).

  – The plural of taxon is *taxa*.

*Hierarchy of Taxa*:

  – Biologists have developed a hierarchy of taxa with ranks from *species* to *kingdom*.

  – Example of hierarchy:

    – *Genus* contains one or more *species*.

    – *Family* contains one or more *genera*.

    – As you move up, taxa contain larger numbers of species with fewer shared traits.

*Challenges in Classification*:

  – Classifying organisms into the traditional hierarchy can be difficult.

  – Taxonomists often agree on which species belong together but disagree on the *taxonomic rank*.

    – Example: One taxonomist might classify similar species as a *genus*, while another might classify them as a *family*.

*Cause of Uncertainty*:

  – Uncertainties arise due to the *gradual divergence* of species and larger groups over time.

  – Over time, species in a genus may diverge enough to form separate genera.

  – Continued divergence over millions of years may lead to genera being placed in different families.

*Boundary Paradox*:

  – The exact point at which species should be classified into new groups is not objectively determined.

  – This is known as the *boundary paradox*.

  – Because of this, taxonomic rankings are considered *arbitrary*.

A3.2.3 Advantages of classification corresponding to evolutionary relationships

– *Goal of Classification*:

  – Classification should mirror the **evolutionary origins** of species.

– *Criteria for Evolutionary Classification*:

1. *Common Ancestor*: Organisms evolved from a common ancestor should belong to the same *taxonomic group*.
2. *Shared Evolutionary Origin*: All species within a group must have evolved from the same common ancestor.

– *Synapomorphies*:

  – *Synapomorphies* are shared traits inherited from a common ancestor.

  – These traits define taxonomic groups.

– *Predictive Power*:

  – Classification based on evolutionary relationships allows biologists to *predict* traits and behaviors of species.

– *Examples*:

1. *Bats*:

     – Since bats are classified as mammals, it is predictable that new species of bats will have:

       – A *four-chambered heart*

       – *Hair*

       – *Mammary glands*

       – *Placenta* (and thus a *navel*)

       – Other mammalian characteristics.

2. *Daffodils (Narcissus species )*:

     – All species in the genus *Narcissus* evolved from a common ancestor.

     – It is predicted that Narcissus species produce *alkaloids*, including *galanthamine*.

A3.2.4 Clades as groups of organisms with common ancestry and shared characteristics

                                                               (Cladograms are tree diagrams where each branch point represents the splitting of two new groups from a common ancestor, each branch point (node) represents a speciation event by which distinct species are formed via divergent evolution)

– *Evolution of Species*:

  – Species can evolve over time and split to form new species.

  – Some species evolve repeatedly, forming large groups derived from a *common ancestor*.

– *Definition of Clade*:

  – A clade is a group of organisms that evolved from a *common ancestor* and share specific characteristics.

  – Clades include:

    – All *living species* derived from the common ancestor.

    – The *ancestral species*.

    – Any extinct species that evolved from the common ancestor.

– *Size of Clades*:

  – Clades can be *large* (e.g., birds, with ~10,000 species).

  – Clades can also be *small* (e.g., Ginkgo biloba, the only living member of a clade that evolved 270 million years ago).

– *Identifying Clades*:

  – It is not always obvious which species belong to a clade.

  – The most objective evidence for clades comes from **genetic data**:

    – *Base sequences of genes* or *amino acid sequences** of proteins.

  – When genetic data is unavailable, **morphological traits** (physical characteristics) are used, especially for extinct species based on fossils.

– *Nested Clades*:

  – Every species belongs to multiple clades, with smaller clades nested within larger ones.

  – Example: *Gymnosperms (non-flowering seed plants)*:

    – *Araucaria araucana* (monkey puzzle tree) and *Podocarpus totara* form a small clade due to common ancestry.

    – This small clade is nested within a larger clade with *Taxus baccata* and other species.

    – The entire group (including *Pinus radiata* and others) is part of a larger clade that includes all gymnosperms, including *Ginkgo biloba*.

A3.2.5 Gradual accumulation of sequence differences as the basis for estimates of when clades diverged from a common ancestor

– *DNA and Protein Sequence Differences*:

  – *Mutations* cause differences in the base sequence of DNA, which leads to differences in the amino acid sequence of proteins.

  – These differences accumulate *gradually* over long periods.

– *Molecular Clock*:

  – The *molecular clock* is a method for estimating the time since two species diverged from a common ancestor.

  – Assumes that mutations accumulate at a *roughly constant rate*.

  – The larger the number of sequence differences, the longer it has been since the species diverged.

– *Assumptions and Variability*:

  – The molecular clock assumes mutations accumulate at a constant rate, but this rate can vary.

  – The rate of mutation is influenced by factors like:

    – *Generation time*

    – *Population size*

    – *Selective pressure* and other environmental factors.

  – As a result, molecular clock estimates are *approximate* and subject to variability.

– *Example of Molecular Clock in Humans*:

  – *Humans and nearest relatives*: Based on a mutation rate of 10^-9 per year, humans are estimated to have split from their nearest living relatives about *4.5 million years ago*.

  – *Chimpanzees and bonobos*: The split between common chimpanzees and bonobos occurred around *1 million years ago*.

– *Recent Common Ancestor of Humans*:

  – By studying variations in the *mitochondrial DN* sequence, it is estimated that the most recent common ancestor of all modern humans lived around *150,000 years ago*.

A3.2.6 Base sequences of genes or amino acid sequences of proteins as the basis for constructing cladograms

– *Species within a Clade*:

  – Species within a clade can be *more closely related* or *distantly related* depending on how recently they diverged from a common ancestor.

  – *Closely related species* have fewer differences in their *base sequences* or *amino acid sequences*.

  – *Distantly related species* have more differences due to a longer time since divergence.

– *Estimating Divergence Time*:

  – By comparing *base sequences* or *amino acid sequences*, we can estimate how long ago two species diverged.

  – These estimates help to suggest the *order of divergence* between species.

– *Sophisticated Analysis with Software*:

  – Modern *software* allows for more sophisticated analysis:

    – Sequences from all species in a clade are compared simultaneously.

    – The software calculates the *smallest number of sequence changes* needed to explain the evolutionary relationships. This method is called the *parsimony criterion*.

– *Parsimony Criterion*:

  – The *parsimony criterion* aims to identify the most *probable pattern of divergence* by minimizing the number of evolutionary changes.

  – It does not prove the exact sequence of events but suggests the most likely scenario.

– *Cladogram Construction*:

  – *Cladograms* are branching diagrams used to represent *ancestor-descendant relationships*.

  – Sequence analysis (base or amino acid sequences) is used to construct these cladograms, showing the evolutionary relationships within a clade.

A3.2.7 Analysing cladograms

When analysing cladograms, remember:

• A cladogram is a tree diagram with a number of branches

• The terminal branches are ends that represent individual clades. These may be species or groups of species that are not subdivided on the cladogram

• The branching points on a cladogram are called nodes. Usually, two clades branch off at a node but sometimes there are three or more. A node represents the point at which a hypothetical ancestral species split to form two or more clades.

• Two clades that are linked at a node are relatively closely related. Clades that are only connected via a series of nodes are less closely related.

• The root is the base of the cladogram. This is the hypothetical common ancestor of all the clades.

• Some cladograms include numbers to indicate numbers of sequence differences.

• Some cladograms are drawn to scale, based on estimates of the time since each split occurred.

• The pattern of branching in a cladogram is assumed to match phylogeny of the organisms—the evolutionary origins of each species.

A3.2.8 Using cladistics to investigate whether the classification of groups corresponds to evolutionary relationships

– *Cladistics and Evolutionary Relationships*: 

  – Cladistics is used to investigate if traditional classifications align with evolutionary relationships.

– *Advancement in Genomic Data*: 

  – Since the 1990s, genomic sequencing (gene and whole genome data) has become more accessible.

  – This data allows researchers to test traditional taxonomic classifications through cladistic analysis.

– *Cladistics and Confirmation of Classification*: 

  – In many cases, cladistics confirms that traditional classifications align with evolutionary pathways.

-*Cases of Misclassification*: 

  – Some taxonomic groups do not consist of species that share a common ancestor.

  – Alternatively, species that share a common ancestor may have been placed in separate groups.

– *Justification for Reclassification*: 

  – When species are misclassified, reclassification is necessary to reflect evolutionary relationships accurately.

A3.2.9 Classification of all organisms into three domains using evidence from rRNA base sequences

– *Traditional Classification*: 

  – Historically, organisms were classified into two categories: *eukaryotes** and *prokaryotes* based on cell types.

– *Limitations of Traditional Classification*: 

  – This system is now considered inappropriate because *prokaryotes* are highly diverse.

– *Discovery of Two Prokaryotic Groups*: 

  – Analysis of ribosomal RNA base sequences revealed two distinct groups within prokaryotes:

    – *Eubacteria*

    – *Archaea*

– *Current Classification System*: 

  – Modern systems recognize *three major categories (domains)* of organisms:

1. *Eubacteria*
2. *Archaea*
3. *Eukaryota*

– *Domain Names*: 

  – Organisms are classified into these three domains, and members are referred to as:

    – *Bacteria* (Eubacteria)

    – *Archaeans* (Archaea)

    – *Eukaryotes* (Eukaryota)

– *Familiarity of Domains*: 

  – *Bacteria* and *eukaryotes* are well-known to most biologists.

  – *Archaeans* are often less familiar.