17.10 Evolutionary Relationships

1. DNA Comparisons and Evolutionary Relationships

1.1. DNA Structure and Function

• DNA (Deoxyribonucleic Acid): The molecule that carries genetic information in living organisms.
• Nucleotides: Building blocks of DNA, comprising a phosphate group, deoxyribose sugar, and one of four nitrogenous bases (adenine [A], thymine [T], cytosine [C], guanine [G]).
• Double Helix: DNA’s structure, where two strands coil around each other, with base pairing (A-T and C-G).

1.2. Similarities in DNA Sequences

• Genetic Similarity: The degree of similarity in nucleotide sequences between different species indicates their evolutionary relatedness.
  • High Similarity: Suggests a recent common ancestor.
  • Low Similarity: Implies a more distant common ancestor.

1.3. Measuring DNA Similarity

• Sequence Alignment: Comparing DNA sequences to identify regions of similarity.
• Percentage Identity: Calculating the percentage of identical nucleotides over a specific DNA region.

1.4. Implications of DNA Comparisons

• Phylogenetic Relationships: Understanding how species are related through evolutionary history.
• Divergence Time Estimates: Assessing how long ago two species split from a common ancestor based on genetic differences.

2. Types of DNA Used in Analysis

2.1. Nuclear DNA

• Location: Resides in the cell nucleus.
• Content: Contains the majority of an organism’s genetic information, organized into chromosomes.
• Usage: Ideal for comparing overall genetic makeup between species.

2.2. Mitochondrial DNA (mtDNA)

• Location: Found in mitochondria, the energy-producing organelles in cells.
• Inheritance: Maternally inherited; passed from mother to offspring without recombination.
• Mutation Rate: Higher than nuclear DNA, accumulating mutations approximately every 25,000 years.
• Applications:
  • Tracing Maternal Lineage: Useful for studying maternal ancestry.
  • Human Evolution Studies: Identifying relationships between modern humans and ancient hominins.

2.3. Chloroplast DNA (cpDNA) – (Specific to Plants)

• Location: Found in chloroplasts, the photosynthetic organelles in plant cells.
• Structure: Typically circular, similar to mitochondrial DNA.
• Usage: Studying plant evolution and phylogenetic relationships.

3. Applications in Human Evolution

3.1. Human and Chimpanzee DNA Comparisons

• Genetic Similarity: Humans share approximately 98% of their DNA with chimpanzees.
• Implication: Indicates a recent common ancestor, estimated to have lived around 6-7 million years ago.

3.2. Human-Neanderthal DNA Comparisons

• Genetic Overlap: Modern humans share a significant portion of their DNA with Neanderthals.
• Divergence Time: Evidence suggests that humans and Neanderthals diverged approximately 500,000 years ago.
• Interbreeding Evidence: Genetic data indicates occasional interbreeding between Homo sapiens and Neanderthals.

3.3. Mitochondrial Eve

• Definition: The most recent common matrilineal ancestor of all living humans.
• Estimation: Lived in Africa approximately 150,000–200,000 years ago.
• Significance: Supports the “Out of Africa” theory of human evolution.

3.4. Y-Chromosome Adam

• Definition: The most recent common patrilineal ancestor of all living humans.
• Comparison with Mitochondrial Eve: Y-Chromosome Adam and Mitochondrial Eve did not necessarily live at the same time.

4. Mitochondrial DNA (mtDNA) and Evolutionary Studies

4.1. Inheritance of mtDNA

• Maternal Inheritance: mtDNA is inherited exclusively from the mother, as sperm mitochondria do not typically enter the egg during fertilization.
• No Recombination: mtDNA does not undergo recombination, making it a stable marker for tracing lineage.

4.2. Mutation Rate and the Molecular Clock

• Higher Mutation Rate: mtDNA accumulates mutations faster than nuclear DNA.
• Molecular Clock Hypothesis: Assumes a relatively constant mutation rate over time, allowing scientists to estimate divergence times between species.
• Calibration: Molecular clock estimates are refined using fossil records and known divergence events.

4.3. Tracking Human Migration

• Population Variations: Different populations have distinct mtDNA haplogroups.
• Migration Patterns: By analyzing mtDNA variations, scientists can trace human migrations and determine origin points.
• Out of Africa: Genetic evidence from mtDNA supports the theory that modern humans originated in Africa and dispersed globally.

5. Constructing Evolutionary Trees (Phylogenetic Trees)

5.1. Purpose of Phylogenetic Trees

• Visualization: Illustrate the evolutionary relationships among various species or groups.
• Common Ancestor: All branches of the tree trace back to a single common ancestor.
• Divergence Points: Points where lineages split, indicating speciation events.

5.2. Building Phylogenetic Trees Using DNA Data

• Data Collection: Obtain DNA sequences from the species of interest.
• Sequence Alignment: Align sequences to identify similarities and differences.
• Tree Construction Methods:
  • Cladistics: Groups organisms based on shared derived characteristics.
  • Distance-Matrix Methods: Calculate genetic distances and build trees based on these distances.
  • Maximum Parsimony: Select the tree with the least number of evolutionary changes.
  • Maximum Likelihood: Choose the tree that is most probable given the data and a model of evolution.

5.3. Interpretation of Phylogenetic Trees

• Branch Lengths: Represent genetic differences; longer branches indicate more differences.
• Clades: Groups consisting of an ancestor and all its descendants.
• Monophyletic Groups: Clades that include all descendants of a common ancestor.

5.4. Example: Lizard Family Tree

• Lineage Division:
  • Primitive Lineage: Leads to the Sphenodon genus (e.g., tuatara in New Zealand).
  • Other Genera: Branches lead to Heloderma (e.g., Gila monster), Agama, Chamaleo (chameleons), Oplurus, and Anolis.
• Implications: Demonstrates evolutionary divergence and specialization within lizards.

6. Case Study: Anole Lizards in the Caribbean

6.1. Genetic Isolation and Speciation

• Allopatric Speciation: Occurs when populations are geographically separated, preventing gene flow.
• Caribbean Anoles: Genetic drift and founder effects have led to distinct phenotypes in isolated island populations.

6.2. mtDNA Analysis in Anoles

• Sequence Comparison: mtDNA sequences reveal genetic differences among anole species.
• Evolutionary Paths: Isolated populations on different islands follow unique evolutionary trajectories.

6.3. Colonization Events

• Multiple Colonizations: Species like Anolis porcatus have colonized different islands in separate events.
• Genetic Similarity: Anolis brunneus, A. smaragdinus, and A. carolinensis show varying degrees of mtDNA similarity with A. porcatus, indicating separate colonization histories.

6.4. Example of mtDNA Comparison Results

• Table A (Hypothetical): Displays sequence differences among anole species.
  • Smaller Differences: Between A. smaragdinus and A. porcatus suggest a recent common ancestor.
  • Larger Differences: Between A. carolinensis and A. brunneus imply an older divergence.

7. Key Terms and Definitions

• Evolutionary Tree (Phylogenetic Tree): A diagram illustrating the evolutionary relationships among species based on genetic or morphological data.
• Molecular Clock: A method that uses the mutation rate of biomolecules to deduce the time in prehistory when two species diverged.
• Mitochondrial DNA (mtDNA): Genetic material found in mitochondria, inherited maternally and used in tracing ancestry and evolutionary relationships.
• Mitochondrial Eve: The most recent common matrilineal ancestor of all living humans, believed to have lived in Africa around 150,000–200,000 years ago.
• Allopatric Speciation: The process by which new species evolve in geographic isolation from their ancestral population.
• Cladistics: A method of classifying species based on common ancestry and branching from a single root.
• Haplotype: A group of genes within an organism that was inherited together from a single parent.
• Genetic Drift: Random changes in allele frequencies within a population, which can lead to significant genetic differentiation over time.
• Founder Effect: The loss of genetic variation that occurs when a new population is established by a very small number of individuals from a larger population.
• Haplotype Networks: Graphical representations that show the relationships between different haplotypes within a species or group.

8. Techniques in DNA Analysis

8.1. Polymerase Chain Reaction (PCR)

• Purpose: Amplify specific DNA segments to obtain sufficient quantities for analysis.
• Process: Denaturation, annealing, and extension cycles.
• Applications: Identifying genetic similarities, detecting mutations, forensic analysis.

8.2. DNA Sequencing

• Methods: Sanger sequencing, Next-Generation Sequencing (NGS).
• Purpose: Determine the exact sequence of nucleotides in a DNA fragment.
• Applications: Comparative genomics, evolutionary studies, medical diagnostics.

8.3. Restriction Fragment Length Polymorphism (RFLP)

• Process: Use of restriction enzymes to cut DNA at specific sequences, resulting in fragments of varying lengths.
• Analysis: Comparing fragment patterns to identify genetic differences.
• Applications: Genetic mapping, paternity testing, disease diagnosis.

8.4. Single Nucleotide Polymorphism (SNP) Analysis

• Definition: Variation at a single nucleotide position in the DNA sequence among individuals.
• Usage: Genome-wide association studies, population genetics, personalized medicine.

9. Limitations and Considerations in Molecular Evidence

9.1. Incomplete Lineage Sorting

• Definition: When gene trees do not match species trees due to ancestral genetic polymorphism.
• Implications: Can complicate the interpretation of phylogenetic relationships.

9.2. Horizontal Gene Transfer

• Definition: Transfer of genetic material between unrelated species.
• Impact: Particularly relevant in microorganisms; can obscure evolutionary relationships.

9.3. Mutation Rate Variability

• Issue: Assumed constant in the molecular clock hypothesis; however, mutation rates can vary among lineages and over time.
• Solution: Use calibration with fossil data and multiple genetic markers to improve accuracy.

9.4. Incomplete Fossil Record

• Problem: Gaps in the fossil record can limit the ability to calibrate molecular clocks and validate phylogenetic trees.
• Approach: Integrate multiple lines of evidence, including morphological and molecular data.