BB638 Evolution Notes

Course Aims

• Provide an overview of evolutionary facts: history, controversies
• Understand principles of evolution at the molecular level in greater detail
• Discuss research papers (historic breakthroughs and current literature)
• Explore open or unanswered questions in evolution

Semester Structure

First Half of the Semester

• Introductory lecture themes

• What is Natural Selection?

• Classic examples of natural selection

• Mechanics of evolution: how evolution operates

• Pathways of evolution: different ways species can evolve

• Observing evolution in real time: is it possible?

• Concepts of fitness and fitness landscapes

• How to measure evolution

• Artificial selection and directed evolution: can we engineer proteins/organisms in the lab based on evolutionary principles?

• Quiz-1 scheduled on 22-August-2025

Second Half of the Semester

• How did life start on Earth?
• Can we trace all life to a single ancestor?
• How are species related to each other?
• How did multicellularity evolve?
• How did sex evolve?
• What do we know about human evolution?
• Did culture play a role in human evolution?
• Do altruism, homosexuality, and consciousness play a role in how we are evolving?
• Virus evolution: origins of viruses and what COVID-19 taught us about evolution
• Student projects/assignments: typically 3–4 classes

Readings and Textbooks

• Evolution. Nicholas H. Barton, Derek E. G. Briggs, Jonathan A. Elison, Nipam H. Patel. Cold Spring Harbor Laboratory Press, 2007. Available in the library.

• Strickberger's Evolution. Brian K. Hall & Bendikt Hallgrimsson. Jones and Bartlett Publishers, 4th edition, 2007. Available in the library.

  • An excellent book covering all aspects of evolution.

• Sequence - Evolution – Function: Computational Approaches in Comparative Genomics. Eugene V. Koonin and Michael Y. Galperin. NCBI, NLM, NIH, Boston: Kluwer Academic, 2003.

  • Complete textbook available free online. URL: $\url{http://www.ncbi.nlm.nih.gov/books/NBK20260/}$

• On the Origin of Species. Charles Darwin, 1859.

• Biochemical Evolution (Second Edition) and related volumes such as The Pursuit of Perfection. Athel Cornish-Bowden

• The Extended Phenotype (Dawkins) [with an afterword by Daniel Dennett]

• The Selfish Gene (Dawkins)

• The Long Reach of the Gene

• Sapiens, Homo Deus, A Brief History of Humankind, A Brief History of Tomorrow (Yuval Noah Harari)

Reading Strategy and Classroom Expectations

• We will read research papers, reviews, and opinion pieces as we go along.
• Some papers will be current; some historic.
• You are welcome to suggest breakthrough papers that you encounter.
• You are responsible for all course materials.
• You are expected to download suggested papers, read them, and come prepared for discussion.
• A quiz will be conducted only once.

Evaluation and Grading (BB638 / BB647)

• Course Participation & Communication: $20\% / 30\%$

• Quiz-1: $15\% / 30\%$

• Mid-Semester Exam: $15\% / 40\%$

• Course Assignment/Project: $20\% / --$

• End-Semester Exam: $30\% / --$

• Grade mapping (overall):

  • >$95\%$: AA
  • >$85\%$: AB
  • >$75\%$: BB
  • >$65\%$: BC
  • >$55\%$: CC
  • >$45\%$: CD
  • >$35\%$: DD
  • <$35\%$: FF

• Attendance shortage: II

• No request for re-quiz will be entertained

• How can we make this course less of a monologue and more active involvement? Options include activity-based learning, project-based assignments, classic paper/reading-based discussions.

Virus Evolution and Giant Viruses (Key Case Studies)

• Viruses and notable large DNA viruses:
  • Vaccinia Virus (1796): ~$190\,\mathrm{kb}$ genome
  • Pandora virus (2013): ~$2.5\,\mathrm{Mb}$ genome
  • Mimivirus (2003): ~$1.2\,\mathrm{Mb}$ genome
  • HCMV (Human Cytomegalovirus) (1881): ~$230\,\mathrm{kb}$ genome
• Discussion prompts:
  • Are giant viruses alive?
  • Genome evolution of giant viruses
  • How did the complexity in giant viruses arise?
  • Structural biology of giant viruses
• Broader topic: Evolutionary adaptation and engineering of phages for therapeutic use

Historical Perspectives on Life’s Organization

Scala Naturae and the Great Chain of Being

• Aristotle’s scala naturae attempted to assign living things a hierarchical position representing a degree of perfection.
• It was thought to be fixed and reflect the mind of a creator; it portrayed a linear ladder of complexity.
• This view influenced early thinking about evolution and natural order.

Haeckel’s Pedigree

• Traced the lineage of humans downward in a hypothetical pictorial pedigree.
• The idea was that evolution progresses toward more perfect forms.

Interactive and Conceptual Exercises

• Wooclap activity: Labeling graphs related to Darwin, Lamarck, selective vs non-selective models, mutation directing mechanisms, and ancestor scenarios (single vs multiple ancestors).
• Concepts tested included mutation, time, selective pressures, and genealogical relationships.

Lamarck vs Darwin: Inheritance and Hypotheses

Lamarck’s Hypothesis (Theory of Inheritance of Acquired Characteristics)

• Change is driven by what organisms want or need; changes during life to adapt are passed on to offspring.
• Life originated many times; distinct lines without genealogical relationships; complexification over time.
• Transmission of acquired characters; spontaneous formation of new species; multiple origins.
• Lamarck also posited evolution follows a predetermined plan.

Darwin’s Theory (Natural Selection) vs Non-selective Model

• Darwin’s theory emphasizes natural selection acting on variation generated by random processes.

• Non-selective model vs selective model distinctions (which changes are inherited or directed by selection).

• Later in the course, the slide contrasts: spontaneous formation of new species, life originated many times, multiple ancestors vs single ancestor, mutation directing mechanisms vs random mutagenesis.

Epigenetics and Lamarckism

• Epigenetics: study of heritable changes in gene expression that do not involve changes to the DNA sequence.
• Mechanisms include covalent modifications to chromatin, such as DNA methylation and histone modifications.
• Environmental factors can directly influence phenotypic variation and its inheritance through epigenetic marks.
• Epigenetic changes are thought to play a role in development and biological processes and may fine-tune traits rather than drive major evolutionary leaps.
• Epigenetics operates within the framework of evolution by natural selection.

Chromatin Regulation and Gene Accessibility

• Chromatin structure and transcriptional accessibility are regulated by DNA and histone tail modifications.
• Open/relaxed chromatin is transcriptionally active; histone tail acetylation promotes an active state.
• Deacetylation leads to a repressed transcription state.

Histone Modifications and Environmental Influences

• Histone modifications can promote gene activation or repression.
• External factors (metals, pesticides) can affect histone modification pathways or enzymes involved (e.g., HATs and HDACs), often via oxidative stress.
• Dietary factors can interfere with histone acetylation by inhibiting histone acetyltransferase (HAT) or deacetylase (HDAC) activities.

Dutch Famine and Epigenetic Effects

• Prenatal exposure to famine has lasting health effects later in life for offspring.
• In utero exposure linked to higher mortality and various physical/mental health issues in adulthood.
• Source: New York Times coverage of the Dutch Winter Hunger studies (historical epigenetic implications).

Adaptation and The Origin: Principle of Divergence

• Diagrammatic concept illustrating how natural selection can diversify a lineage by occupying different ecological niches.
• Example: moisture requirements in a hypothetical plant genus; divergence leads to a broader occupancy of environments and an increased species count.
• Key takeaway: natural selection can favor traits that reduce competition and promote niche differentiation.
• Reference to historical diagrams (Darwinian adaptation and divergence; Stauffer 1975; Cambridge University Press permission).

Tree of Life and the Scope of Evolutionary Biology

• Evolution as change in properties of populations over time.
• Open-ended question: what is the scope of evolutionary biology?
• Notable quotes:
  • "Nothing in biology makes sense except in the light of evolution" — Theodosius Dobzhansky (1900–1975)
  • "Biology is Evolution!" — Eugene Koonin (1956–)
• Resources include online tools such as Open Tree of Life for exploring phylogenies.

Parthenogenesis and Virgin Births: Case Studies

• Python example (Thelma in Louisville Zoo): parthenogenesis observed in snakes; Thelma produced fertile eggs without male contact.
• Mechanism: polar bodies normally die but can fuse with the egg and trigger cell division, producing clones.
• Parthenogenesis observed in other snakes, birds, and sharks; first documented in the world’s longest snake in this case.
• Komodo dragons are also capable of virgin births.

Virgin Births in Mammals: Media Coverage and Ethics

• Case study: mice produced from two female parents (Kaguya) reported in 2004 media coverage.
• Concepts involved: imprinting and sex-specific gene expression in eggs vs sperm; two female genomes can contribute to viable offspring under certain conditions.
• Ethical and scientific implications include re-examining reproductive biology and potential implications for cloning and human assisted reproduction.

Parthenogenesis, Virgin Births, and Modern Media

• Media discussions (BBC, Daily Mail) cover breakthroughs in virgin births and related genetic mechanisms.
• Important to distinguish sensational claims from peer-reviewed evidence; verify with primary literature.

Microorganisms and Extremophiles: Artemia and Bacteria in Permafrost

• Brine shrimp Artemia salina demonstrate extreme resilience:
  • Can survive desiccation, extreme pH, high salt, UV exposure, and vacuum of space.
  • Anhydrobiosis allows survival under extreme dehydration (up to ~97% water loss).
• Some adult female mayflies have short lifespans (as little as 5 minutes).
• Bacteria in permafrost can remain viable for very long times (claims of up to hundreds of thousands to millions of years under certain conditions).
• Implications for understanding longevity, aging, and the limits of life in extreme environments.

Some Notable Milestones and News in Microbiology

• Reports of extremely old viable bacteria in permafrost; implications for aging, regeneration, and the persistence of life.
• Media coverage of extraordinary results (e.g., long-term viability, potential applications in aging research and astrobiology).

Summary of Key Ideas and Concepts

• Evolution is a unifying framework for biology, linking history, genetics, and ecology.
• Natural selection drives adaptation and diversification, while genetic drift, gene flow, and mutation contribute to variation.
• Epigenetics adds a layer where environment can influence gene expression across generations, though major leaps in evolution are still framed within natural selection.
• Historical concepts (Scala Naturae, Haeckel’s Pedigree) illustrate how scientific thinking has evolved from linear hierarchies to branching phylogenies.
• Parthenogenesis and virgin births show that extreme forms of asexual reproduction exist in vertebrates and invertebrates, raising questions about genetic diversity and reproductive strategies.
• Giant viruses challenge traditional distinctions between cellular life and viruses; their large genomes raise questions about the origins and evolution of complexity.
• The Tree of Life and online phylogenetic tools enable modern synthesis of diverse data types into a cohesive view of life's relationships.

References and Web Resources (examples cited in slides)

• Open Tree of Life: https://tree.opentreeoflife.org/opentree/tree
• NYTimes article on Dutch famine and prenatal epigenetic effects: https://www.nytimes.com/2018/01/31/science/dutch-famine-genes.html
• Darwin, On the Origin of Species (1859)
• Koonin & Galperin, Sequence - Evolution – Function: Computational Approaches in Comparative Genomics, 2003, NCBI/NLM/NIH
• Darwin: On the Origin of Species (Darwin, 1859)
• Dawkins, The Extended Phenotype; The Selfish Gene

Quick Reference: Key Terms and Concepts

• Natural selection, fitness, fitness landscapes
• Artificial selection and directed evolution
• Origin of life and ancestry tracing
• Multicellularity and sex evolution
• Human evolution and culture interactions
• Altruism, homosexuality, consciousness in evolution
• Viral evolution and giant viruses
• Scala naturae; Great Chain of Being
• Lamarckian vs Darwinian inheritance; inheritance of acquired characteristics
• Epigenetics; DNA methylation; histone modification; HAT/HDAC
• Chromatin accessibility; open vs closed chromatin
• Imprinting in mammals
• Parthenogenesis; polar bodies; cloning concepts
• Anhydrobiosis; extremophiles; permafrost bacteria

Notes on Formulas and Quantitative Elements

• Genome sizes (examples):
  • Vaccinia Virus: $190\,\mathrm{kb}$
  • Pandora virus: $2.5\,\mathrm{Mb}$
  • Mimivirus: $1.2\,\mathrm{Mb}$
  • HCMV: $230\,\mathrm{kb}$
• Grade cutoffs (example):
  • $95\%$ -> AA; $85\%$ -> AB; $75\%$ -> BB; $65\%$ -> BC; $55\%$ -> CC; $45\%$ -> CD; $35\%$ -> DD; $<35\%$ -> FF