BIOL 3321 – Evolution - Study Guide – Part 4

Origins of Life

The First Living Things

Ribozymes: Their discovery was important in hypothesizing the origin of life because they can act as catalysts and carry genetic information, suggesting RNA could have been a primary substance for early life.

• Ribozymes are RNA molecules capable of catalyzing specific biochemical reactions, similar to enzymes. This catalytic ability, combined with their capacity to carry genetic information, posits that RNA might have been central in early life forms before the evolution of DNA and proteins.

RNA World: The hypothesis that RNA was a necessary first step; its building blocks were essential for life.

• The RNA world hypothesis suggests that RNA, not DNA, was the primary form of genetic material in early life due to its simpler structure and ability to act as both a carrier of genetic information and a catalyst.

Defining Life

Genotype vs. Phenotype: Genotype is the genetic makeup, while phenotype is the observable characteristics.

• Genotype refers to the genetic constitution of an organism, describing the complete set of genes it possesses. Phenotype, on the other hand, is the observable expression of the genotype, influenced by both genes and environmental factors; it includes physical traits, behavior, and physiological characteristics.

Ability to Reproduce: A core characteristic of life.

• Reproduction is a fundamental attribute of life, enabling organisms to produce offspring and pass on genetic information, ensuring the continuity of species. This can occur through various mechanisms, including sexual and asexual reproduction.

Ability to Evolve: Requires heritable variation and selection.

• Evolution, the change in heritable characteristics of biological populations over successive generations, is driven by mechanisms such as natural selection, genetic drift, mutation, and gene flow. These mechanisms rely on genetic variation within populations to enable adaptation to changing environments.

What makes evolution possible?

RNA World Early Experimental Evidence

Progress towards self-replicating RNA.

• Significant progress has been made in synthesizing RNA molecules that can self-replicate under laboratory conditions. These experiments provide support for the RNA world hypothesis, demonstrating the potential for RNA to independently catalyze its replication without the need for proteins.

Where Did the First Living Things Come From?

Four Issues to Address:

Origin of building blocks.

• How did the basic molecular components of life, such as amino acids, nucleobases, and sugars, arise on early Earth? What were the possible sources—were they synthesized on Earth through geochemical processes, or did they arrive from extraterrestrial sources such as meteorites and comets? Understanding the origin of these building blocks is crucial for understanding how life could have started.
  Polymerization of monomers into polymers.
• What mechanisms facilitated the assembly of simple organic molecules (monomers) into complex polymers like proteins, nucleic acids, and polysaccharides? How did this polymerization occur in the aqueous conditions of early Earth, which typically favor hydrolysis over polymerization? What role did mineral surfaces, or cycles of dehydration and rehydration, play in promoting polymerization?
  Origin of self-replication.
• How did the first self-replicating molecules emerge, capable of copying themselves and passing on genetic information? What were the key steps in the evolution of self-replication, and what role did RNA or other molecules play in this process? Did self-replication arise from a single molecule, or did it require a community of molecules working together? The transition from simple building blocks to self-replicating systems is one of the most challenging questions in origin-of-life research.
  Compartmentalization to form a cell.
• How did the essential biochemical reactions become enclosed within a cellular membrane, creating the first protocells? What mechanisms led to the formation of lipid bilayers or other structures that could encapsulate biological molecules and maintain a stable internal environment? How did these protocells acquire the ability to grow, divide, and evolve? Compartmentalization was a critical step in the origin of life, as it allowed for the concentration of reactants and the development of stable, self-sustaining systems.

Potential Importance of Meteorites:

Murchison Meteorite: Contained amino acids, suggesting extraterrestrial origins of life's building blocks.

• The Murchison meteorite, which fell in Australia in 1969, contained a variety of amino acids, nucleobases, and other organic compounds. Its analysis provided evidence that the building blocks of life could have been synthesized in outer space through photochemical and chemical reactions and delivered to Earth via meteor impacts, contributing to the prebiotic soup.

Amino acid origins.

Earth Before Life: Needed ingredients present.

The Oparin-Haldane Model

Four Steps:2. formation of inorganic compounds under early Earth conditions.

3. Synthesis of simple organic molecules from inorganic ones.
4. Polymerization of organic monomers into polymers.
5. Enclosure of polymers into protocells.

Experiments addressed the potential of the model and tested the conditions for the formation of organic molecules.

• The Miller-Urey experiment, conducted in 1952, simulated early Earth conditions to test the Oparin-Haldane model. By combining gases believed to be present in the early atmosphere (such as methane, ammonia, hydrogen, and water vapor) and subjecting them to electrical sparks (simulating lightning), they successfully produced amino acids, the building blocks of proteins. This experiment provided compelling evidence that organic molecules could form spontaneously from inorganic substances under the conditions of early Earth, although the exact composition of the early atmosphere is still debated.

Finding the Common Ancestor of Extant Organisms

Cell Membranes:

The first cells and experiments on their formation.

Oldest Fossil Cells

Significance of ^{12}C vs. ^{13}C:

Found in old rocks; ^{12}C is preferentially used by living organisms, indicating biological activity.

• Living organisms preferentially use the lighter isotope ^{12}C over the heavier isotope ^{13}C during metabolic processes, leading to a higher ^{12}C:^{13}C ratio in biological materials compared to inorganic substances. This isotopic fractionation results from the kinetic isotope effect, where lighter isotopes react faster than heavier isotopes. The detection of elevated ^{12}C levels in ancient rocks serves as a biosignature, providing evidence of early life forms and their metabolic activities.

LUCA: Last Universal Common Ancestor

Building the Tree of Life:

Importance for discovery of LUCA.

Ribosomes and rRNA:

Significance for constructing the tree of life due to their universal presence and conserved sequences.

• Ribosomes and ribosomal RNA (rRNA) are essential components of all known living cells, playing a central role in protein synthesis. The universality and conserved sequences of rRNA genes make them valuable tools for reconstructing phylogenetic relationships and tracing the evolutionary history of life. By comparing rRNA sequences across different species, scientists can infer the degree of relatedness and construct a comprehensive tree of life, providing insights into the ancestry and diversification of all living organisms. The high conservation of rRNA sequences reflects their critical function in the cell, making them reliable markers for evolutionary studies.

LUCA and Hypotheses of the Evolution of Extant Organisms

Woese’s Universal Gene-Exchange Pool

The Ring of Life Hypothesis

Chronocyte Hypothesis

Viruses: Implications of DNA and their role in evolution.

Evolution and the Fossil Record

What are Fossils?

How are they preserved?

Best preservation:

Amber

Freezing

Permineralization

Natural molds

Trace fossils

Sampling Bias:

Why does it occur in the fossil record?

• Sampling bias in the fossil record occurs because the fossilization process is rare and highly dependent on environmental conditions. Certain environments, such as those with rapid burial and low oxygen levels, are more conducive to fossilization than others. Additionally, some organisms are more likely to be preserved due to their hard body parts (e.g., bones, shells). These factors lead to an incomplete and uneven representation of past life forms in the fossil record, with some groups being overrepresented while others are underrepresented.

Lagerstätte

Fossil sites with exceptional preservation.

• Lagerstätten are sedimentary deposits that exhibit extraordinary features, such as exceptional preservation of fossilized organisms or abundance of fossils, dating from a particular interval of geological time. These sites provide crucial insights into the evolution of life due to the highly detailed and complete fossils they contain.

Life on a Changing Earth

Major Environmental Changes:

Why and when they occurred.

• Major environmental changes on Earth, such as shifts in atmospheric composition, climate fluctuations, and alterations in sea level, have occurred due to a combination of factors, including volcanic activity, tectonic movements, astronomical events, and biological processes. These changes have had profound effects on the distribution and evolution of life, often triggering extinction events and adaptive radiations.

Eras and Periods:

Approximate timing of major events.

• Earth's geological history is divided into a series of eras and periods, each characterized by distinct environmental conditions and biological assemblages. The approximate timing of major events, such as the emergence of new life forms, mass extinctions, and significant geological changes, is determined through radiometric dating and other geological techniques.

Familiarize with historical timeline of Fig. 18.5 (not provided).

Ediacaran Fossils:

Significant diversity during this time.

• The Ediacaran period (approximately 635 to 541 million years ago) was marked by the appearance of the first large, complex multicellular organisms, known as the Ediacaran biota. These fossils exhibit a wide range of unusual morphologies, representing an early experiment in multicellular life. The end of the Ediacaran period is defined by the Cambrian explosion.

Burgess Shale and the Cambrian Explosion:

Diversification of major extant lineages.

• The Cambrian explosion was a period of rapid evolutionary innovation that occurred approximately 541 million years ago. During this time, many of the major animal phyla that exist today appeared in the fossil record for the first time. The Burgess Shale, a Lagerstätte in British Columbia, Canada, provides a remarkable window into this period, preserving a diverse array of soft-bodied organisms that are rarely found elsewhere.

Major Lineage Transitions:

How, why, and when they occurred.

• Major lineage transitions, such as the transition from fish to tetrapods, dinosaurs to birds, and early reptiles to mammals, represent significant shifts in body plan, physiology, and behavior. These transitions occurred through a combination of genetic changes, natural selection, and environmental pressures, often over millions of years. Fossils provide direct evidence of these transitions, while molecular data can help to reconstruct the evolutionary relationships among different groups.

Fish-Tetrapod

Dinosaur-Bird

Mammals

Extinction Events:

Mass vs. Background.

• Extinction events can be classified as either mass extinctions or background extinctions. Mass extinctions are characterized by a widespread and rapid loss of biodiversity, typically affecting a large number of different groups of organisms. Background extinctions, on the other hand, occur continuously over time, representing the normal rate of species turnover. Mass extinctions are often caused by catastrophic events, such as asteroid impacts or volcanic eruptions, while background extinctions are driven by a variety of factors, including competition, disease, and environmental change.

Mass Extinctions:

Why and when they occurred.

• Mass extinctions have occurred several times throughout Earth's history, each resulting in a significant reduction in global biodiversity. These events were caused by a variety of factors, including asteroid impacts, volcanic eruptions, climate change, and sea level fluctuations. The timing of mass extinctions is determined through radiometric dating and other geological techniques.

Evidence supporting them.

• Evidence supporting mass extinctions comes from a variety of sources, including the fossil record, geological data, and geochemical analyses. The fossil record shows a sharp decline in the number of different species at the time of mass extinctions, while geological data provide evidence of the catastrophic events that caused these extinctions. Geochemical analyses can reveal changes in the Earth's atmosphere and oceans that occurred during mass extinctions.

Role of Extinction in Evolution:

Opens up niches for new species.

• Extinction plays a crucial role in evolution by opening up ecological niches for new species to colonize. When existing species disappear, their resources become available to others, allowing for adaptive radiation and the diversification of life. Extinction also drives the evolution of new traits and adaptations, as species must adapt to changing environments in order to survive.

Sixth Mass Extinction:

Why is it occurring?

• The Earth is currently experiencing a sixth mass extinction, driven primarily by human activities. These activities include habitat destruction, pollution, climate change, overexploitation of resources, and the introduction of invasive species. The current rate of extinction is estimated to be 100 to 1,000 times higher than the background rate, and many scientists believe that this crisis poses a serious threat to the future of life on Earth.

Adaptive Radiation

What are the causes and consequences?

• Adaptive radiation is an evolutionary process in which a single lineage diversifies rapidly into many different forms, each adapted to a specific ecological niche. Adaptive radiation is often triggered by the availability of new resources, the absence of competition, or the evolution of a key innovation. The consequences of adaptive radiation include an increase in biodiversity, the evolution of new traits and adaptations, and the colonization of new environments.

Phylogeny and Fossils

Does molecular and fossil evidence always agree on timing of events? Why?

• Molecular and fossil evidence do not always agree on the timing of evolutionary events. Fossil evidence provides direct evidence of past life forms, but it is often incomplete and subject to sampling bias. Molecular evidence, on the other hand, is based on the analysis of DNA and RNA sequences, which can provide insights into the evolutionary relationships among different groups, but it is also subject to interpretation and uncertainty. Discrepancies between molecular and fossil evidence can arise due to incomplete fossil records, differences in mutation rates among different groups, and the difficulty of calibrating molecular clocks.

Case Studies:

Timing of Cambrian Explosion.

• The timing of the Cambrian explosion is a subject of ongoing debate, with molecular and fossil evidence providing different estimates. Fossil evidence suggests that the Cambrian explosion occurred over a relatively short period of time, while molecular evidence suggests that the diversification of animals may have begun much earlier.

Diversification of Mammals.

• The diversification of mammals is another example of an evolutionary event where molecular and fossil evidence do not always agree. Fossil evidence suggests that mammals began to diversify shortly after the extinction of the dinosaurs, while molecular evidence suggests that the diversification of mammals may have begun much earlier.

Human Evolution

Beginnings

What is the evidence?

• The evidence for human evolution comes from a variety of sources, including fossils, genetics, archaeology, and comparative anatomy. Fossils provide direct evidence of our extinct ancestors, while genetic data reveal the evolutionary relationships among different human populations. Archaeological evidence provides insights into the behavior and culture of early humans, while comparative anatomy reveals similarities and differences between humans and other primates.

Phylogeny of the Apes

Synapomorphies for the Clade:

Shared derived traits.

• Synapomorphies are shared derived traits that are unique to a particular group of organisms and their common ancestor. These traits provide evidence of evolutionary relationships and can be used to construct phylogenetic trees.

Evidence for the Clade:

Molecular

Morphology

The African Great Apes (Humans + Chimps + Gorillas)

Synapomorphies

Conflicting Molecular Evidence?

Overall Genetic and Morphological Evidence

Age of Divergence Times Among the Apes

Recent Ancestry and Hominin Diversification

The Fossil Evidence

What do skulls tell us?

What does the skeleton tell us?

The Major Lineages (Paranthropus, Australopithecus, Homo)

General timeline and morphological changes

Diversification, co-existing lineages, dispersal

Homo Sapiens – Origins

Evidence of unique lineage

Immigration Models (African Replacement vs. Multiregional Evolution)

What does the data tell us?

Timing:

Molecular and fossil evidence

Population genetics - Allele frequencies and LD (linkage disequilibrium