Bio 466 - Ch 2 Cont. Lecture Notes

Evolutionary Relationships and Ancestry

Littorina Sea Snails

• Species Classification: 8 species of Littorina sea snails:

  • L. brevicula

  • L. scutulata

  • L. littorea (e.g., common periwinkle found on rocky shores)

  • L. obtusata

  • L. mandshurica

  • L. plena

  • L. squalida

  • L. fabalis

• Query Addressed: Exploring evolutionary relationships among these species to understand their divergence and adaptation.

Evidence for Common Ancestry

• Key Evidence Type: Pseudogene homology used to reconstruct evolutionary relationships among species.

  • Pseudogenes are non-functional DNA sequences that resemble functional genes but have lost their protein-coding ability due to mutations. Sharing similar pseudogenes indicates a common ancestor.

Relationships among Primates

• Historical Context: 65 million years ago, a significant divergence occurred among early primates, leading to the distinct groups we see today.

• Groups Identified:

  • Prosimians (e.g., Lemurs, Lorises)

  • Monkeys

  • New World Monkeys (e.g., Capuchin monkey, Spider monkey - found in Central and South America, characterized by prehensile tails)

  • Old World Monkeys (e.g., Rhesus monkey, Baboon - found in Africa and Asia, no prehensile tails)

  • Tarsiers

  • Apes

  • Lesser Apes (e.g., Gibbons, Siamangs - known for brachiation)

  • Great Apes (e.g., Orangutans, Gorillas, Chimpanzees, Bonobos, Humans)

• Evolutionary Timeline:

  • Lemurs and Lorises: Their evolutionary lineage began diverging from other primates approximately 65 million years ago, representing some of the earliest primate branches.

  • Last Common Ancestor of Monkeys and Apes: Lived approximately 25 million years ago, marking a pivotal split between these two major primate groups.

  • Last Common Ancestor of Humans and Chimpanzees: Estimated living periods between 8 and 6 million years ago (remains not yet discovered), this ancestor is crucial for understanding hominid evolution.

• Specific Examples of Monkeys:

  • Capuchin monkey (known for tool use)

  • Rhesus monkey (commonly used in scientific research)

• Hierarchy of Primates Today:

  • Humans share a very recent common lineage with Chimpanzees and Bonobos.

  • Distinct lineages for Orangutan, Gorilla, and other Great Apes emphasize their unique evolutionary paths.

Insights on Pseudogenes

• Tip #1: Older pseudogenes are present in more lineages because they arose earlier in evolutionary history and were passed down to a wider array of descendant species; younger pseudogenes occur in fewer lineages.

• Tip #2: Closely related species share more similar pseudogene collections because they diverged more recently from a common ancestor, inheriting a similar set of non-functional genes.

• Tip #3: More recently evolved taxa exhibit a greater number of shared pseudogenes compared to older taxa, reflecting continuous gene duplication and inactivation events over time.

Coding of Pseudogene Patterns for Littorina Species

• Pseudogene Presence: Notation of presence and absence of pseudogenes among Littorina species marked as YAY (present) and BOO (absent).

• Species and Pseudogenes:

  • A: YAY

  • B: BOO

  • C: YAY

  • D: YAY

  • E: YAY

  • F: YAY

  • G: NAY

  • H: YAY

Phylogenetic Analysis via mtDNA

• Analysis Basis: Phylogenetic trees constructed using partial mitochondrial DNA (mtDNA) sequences referenced from Lee et al. 2018. mtDNA is particularly useful due to its maternal inheritance, lack of recombination, and relatively fast mutation rate, making it suitable for tracking recent evolutionary divergences.

• Photos Cited: Rolán-Alvarez et al. 2015.

• Terminology: MRCA refers to the Most Recent Common Ancestor, the latest individual from which all organisms in a group are directly descended.

Evidence Types for Evolution

1. Microevolution - Small-scale changes in allele frequencies within a population over a few generations (e.g., the development of antibiotic resistance in bacteria).

2. Speciation - The formation of new and distinct species through evolutionary processes, often involving reproductive isolation (e.g., the divergence of finch species on the Galápagos Islands).

3. Macroevolution - Large-scale evolutionary changes, usually over geological time, leading to the formation of new taxonomic groups (e.g., the evolution of birds from dinosaurs).

4. Common Ancestry - All life traces back to shared ancestors, supported by homologous structures, genetic similarities, and fossil records (e.g., the pentadactyl limb structure found in vertebrates like humans, bats, and whales).

• Patterns of Change: Increased time for significant changes in the evolutionary record is evident with geological processes, illustrating that profound evolutionary shifts require vast timescales.

Dating the Earth

• Technique Types:

  • Relative Dating: Based on the position of sediment layers (stratigraphy). Older layers are generally found beneath younger layers (Law of Superposition). This method determines if one fossil or rock is older or younger than another, but not its exact age.

  • Absolute Dating: Involves measuring radioactive decay rates of unstable isotopes within rocks or fossils to determine an exact numerical age (e.g., using Carbon-14 dating for organic materials).

  • Molecular Dating: Analyzing neutral genetic variation among species and assuming a constant rate of mutation (molecular clock) to estimate divergence times between lineages.

• Goal of Dating: Estimating the age of the Earth and geological events with the presumption of consistent rates in geological processes (e.g., sedimentation, radioactive decay) over time.

Geological Time Scale - Layers and Fossils

• Geologic Strata: Layers of rock that contain fossils, aiding in defining periods with shared geological and biological characteristics. Each stratum can represent a distinct time period.

• Major Evolutionary Events:

  • Hadean Era: (approx. $4.6 - 4.0$ billion years ago) Formation of Earth; conditions were extremely hot with volcanic activity.

  • Archean Era: (approx. $4.0 - 2.5$ billion years ago) Oldest rocks begin to form; formation of Earth's crust; appearance of the earliest life forms (prokaryotes).

  • Proterozoic Era: (approx. $2.5$ billion - $541$ million years ago) Life begins in seas, including the evolution of eukaryotes and early multicellular organisms.

  • Paleozoic Era: (approx. $541 - 252$ million years ago) Evolution of early life forms from marine invertebrates to amphibians and reptiles; major diversification of life (Cambrian Explosion).

  • Mesozoic Era: (approx. $252 - 66$ million years ago) Rise of dinosaurs and first mammals; Pangea breaks apart (known as the "Age of Reptiles").

  • Cenozoic Era: (approx. $66$ million years ago - present) Dominance of mammals and extensive human evolution after the extinction of dinosaurs (known as the "Age of Mammals").

Radiometric Dating Explained

• Principle: Measurement of the parent isotope to daughter isotope ratio within a sample. Parent isotopes are unstable and decay into stable daughter isotopes at a predictable rate.

• Decay Process: Half-lives are fundamental to understanding how long it takes for half of the parent isotopes in a sample to decay into daughter isotopes. For example, Carbon-14 has a half-life of $5,730$ years.

• Graphical Representation: Depicting the stages from $100\%$ parent isotope through various stages of decay (e.g., $50\%$ parent after one half-life, $25\%$ parent after two half-lives) to measure absolute age. This allows for precise calculations of how many half-lives have passed.

Calibration of Molecular Clocks

• Benchmarking Common Ancestors: Understanding how long ago common ancestors lived (often through fossil evidence) aids in calibrating molecular clocks, providing a reference point for mutation rates.

• Addressing Fossil Gaps: Molecular clocks offer a way to infer the timing of divergences among species even in the absence of a complete fossil record, by analyzing genetic differences.

• Genetic Marker Evolution Rates: Knowing the evolution rates of specific genetic markers (e.g., genes for ribosomal RNA or mitochondrial DNA) allows the calculation of divergence time based on the observed genetic differences between groups. The greater the genetic difference, the longer the time since divergence (assuming a constant mutation rate).