5.4 Cladistics

Question 1

What is a clade?

Answer 1

A group of organisms that have evolved from a common ancestor

Question 2

What is cladistics?

Answer 2

• A method of classifying organisms into groups of species called clades
• Each clade consists of an ancestral organism and all of its evolutionary descendants
• Members of a clade will possess common characteristics as a result of their shared evolutionary lineage

Question 3

How can clades be organized?

Answer 3

Clades can be organized according to branching diagrams (cladograms) to show evolutionary relationships

Question 4

Examples of clades

Answer 4

Question 5

Other examples of clades

Answer 5

Question 6

What are cladograms?

Answer 6

• 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

Question 7

What do cladograms show?

Answer 7

• The probable sequence of divergence and hence the likely evolutionary history (phylogeny) of a clade
• The fewer the number of nodes between two groups, the more closely related they are expected to be

Question 8

Diagram of phylogenic comparison of cladograms

Answer 8

Question 9

Cladograms can show ___ relationships

Answer 9

Evolutionary

Question 10

Explain how cladograms can show evolutionary relationships

Answer 10

• Cladograms can show evolutionary relationships and demonstrate how recently two groups shared a common ancestry
• As each node represents a point of divergence, closely related species will be separated by fewer nodes
• According to a cladogram outlining the evolutionary history of humans and other primates:
• Humans, chimpanzees, gorillas, orangutans, and gibbons all belong to a common clade – the Hominoids
• The Hominoid clade forms part of a larger clade – the Anthropoids – which includes Old World and New World monkeys

Question 11

Diagram showing a cladogram for humans and other primates

Answer 11

Question 12

What key features do constructed cladograms all typically share?

Answer 12

• Root – The initial ancestor common to all organisms within the cladogram (incoming line shows it originates from a larger clade)
• Nodes – Each node corresponds to a hypothetical common ancestor that speciated to give rise to two (or more) daughter taxa
• Outgroup – The most distantly related species in the cladogram which functions as a point of comparison and reference group
• Clades – A common ancestor and all of its descendants (i.e. a node and all of its connected branches)

Question 13

Diagram showing the key features of a cladogram

Answer 13

Question 14

How can cladograms be constructed?

Answer 14

• Based on either a comparison of morphological (structural) features or molecular evidence
• Historically, structural features were used to construct cladograms, but molecular evidence is now more commonly used

Question 15

Using structural evidence to construct cladograms

Answer 15

Step 1: Organise selected organisms according to defined characteristics

• Use characteristics that are developmentally fixed (i.e. innate) and not influenced by environmental pressures

Step 2: Sequentially order organisms according to shared characteristics to construct a cladogram

• Grouping of organisms may be facilitated by constructing a Venn diagram before developing a cladogram
• Each characteristic will be represented by a node, with more common characteristics representing earlier nodes
• The species with the least number of characteristics in common will represent the outgroup (establishes baseline properties)

Question 16

Diagram of cladogram according to structural evidence

Answer 16

Question 17

Using molecular evidence to construct a cladogram

Answer 17

Step 1: Select a gene or protein common to a range of selected organisms

• Examples of molecules which are ubiquitously found in many animals include haemoglobin and cytochrome c

Step 2: Copy the molecular sequence (DNA or amino acid) for each of the selected organisms

• Use online databases such as Genbank or Ensembl to identify relevant DNA or amino acid sequences
• Sequences can be collated in a Word document and then saved as a document in plain text format (.txt)
• Before each sequence, designate a species name preceded by a forward arrow (e.g. ‘>Human’ or ‘>Chimpanzee’)

Step 3: Run a multiple alignment to compare molecular sequences (DNA or amino acid)

• Multiple alignment software compares DNA or protein sequences for similarities and differences
• Closely related species are expected to have a higher degree of similarity in their molecular sequence
• Clustal Omega is a free online tool that will align multiple DNA or amino acid sequences for comparison

Step 4: Generate a phylogeny tree (cladogram) from multiple alignment data

• Clustal Omega can generate branched phylograms after a sequence alignment is completed (select ‘Phylogenetic Tree’)
• Below is a plain text file that can be uploaded to compare amino acid sequences from different species:
• HBA – Haemoglobin alpha chain (amino acid sequence) from various species

Question 18

Multiple alignment of a protein sequence from various species

Answer 18

Question 19

Explain how evidence for which species are part of a clade can be obtained from the base sequence of a gene or the corresponding amino acid sequence of a protein

Answer 19

• All organisms use DNA and RNA as genetic material and the genetic code by which proteins are synthesized is (almost) universal
• This shared molecular heritage means that base and amino acid sequences can be compared to ascertain levels of relatedness
• Over the course of millions of years, mutations will accumulate within any given segment of DNA
• The number of differences between comparable base sequences demonstrates the degree of evolutionary divergence
• A greater number of differences between comparable base sequences suggests more time has passed since the two species diverged
• Hence, the more similar the base sequences of two species are, the more closely related the two species are expected to be
• When comparing molecular sequences, scientists may use non-coding DNA, gene sequences, or amino acid sequences
• Non-coding DNA provides the best means of comparison as mutations will occur more readily in these sequences
• Gene sequences mutate at a slower rate, as changes to base sequence may potentially affect protein structure and function
• Amino acid sequences may also be used for comparison but will have the slowest rate of change due to codon degeneracy
• Amino acid sequences are typically used to compare distantly related species (i.e. different taxa), while DNA or RNA base sequences are often used to compare closely related organisms (e.g. different haplogroups – such as various human ethnic groups)

Question 20

Comparison of the hemoglobin beta chain in different species

Answer 20

Question 21

Explain the concept of the molecular clock

Answer 21

• Some genes or protein sequences may accumulate mutations at a relatively constant rate (e.g. 1 change per million years)
• If this rate of change is reliable, scientists can calculate the time of divergence according to the number of differences
• E.g. If a gene that mutates at a rate of 1 bp per 100,000 years has 6 bp different, divergence occurred 600,000 years ago
• This concept is called the molecular clock and is limited by many factors:
• Different genes or proteins may change at different rates (e.g. hemoglobin mutates more rapidly than cytochrome c)
• The rate of change for a particular gene may differ between different groups of organisms
• Over long periods, earlier changes may be reversed by later changes, potentially confounding the accuracy of predictions

Question 22

Diagram of molecular clocks

Answer 22

Question 23

What was classification primarily based on historically?

Answer 23

• On morphological differences (i.e. structural characteristics)
• Closely related species were expected to show similar structural features, indicating common ancestry

Question 24

What are the two key limitations to using morphological differences as a basis for classification?

Answer 24

• Closely related organisms can exhibit very different structural features due to adaptive radiation (e.g. pentadactyl limb)
• Distantly related organisms can display very similar structural features due to convergent evolution

Question 25

Explain convergent evolution

Answer 25

• Convergent evolution is the independent evolution of similar features in species with distinct lineages
• It may occur when different species occupy the same habitat and are thus subjected to the same selection pressures
• The shared conditions cause common adaptations to be selected in different species, resulting in structural similarity
• An example of convergent evolution is the development of wings in birds, bats, and insects

Question 26

Diagram showing convergent evolution

Answer 26

Question 27

Explain homologous and analogous structures

Answer 27

• Structural traits are not commonly used to determine clades as such features may not necessarily indicate shared heritage
• Traits that are similar because they are derived from common ancestry are termed homologous structures
• Traits that are superficially similar but were derived through separate evolutionary pathways are termed analogous structures

Question 28

Table explaining homologous and analogous structures

Answer 28

Question 29

What have scientists discovered using molecular evidence?

Answer 29

• That many species thought to be closely related based on shared structural characteristics actually demonstrate distinct evolutionary origins
• Crocodiles have been shown to be more closely related to birds than lizards, despite closely resembling lizards in structure
• Many species of plants previously classified as figworts have been reclassified based on molecular evidence

Question 30

Diagram showing homologous vs. analogous structures

Answer 30

Question 31

Reclassification of the figwort family using evidence from cladistics

Answer 31

• Until recently, figworts were the 8th largest family of flowering plants (angiosperms), containing 275 different genera
• This was problematic as many of the figwort plants were too dissimilar in structure to function as a meaningful grouping
• Taxonomists examined the chloroplast gene in figworts and decided to split the figwort species into five different clades
• Now, less than half of the species remain in the figwort family – which is now the 36th largest among angiosperms

Question 32

Diagram showing the reclassification of the figwort family (Family Scrophulariaceae)

Answer 32