4.6.5 Investigating Diversity

• A species can be defined as a group of organisms that are able to interbreed and produce fertile offspring
• Members of one species are reproductively isolated from members of another species
• In reality, it is quite hard to define ‘species’ and the determination of whether two organisms belong to the same species is dependent on investigation
• Individuals of the same species have similar behavioural, morphological (structural) and physiological (metabolic) features
• A common example used to illustrate this concept are mules; the infertile offspring produced when a male donkey and a female horse mate

Genetic isolation

• Two groups, when reproductively isolated from each other, become genetically isolated
• If two groups are no longer reproducing with each other, then they do not interchange genes with each other in the production of offspring
• Changes that occur in the allele frequencies of each group are not shared, so they evolve independently of each other which can lead to the formation of two groups that are no longer successfully able to interbreed

Genetic diversity

• Genetic diversity is the number of different alleles of genes
• Genetic diversity within and between species can be measured by looking at the following:
  • Displays of measurable characteristics
  • The nucleotide base sequence of DNA
  • The nucleotide base sequence of mRNA
  • The amino acid sequence of proteins

Measurable and Observable Characteristics

• Comparing characteristics of different individuals is usually the quickest but least reliable form of determining genetic diversity
  • The genetic differences between individuals can only be implied using this technique

• This method was used successfully to classify organisms into the taxonomic hierarchy for hundreds of years before DNA sequencing
• Characteristics that could be measured include:
  • Number of legs
  • Number of seeds in a berry
  • Number of petals
  • Number of leaf indentations

• Characteristics that could be observed:
  • Colour
  • Patterns on fur/scales/feathers
  • Habitat
  • Presence of hair/wings/fins

• The problem with this method is that it is not precise enough if only one characteristic is looked at, for example, many animals have four legs
• It can be useful if a species has unique characteristics such as tigers
• Often if two species cannot be distinguished from their observable characteristics, measurable characteristics will give a better understanding of the similarities and differences

DNA Analysis and Comparison

• DNA sequence analysis has replaced using characteristics as a means of determining genetic diversity
• DNA is extracted from the nuclei of cells taken from an organism
  • DNA can be extracted from blood or skin samples from living organisms or from fossils

• The extracted DNA is processed, analysed and the base sequence is obtained
• The base sequence is compared to that of other organisms to determine evolutionary relationships
  • The more similarities there are in the DNA base sequence, the more closely related (in that the less distant the species separation) members of different species are
  • Computers can be used to highlight matches between the DNA samples

• In 2005, the chimpanzee genome was sequenced, and when compared to the human genome it was discovered that humans and chimpanzees share almost 99% of their DNA sequences, making them our closest living relatives
  • In 2012, the sequencing of the bonobo genome also revealed that humans and bonobos also share 98% of their genome (with slight differences to the differences seen in chimpanzees)

• The differences between the nucleotide sequences (DNA) of different individuals can provide a lot of information:
  • The more similar the sequence the more closely related the species are
  • Two groups of organisms with very similar DNA will have separated into separate species more recently than two groups with less similarity in their DNA sequences

• DNA sequence analysis and comparison can also be used to create family trees that show the evolutionary relationships between species

• When analysing DNA from the mitochondria is is important to remember that:
  • A zygote only contains the mitochondria of the egg and none from the sperm so only maternal mitochondrial DNA is present in a zygote
  • There is no crossing over that occurs in mtDNA so the base sequence can only change by mutation

• The lack of crossing over in mtDNA has allowed scientists to research the origins of species, genetic drift and migration events
• It has even been possible to estimate how long ago the first human lived and where
  • Mitochondrial Eve is thought to have lived in Africa ~200,000 years ago
  • The estimation of this date relies on the molecular clock theory which assumes there is a constant rate of mutation over time
  • The greater the number of differences there are between nucleotide sequences, the longer ago the common ancestor of both species existed
  • The molecular clock is calibrated by using fossils and carbon dating
  • A fossil of a known species is carbon-dated to estimate how long ago that organism lived
  • This mtDNA of this species is then used as a baseline for comparison with the mtDNA of other species

• Although for your exams you should say that only maternal mitochondrial DNA can be passed on or inherited by the zygote, recent research suggests that paternal mDNA may also be present in zygotes

mRNA Analysis and Comparison

• mRNA is often easier to isolate from cells than DNA as it is found in the cytoplasm and there are usually multiple copies of the same mRNA
• Collected mRNA from an individual can be used as a template to produce cDNA (complementary DNA)
  • The first strand of cDNA produced is complementary to the mRNA (the same as the template strand of the DNA)
  • The first strand is then used to produce a second cDNA strand which is the same as the coding strand of DNA
  • Unlike the original DNA in the nucleus, the cDNA contains only the coding regions of the gene (exons) and no introns

• It is important to compare the same mRNA between samples
  • mRNA for a known, universal protein is often used and compared, for example, cytochrome-c (from the electron transport chain)
  • Primers can be used that bind to specific sequences

Amino Acid Sequence Analysis and Comparison

• Similarly to mRNA, proteins are often easier to isolate from the cell than DNA
• The sequence of amino acids of the same protein can be compared between individuals
  • The protein chosen must be found in all the individuals/species being compared eg. haemoglobin is used for many animals

• Amino acid sequences can also be determined from mRNA sequencing if the 'frame' is known (the correct start codon is determined)
• Amino acid sequences of proteins evolve much slower than DNA, especially if the protein is of high importance
  • Therefore, it is likely that closely related species (eg. humans and chimpanzees) will have the same amino acid sequence even though these species split from their common ancestors millions of years ago
  • This is because the shape, and therefore function and specificity, of a protein is determined by the amino acid sequence as the position of amino acids determines the intermolecular forces between R groups