BIOL380 Lecture Notes I   (Material covered before the first test)

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Evolution - look up in a dictionary

• simplest - change (Greek for unfold)
• biological - descent with modification >150 yrs. (descent: grandpa=>pa=>me=>kids; modification: they are different)
• modern - a change in allele frequencies (~ same definition but more specific; allele - an alternative form of a gene, a piece of DNA that determines some character)
• evolution is a population level phenomenon (one organism does not undergo evolution by definition, because alleles don't change.

1. understand the nature of biological change; understand the unique history of life in Earth (~ 1.5 million species)
2. test hypotheses about the mechanisms we think are responsible for biological evolution
3. account for variation and diversity
4. understand the pattern of relationships to formulate and test hypotheses of relationships

Traditions from Greeks -

Plato (web) - philosophical perspective called "idealism" ("essentialism"). The concept of "ideal" is very important. In the world of abstract ideas, there was a perfect form of everything (ideal). Here, on Earth, we see imperfect mimics of ideal forms; any variation we see on Earth is just an imperfect representation => variation is of no consequence.

"Animate cosmos" - everything works as one unit on Earth, tied together in a living harmony; change in the world is bad.

Point: from Plato's perspective evolution is not possible.

Aristotle (web) - father of biology, was influenced by Plato's ideas to some degree. Concluded that the groups of organisms were very well defined, might be some variation, but it is a "noise in the system" because ideal exists. Therefore, living organisms are fixed and unchanging. They neither could vanish (extinct) nor be created.

Aristotle proposed a directionality to life (there were lower forms and higher forms), was able to arrange them in some kind of sequence and developed the Scale of Nature (the great chain of being) - H/A.

So, the concept is still prevalent - that there is a change and life is dynamic.

Aristotle, Plato, other philosophers => christian philosophy, which greatly influenced science and biology. God created the universe, it happened relatively recently; they extended the Scale of Nature up one step to give some room for god.

The christian philosophy supports that order is much superior to disorder. God could not make mistakes. From here a school called natural theology has appeared (god started the world).

Natural Theology

• you can better understand god by going out and studying nature
• assumption that there is no conflict between science and god
• scientists were out to get better grasp of what was the nature
• to many questions, simple answers were already known - god created it. Natural theology was championed by Reverend John Ray (1628-1705, web). He wrote a book called "The Wisdom of God Manifested in the Works of Creation."
• a lot of info to fill in gaps of great chain. Also getting notions that lead to medicine. This all provided the basis for the science given their contemporary tools.

People started to wonder about the Earth's age. Bishop of Usher has calculated that the Earth was created by God in the year 4004 BC ( now - 4.5 billion years old). Translates into a concept that the Earth is young (which still influence thinking of a lot of people). But there were people who thought differently. They question Natural Theology. (Age of reason, age of enlightment). Next, happens a shift to the rise of

Empirical Science

It's a very different perspective. Notion that there are natural explanations for natural phenomena (as opposed to supernatural explanations). Copernicus, Kepler, Newton, Galileo, Descartes - there is an overlap with natural theology. Shift first occurs in physical science; biologists still are going with natural theology.

Geology - 1700's - 1800's - some geologists conclude that the Earth is much older then previously thought age is 10000-100000 years.

1779 - Buffon (web) published a work that age is 168000 years. In an unpublished work he hypothesized 500000 years. He wrote Histoire Naturelle - Natural History, where he toyed with the idea (but rejected) of common ancestry for organisms. Knew that variation exists, and speculated that it's possible to produce new varieties from this variation. Back in this time, people are starting to think in some new light in the area of biology.

Geologists have 2 schools of thought:

1. catastrophists - glaciations, floods - very violent and widespread catastrophes (sometimes involving the entire Earth) - some thought of multiple creations. Fits nicely with christian and judaism (flood). Some thought of a progress - fits with scala natura (H/A table 1)
2. uniformitarianists - do not disagree that there are catastrophes, but disagree in the causes of explanations of these geological events (2a vs. 2b) (5a vs. 5b) (1a vs. 1b vs. 1c) They say no data to suggest that at one time the entire Earth was involved in a catastrophe. Charles Lyelle (web) - uniformitarianist (important and influential in 1797-1875) - his ideas greatly influenced Darwin.

Comparative anatomy - 16 - 17 00's - empires ship strange animals from all over the world - but they look alike! But the notion of the biological evolution is rejected - because there was no mechanism to explain how these changes could occur - people were not willing to accept the idea of change and evolution. But it was changed by

Jean Baptiste Lamarck (1744-1829, web) - first to really promote the notion of biological evolution. "The father of evolution" - in front of French Museum of Natural History in Paris. Proposed a mechanism to account for biological evolution. The mechanism is called the inheritance of acquired characteristics. 2 major causes of biological evolution:

1. innate power or innate need which provided for acquisition of greater complexity (presumably came from god)
2. a capacity to react to special conditions in the environment

1. a change in environment results in a change in the "needs" of the organism
2. it must change to satisfy the new needs
3. change will occur via use or disuse of body parts. This causes them to get bigger or smaller. But a lot of other people knew it; Lamarck had a mechanism to explain how it happens. (H/A on giraffes).

• different factors from different parts of a body travell via bloof - collect in germ cells (top) - not correct, but that's how Lamarck thought. But he wasn't a "moron" - he had a hypothesis which was to explain the phenomenon (variability) which he said was true.

Lamarck's mechanism was rejected untill 1858 - notion of bioevolution comes into play again. Proposed by Charles Darwin (1809-1882, web) + Alfred Russell Wallace (1823-1913, web) - independently develop the idea of bioevolution via Natural Selection. NS is not new, the "via" is -> it's a mechanism; nothing more or less than differential survival for the sake of reproduction. Back to giraffes (bottom).

Comparing bottom to top - there is no inner need, it's a simple natural phenomenon. Lamarck - level of individual. Darwin - level of population.

Darwin:

• organisms evolved

• primary mechanism is Natural Selection
• common ancestry + descent among organisms
• explain biodiversity, miltiplication of species
• changes occurred gradually, over time

Se table 2

Evolutionary (Modern) Synthesis (Neo-Darwinian Theology)

1. population-level thinking becomes emphasized
2. population genetics developed
3. coupling Mendelian genetics with Darwinian evolution
4. population genetics involved mathematical models which described and predicted the behavior of genes in populations
5. systematists - development of biological species concept, importance of genetic variation is further emphasized - variation is a norm and not an exception, exists at phenotypic and genotypic levels
6. paleontology, study of fossil record - coupled with Dawinian or neo-Darwinian ideas.

Text pp. 26-28 (20 points)

Summary of the six major components of the modern synthesis (what happened conceptually):

1. Populations contain variation.
2. Variation arises by random (not directed) mutations and recombinations.
3. Evolutionary factors such as genetic drift and natural selection can alter allele frequencies ( + mutations, gene flow, segregation-distortion).
4. Changes are slight and generally occur gradually.
5. Diversification between populations occurs via speciation (cladogenesis).
6. Speciation occurs primarily through reproductive isolation.

Additionally, changes in ideas about genetics and inheritance. Example: McClintock with jumping genes. Jumping genes are the ones that move from one non-homologous chromosome to another one (via plasmids); even sometimes between organisms of different species.

Summary see H/A.

Part II Chapter 5

Also, pp. 122-123 (read and know it)

Biodiversity within and among species. Number of known, unknown, and previously existed species.

Systematics

Systematics - study of biodiversity, explains the history of life on planet, formulate and test hypotheses of relationships.

Taxonomy - study of biological nomenclature, naming of organisms, their assignment to a taxon (taxa). It's about how to name a new organism (boring) - there are rules, lots of Latin names, complicated.

Classifiction - the practice of taxonomy; the way by which we arrange the organisms into a hirearchy.

Dr. Matson: vertebrates, pond scum, plants; Ecologists: plants with different subcategories. Today, we use a standard Linnean hierarchy (a modified form of it). Standard mean of communication. We make a classification that tells us something about evolution. There are seven major categories: kingdom, phylum, class, order, family, genus, species (keep people clear of fuzzy green snakes). Classifications can and do change the kmowledge of living organisms changes. Before thought - 5 kingdoms, now - 7 kingdoms.

The lower you go down on KPOFGS, the more variability.

Systematics - study of a historical, evolutionary, and genetic relationships among organisms. Controversial areas (2 examples):

1. what does the word "relationship" mean?

1. similarity
2. genealogy (genetic inheritance) - siblings look alike (1998 - most biologists will tell b)

1. the role of classification?

1. should a classification reflect genealogy or not?
2. should a classification reflect the degree of difference or not?

The majority of biologists think a - historically, in the majority of textbooks, but the majority of the biologists think that should be b. Linneaus - no evolution tried to be shown. The more info you get, the more b makes sense and a looks wrong.

Fig. 5.2 + Ernest Heckel classification ~"bush" (1875) - birds and dinosaurs are related (among other points).

We need: go out, id animals, then put them together and classify. To do this, use comparative biology, which started with Cuvier, but he wasn't evolutionist. Compare: biology, anatomy, physiology, genetics.

Character - feature, trait, attribute; can be measured, described, and shared with other scientists; can see with eyes or sophisticated instruments. Kinds of characters - see H/A.

Character state is the condition in which one can find that particular character.

Analysing data

Historical perspective - since 1940's there were three schools of thought:

1. Evolutionary Systematics (historically first). Darwin, Heckel, and descendants - wanted to show the relationships, but not the contemporary way. Modern synthesis -> population shifting (genes, behavior, ecological patterns…) Mayr formulated evolutionary systematics.

1. describe evolutionary history of a particular group of animals
2. develop a classification which would reflect both phylogeny and character similarities/differences.

1. Phenetics (1960's) - as a response to "extreme subjectivity" of evolutionary system. This school of thought is more rigorous and less subjective. First, heavily mathematical branch of systematics, used computers (advantages - fast handling of large data sets). Computers with programs which are phenetically based: UPGMA, WPGMA, etc. Some assumptions are built into the programs, and we cannot test the ypotheses of these assumptions.
2. Cladistics (Phylogenetic Systematics, 1950's, but didn't become independent untill 1970's). Most Dr. Matson's friends are cladists. Most difficult - how do we determine who is related to who?

Primitive and derived do not refer to the quality of a character, but to the time when a character evolved. Primitive character evolved earlier in time. Derived character evolved later in time. Primitive and derived are relative terms. Some characters can be primitive and derived depending on how you look at them.

Mammals, birds & crocks are amniotes (have amniotic egg) - it's a derived character as compared to other organisms. But if we compare birds with crocks, both have amniotic egg, and this character is primitive because there are others who have it.

Disadvantages of cladistics: one classification has class and order; another one - 4 different others } people don't like complicated taxa names of phylogenetic classification.

5 basic tenets (ideas, assumptions) in modern cladistics:

1. Relationships leading to the cohesion of living and extinct organisms are genealogical (blood) relationships.
2. These genealogical relationships exist between individual organisms within a population; between populations; between species.
3. All other types of relationships (phenotypic, genetic) are correlated with genealogical descent and are best understood within the content of evolution.
4. These genealogical relationships are recoverable by looking at and comparing characters in different organisms.
5. The best general classification is the one that reflects phylogeny ( = evolutionary history)

H/A Systematic concepts.

Clade - the entire portion of a phylogeny that is descended from a single ancestral species and is therefore a monophyletic group.

Cladogenic event - which causes a splitting in evolution.

Cladistics generate a cladogram (a branching diagram that represents a hypothesis of relationships). It is supported with synapomorphies. We end up with a diagrams that look like branching trees. Doesn't matter how you draw. Nodes represent common ancestors, transverse bars - synapomorphies. If there are several hypothetic "trees" only one can be true (usually) if there is one line of history.

Look at morphological data, gene sequences (independent data sets), etc. - to support or reject the hypothesis.

Parsimony (extreme or excessive economy or frugality, stinginess, niggardliness) - what cladistics usually use as a decision making tool to chose between alternative hypotheses of relationships. Parsimony personally, by itself has nothing to do with physics. Deals with simplicity among alternative explanations, if all other things are equal, chose the most simple explanation. If we have two alternative explanations, we'd pick the one which not only the best supported, but also the one which requires the minimal number of evolutionary changes.

When comparing, use homologous characters to build and test cladograms. Fins are not homologous characters, resemblance is only superficial. Dolphin has bones in fins (~ humerus, radius, ulna, etc.); sharks have cartilages - rays, etc. Dolphin and shark fins are not homologous. Fins give the notion of a false similarity due not to sharing common genetic basis. See fig. 5.15

Sometimes determining what is homologous and what is not can be difficult. In genes, you need to find homologous genes.

1. Compare homologous characters.
2. Homoplasy is common in nature. It produces homoplasious characters (false similarity). These can be produced via:

1. convergent evolution ( = convergence) - appearance of similar structures in not closely related animals usually due to similar selective pressures (similar environment) ~laws of physics.
2. parallel evolution ( = parallelism) - similarity arrived at independently in "closely' related organisms. Ex: marsupial vs. placental mammals: flying squirrels of North America vs. Australia; wolves of Tasmania vs. Norht American.
3. reversal - a character loks similar to ancestral/primitive condition.

How is the evolutionary polarity of a character determined? (evolutionary polarity ~ primitive vs. derived)

Some of the methods are better then others.

1. distribution in the fossil record - a character state in oldest fossil is primitive. Problem: what if we find a fossil record a jaw in mammals before we were finding jawless mammals?
2. ontogeny - embryological development: the character state that appears earliest in ontogeny during the embryological development represents the primtive condition. See H/A with embryos. Re: tail, gill pouch.
3. outgroup method - requires that you have some hypothesis of relationships among the organisms you're studying. Then, pick your "ingroup" - the organisms you are concerned with, and compare the characterswith other organisms' that you are not studying ("outgroups") ~ notion of comparative biolgy. The character state which is the same in both ingroup and outgroup is the primitive condition. But pick something closely related - go one or two steps up in the hierarchy of systematics. If you study genus, pick the sister outgroup from the same family or order. Difficult to determine, do carefully, can use other's work.

1. Homologous characters are derived from a common ancestor
2. Homoplasy is common
3. Mosaic evolution is common - rates of evolution of various characters differ
4. Evolutionary change is often gradual, but there are different rates of evolution
5. Evolutionary changes in the form of an organism are correlated with changes in function.
6. Phylogenetic analysis - document evolutionary trends
7. Clades display adaptive radiation.

Fish adaptive radiation - different types of feeding apparatuses in different habitats of the same area.

P. 122-123 - other characters.

Life evolves, universe evolves. Changes have great effect not only on geography/geology, but also as selective agent to drive selective changes on this planet. Biotic and abiotic components interact with eachother.

Continents move - continental drift. We think we understand (in part) the mechanism which causes them to move - Plate Tectonics Theory. It explains how continents move. See fig. 7.22, fig. 6.1 (subduction). Point: Earth changes, it's dynamic.

The age of Universe: astrophysicists say 14 billion years. How do we get that? - the way stars move closer/apart.

The age of Solar System: 4.6 billion years - the oldest dated rocks on Earth are only 3.8 billion years old. How do we know the age of Earth? - fig. 6.2. Geochemical/geophysical processes - concept of radioactive decay, half-lifes.

RA decay of U²³⁸ ->Pb²⁰⁶ half-life is 4.5 billion years. Carbon¹⁴ is not a method to date Earth because has a very short half-life, but a technique for dating living systems - only 50 thousand years.

The earliest fossils are dated from rocks to be ~3.5 billion years old. They are of prokaryotic organisms (presumably anaerobs). Aminoacids are found in comets, asteroids <= biological compounds, can be originated abiotically from abiotic substances.

Spontaneous compartmentalization: RNA can be both catalyst and self-replicated - RNA could be the first biotic molecule. Notion of monophyletic origin of life.

Earliest eucaryotes - 1.5 billion years ago. Modern "phyla" animals - 550 million years ago.

Chapters 1, 2, 5, 6, 7.