Chapter 1: Ecology, Evolution, and the Scientific Method

Ecology, Evolution, and the Scientific Method

• Acknowledgment of place and context (from Module introduction): University of Arizona on Indigenous lands; 22 federally recognized tribes in Arizona; Tucson hosts O’odham and Yaqui; emphasis on sustainable relationships with Indigenous communities.

• Course housekeeping: complete pre-quiz on D2L (ungraded but required); Chapter 1 short quiz opens after class and closes Friday 11:59 pm.

Chapter 1 Learning Objectives

• Ecological systems exist in a hierarchical organization.

• Ecological systems are governed by physical and biological principles.

• Different organisms play diverse roles in ecological systems.

• Scientists use several approaches to studying ecology.

• Humans influence ecological systems.

What is Ecology?

• Etymology: Greek oikos = house, logia = study of.

• Definition: the scientific study of the abundance and distribution of organisms in relation to other organisms and environmental conditions.

Hierarchical Organization of Ecological Systems

• Major biological entities (in order):

  • Individual

  • Population

  • Community

  • Ecosystem

  • Biosphere

• These form Ecological Systems at different scales.

Individual

• An organism with a membrane boundary that separates internal processes from the external environment (e.g., bacterium, lizard, human).

• Individuals acquire nutrients and energy, and produce waste.

• Research focus: how adaptations in morphology, physiology, and behavior enable survival in a given environment.

Population

• All members of a species in a given area at a given time (e.g., all bighorn sheep in the Santa Catalina Mountains).

• The unit of evolution through natural selection.

• Research focus: variation in number, density, and demographic composition; how individuals adapt leads to populations evolving.

Community

• Association of interacting populations defined by interactions or the place they live.

• Boundaries are not rigid and are often artificial for research.

• Research focus: diversity and relative abundance of species; species interactions (predation, competition).

Ecosystem

• Assemblage of biotic communities plus abiotic physical and chemical environment (e.g., lake, desert, forest).

• Research focus: energy flow and nutrient cycling through organisms and environment; element pools (C, O, H, N, P).

Biosphere

• Integrated system of all environments and organisms on Earth.

• Teleconnection: distant ecosystems linked by wind, water, and movement of organisms.

• Research focus: global movement of air and water (energy and elements), influencing organism distribution, population dynamics, community composition, and ecosystem productivity.

Chapter 1: Governing Physical Principles in Ecology

• Matter and energy cannot be created or destroyed but can change form.

• Law of Conservation of Matter: mass is conserved.

• First Law of Thermodynamics (Conservation of Energy): energy is conserved.

• Ecological systems gain and lose matter and energy; dynamic steady state occurs when gains balance losses.

• Quantitative framing: Gains = Losses in a dynamic steady state.

• Questions in ecology often focus on how gains and losses occur.

Evolution and Its Mechanisms

• Evolution: a change in the genetic composition of a population over time.

• Mechanisms include:

  • Natural Selection

  • Artificial Selection

  • Genetic Drift (random chance)

• Darwin’s perspective on natural selection highlights how variation can be acted upon by environmental pressures over generations.

Genotype, Phenotype, and Natural Selection

• Genotype: genetic makeup of an organism.

• Phenotype: outward expression of environmental effects on genotype, including morphology, development, and behavior.

• Natural Selection: change in gene frequency in a population through differential survival and reproduction of individuals with certain phenotypes.

• Genetically identical twins illustrate that the environment shapes phenotype despite identical genotypes.

Core Foundations of Evolution by Natural Selection (Four Key Points)

1. Individual variation in traits within a species.

2. Some variations are heritable.

3. More offspring are produced than can survive.

4. Variation in traits leads to differences in fitness (survival and reproduction).

• These components underlie evolution via natural selection; mutations, recombination, and allele transmission drive genetic variation.

Evolution Through Natural Selection: Expanded View

• Consequence: individuals with advantageous random variations tend to leave more copies of their genes to the next generation; those advantageous traits become more common over time.

• The process is not planned or perfect; it operates on existing variation in populations.

• The idea that there are ~3.8 billion years of life and ~10 million extinct events provides context for the long history of evolutionary change.

Genotype–Environment–Phenotype Interactions

• Genotype: genetic makeup of an organism.

• Phenotype: traits expressed, influenced by environmental effects on genotype.

• Environment can alter expression and trait development, affecting fitness.

• Twins show that identical genotypes can yield different phenotypes under different environments.

The Tree of Life and the Domains of Life

• Current Tree of Life includes three domains:

  • Bacteria

  • Archaea

  • Eukarya

• Number of described species exceeds
  >1.6 \times 10^6
  described species.

• The tree reflects major divisions among life forms and their evolutionary relationships.

Prokaryotes and Eukaryotes; Endosymbiosis

• First organisms were prokaryotes: single-celled bacteria and archaea without membrane-bound organelles.

• Prokaryotes can utilize energy sources inaccessible to many other organisms (e.g., nitrogen fixation by certain microbes, hydrogen sulfide utilization).

• Cyanobacteria are capable of photosynthesis.

• Eukaryotes: organisms with distinct organelles; origin linked to endosymbiosis.

• Endosymbiotic theory: a bacterium/archaea engulfed another bacterium; the engulfed cell became mitochondrion, giving rise to mitochondria and eukaryotic cells.

• Endosymbiosis is a mutualistic relationship that increases fitness.

Habitat vs Niche

• Habitat: the place or physical setting where an organism lives; defined by resources (food, cover, water) and environmental conditions (temperature, precipitation).

• Distinctions between habitats are often blurred; habitats can overlap.

• Niche: the range of abiotic and biotic conditions an organism can tolerate; the function and position of a species in its environment, including interactions with other species.

• No two species share exactly the same niche because each has unique phenotypes that determine tolerances.

• Example: different insects feed on different crop species even when crops are grown in the same field.

Ecological Inquiry and the Scientific Method

• Types of ecological inquiry:

  • Observational: maximizes realism.

  • Experimental: maximizes precision.

  • Theoretical: maximizes generality.

• The Scientific Method is an iterative process of gaining knowledge.

• Figure 1.16 (Ecology: The Economy of Nature) outlines the cycle: Observations → Hypothesis/Predictions → Test the hypothesis → Disseminate findings; use manipulative experiments, natural experiments, models; results either support or refute the hypothesis; revise or generate new hypotheses; iterate.

Step-by-Step: How to Test a Hypothesis in Ecology

• Step 1: Observation – Observe the natural world; ask why a phenomenon is observed.

• Step 2: Hypothesis/Predictions – Propose testable mechanisms explaining the pattern; relate back to Step 1.

• Step 3: Test the Hypothesis – Design experiments with proper controls; consider alternative hypotheses and expected outcomes.

• Step 4: Analyze, Interpret, Repeat – Statistically analyze results; interpret; if results contradict hypotheses, revise and retest; then disseminate findings and generate new predictions.

Case Study: Biodiversity Maintenance and Tropical Forests

• Step 2: Hypothesis (Gillett 1962; Janzen 1970; Connell 1971): Negative feedbacks maintain diversity in communities.

• Observations: Gradient in plant diversity across sites:

  • Las Cuevas, Belize: ~50 tree species per hectare; 1800 mm precipitation.

  • Whytham Woods, UK: ~9 tree species total; 640 mm precipitation.

  • Yasuni, Ecuador: ~300 tree species per hectare; 3800 mm precipitation.

• Question: How is biodiversity maintained in communities and why do tropical forests host so many plant species?

Hypothesis and Predictions (Step 2)

• Hypothesis: Plant pests and diseases caused by insects and fungal pathogens are more prevalent in tropical forests; stronger regulation of plant populations by pests/disease in tropical forests leads to greater species diversity at lower latitudes.

• Prediction: If pests and pathogens help maintain diversity, removing insects and pathogens should lower plant diversity.

Step 3: Testing the Hypothesis

• Develop experimental designs with proper controls; consider alternate hypotheses and their expected outcomes.

• Data types include: observations, manipulative experiments, and theoretical models.

Step 4: Analysis, Interpretation, and Repetition

• Repeat tests, refine hypotheses, analyze statistically, and interpret results in light of new knowledge.

• Outcomes contribute to understanding how biodiversity is maintained across ecosystems.

Types of Data and Experimental Findings in Tropical Forests

• Observational vs experimental data: Observational studies provide realism; experiments provide precision.

• Theory: Theoretical approaches aim for generality across systems.

• Case study results (Bagchi, Gallery et al. 2014, Nature):

  • Pathogens and insect herbivores influence rainforest diversity and composition.

  • Experimental manipulations show: removing fungi decreases plant diversity; removing insects increases plant abundance.

  • Diversity measured as effective species number; density measured as seedling abundance; inverse Simpson's dominance represented as 1/D (with 95% CI).

• General implication: Fungi and insects interact to regulate plant communities; the balance between density-independent and density-dependent processes shapes observed diversity.

Tropical vs Temperate Biodiversity Observations

• Example gradient observations at three sites:

  • Las Cuevas, Belize: 50 tree species/ha; 1800 mm precip.

  • Whytham Woods, UK: 9 tree species total; 640 mm precip.

  • Yasuni, Ecuador: 300 tree species/ha; 3800 mm precip.

• These gradients prompt questions about mechanisms that maintain high tropical diversity.

Maya Civilization Collapse and Climate Variability

• Case: Collapse of Classic Maya civilization related to modest reductions in precipitation.

• Site: El Caracol (ca. 1200 BCE–950 CE) with limited river infrastructure in Yucatán.

• Rainfall reduction: estimated 25–40%; civilizations disappeared within <200 years.

• Implication: Climate variability can have rapid, profound impacts on complex human societies and ecological systems.

Human Influence on Ecological Systems

• Major anthropogenic drivers:

  • Habitat destruction

  • Pollution

  • Climate change

  • Overharvesting of resources

• Concept: Human energy and metabolism are interwoven with planetary metabolism; energy flow through human metabolism contributes to global ecological impacts.

Key References and Foundational Figures

• “On the Origin of Species through Natural Selection” (Darwin) – foundational ideas about variation, selection, and adaptation.

• Figure references: Figure 1.16 (Ecology: The Economy of Nature) – depiction of observational-to-synthesis cycle in the scientific method.

• Notable case study: Bagchi, Gallery et al. (2014) Nature – empirical testing of fungal and insect roles in tropical plant diversity.

Recap: Core Concepts to Remember

• Ecological hierarchy: Individual → Population → Community → Ecosystem → Biosphere.

• Matter and energy are conserved; steady-state dynamics balance inputs and outputs.

• Evolution is driven by variation, heritability, differential survival, and reproduction.

• Genotype and environment shape phenotype; natural selection acts on phenotypes.

• Habitat vs niche: space and resources vs functional role and tolerances.

• Biodiversity arises from complex interactions among organisms and their environment; disturbances, pests, pathogens, and consumer dynamics can maintain or reduce diversity.

• Human activities are major drivers of ecological change; climate, land use, and resource extraction have profound ecological and societal consequences.

Quick Mathematical Notes

• Dynamic steady state condition: Gains = Losses \text{Gains} = \text{Losses}

• Conservation laws:

  • Mass conservation: \Delta M = 0

  • Energy conservation: \Delta E = 0

• Diversity metrics mentioned:

  • 95% CI for estimates; Diversity = effective number of species; Inverse Simpson's dominance: \frac{1}{D} with 95% CI

• Time scales:

  • Age of life: 3.8 \times 10^9\ \text{years}

  • Described species: >1.6 \times 10^6

• Key domains of life: \text{Bacteria}, \text{Archaea}, \text{Eukarya}