What was Ernst Mayr’s gaffe and what fundamental principle of Evo-Devo does this misstatement highlight?  

Mayr thought that homologous genes were only likely to be found among close relatives. However, developmental genes in distantly related species are similar and dictate the same body parts (in animals). 

What do “Modularity”, “Homology” and “Serial Homology” mean?

Modularity – is the compartmentalization of body form consistent among major groups. They all follow a similar pattern. Homology – shared by common descent; when the same derived structure is modified in different ways for each species (limbs). Serial Homology – when structures arise as a repeated series (arms and legs)

What is Williston’s law?  

Over evolutionary time, number of body parts are reduced and become specialized.

What is punctuated equilibrium and who came up with this theory?  

Steven Jay Gould came up with the theory that evolution was marked by long periods of stasis interrupted by brief intervals of rapid change.

Who Motivated Darwin to go to the tropics?  Name two other contemporaries that were similarly motivated?  

Alexander Von Humboldt. Henry Walter Bates (bug collector) and Alfred Russell Wallace (Naturalist).

How did Thomas Huxley participate in the development of Evolutionary Biology as a field of science?  

Huxley emphasized embryology and development as being important to evolution.

What happens if you divide a two celled newt embryo in two?

Parallel to furrow: 2 viable newt tadpoles

Perpendicular to furrow: 1 viable newt tadpole and 1 mass of tissue

What is an “organizer” as it refers to developmental biology?

An organizer is a region of an embryo responsible for development of secondary embryonic axes.

What is a ZPA and what does it do?  

Zone of polarizing activity – (same as the organizer) region of cells affected by morphogens that develop into body parts depending on the distance from the morphogen source.

What did Bateson do for science?  

Bateson catalogued mutant individuals of many species and divided them. He distinguished homeotic variants (body part transformed into the likeness of another) from others.

What is the difference between “homeotic” and “master” genes?

Homeotic genes are the loci where homeotic mutations take place. Master genes govern the differentiation of serially homologous body parts. Homeotic mutations are alleles of master genes, but master genes are not necessarily homeotic alleles.

What is enzyme induction?

The abundant production of an enzyme that takes place when it is needed, but stays dormant when unneeded. (eg. E. coli secretes beta-galacticitase in the presence of lactose)

What is the difference between the Hox genes, the homeobox and the homeodomain?  

The sections of 180 similar base pairs in the homeotic genes of fruit flies were named the homeobox. The homeodomain is the section of amino acids in a set of proteins encoded by a homeobox. The homeotic genes with homeoboxes became known as Hox genes.

What is significant about the order of the Hox genes?  

The order corresponds with the arrangement of body parts in the organism.

How many Hox gene clusters do the fly and mice have?  

4 in mice, 1 in flies

What gene controls appendages?  

Dll (distal-less gene)

What do fly and human heart development have in common?  

They are both governed by an allele of the Tinman gene.

Do transcription factors travel between cells?  

Not in animals, but true for plants.

What does sonic hedgehog have to do with the ZPA and how was this discovered?

The zone of Sonic hedgehog expression wasn’t just part of the ZPA, and the activity of the ZPA was due entirely to Sonic hedgehog expression. Without sonic hedgehog, there is no development.

What does holoprosencephaly mean?  

What is a fate-map of an embryo?  

Chemical staining of cells allow for tracking a parent cell and its daughter cells to determine what structures a particular region of the embryo turn into. Cell fates are determined by position in the body (chemical signals).

Who said, “Embryos are fond of stripes,” and what is the significance of that statement for embryo geography?  

Francis Crick was referring to the tool kit gene expression which often has striped patterns in embryonic cells visualized by dye.

How do the longitudes and latitudes of embryo geography form?  

Hox protein expression makes segments to form longitudes and latitudes. Lateral inhibition makes definition of stripes. Other genes are at play at the same time.

What gene makes the hind wings small in drosophila and how does it achieve this effect?  

The Hox gene Ultrabithorax (Ubx) controls the formation of the hind wings. Ubx suppresses genes that encode development of venation and bristles.

What does BMP-4 do for the developing chicken foot?  

The BMP-4 gene marks the tissue between the digits that will die preventing webbed feet.

What is lateral inhibition and how does it relate to pattern formation in animals?

Certain cells specialize and create a zone in which no other cells within that zone can develop the same as the specialized cell. As other cells outside of the zone specialize, a regular pattern forms. Lateral inhibition forms stripes of Hox gene expression in the embryo.

What percentage of the “dark matter” codes for switches in humans?

2-3%

Are the switches part of the gene?

No, not in the typical use of the word “gene”.

What are “signature sequences?”

They are DNA sequences that are recognized by specific DNA binding tool kit proteins.

How long in bp’s is a typical switch?  How about a signature sequence?  

Switch: Several hundred bp

Signature sequence: 6-9 bp

How many signature sequences are within a switch?  

Usually 6-20

What are BMP’s?

Bone morphogenic proteins; promote cartilage and bone formation.

Describe a wiring diagram of regulatory logic.  

Activators and repressors act on gene switches (circuits), and their products are activators and repressors for other gene switches (forming a network)

Who discovered the Burgess Shale and when?  When did this fauna live (in mya)?

Charles Walcott discovered the fossils in 1909 in British Columbia. Date to 505 mya.

Give some extrinsic and intrinsic causes of the Cambrian radiation.

Extrinsic: Global climate change

Intrinsic: invention of body-building genes

How old is the earth?  When did life begin to evolve?  How long were animals small (<1mm)?  

 4.5 billion years old. Life began evolving 3.5 billion years ago. Animals were small for 3 billion years.

What fauna predated the Cambrian explosion?  

Ediacaran fauna: centimeters long, tube-shaped, radially symmetrical forms

Are arthropods protosomes or deuterosomes?  

Protosomes: mouth develops from the blastopore

What is the name of the ancestor of protostomes and deuterostomes?

Urbilateria – “primitive bilaterian”

When in mya did the Cambrian begin?  

543+/- 1 mya

What creature is it thought that arthropods evolved from?  

Lobopodians

Where do lobopodian relatives of arthropods still live today?  

Onychophorans live in Australia

Breifly explain the genetics of Willistons Law.  

Relative shifting of Hox zones yields different body parts in different zones via change in DNA sequences of signature sequences.

What is the current best date for the origin of vertebrates.  

520 mya; moved onto land 360mya

How many Hox gene clusters were most likely present in the ancestor of vertebrates?  

1

What is a biramous limb?  Give an example from crustaceans.  

“forked” limb in which the two branches have different functions. In crustaceans, the inner branch forms the walking leg, and the outer branch has a role in respiration.

What are two genes important for building insect wings?  

Apterous and Nubbin

Where are Apterous and Nubbin expressed in crustaceans?

In the respiratory lobe of the outer branch of crustacean limbs.

Describe how the evolution of insect wings is a great example of Williston’s law.  

Evolved from a series of gill-like appendages on all segments, to smaller numbers and reduced structures, to two pairs of specialized wings.

Do Hox genes repress or promote wing formation?  

Both Promote (Dll) and Repress (Ubx)

How does a gene get a signature sequence for a Hox protein?  

Inheritance of DNA intron mutations via natural selection that allow a Hox protein to bind.

When did animals move on land?  (period and mya)

Devonian Period (365 mya)

What is an autopod?  

The third, most distal part of the limb.

What vertebrate appendage are the spines of sticklebacks related to? 

The hindlimb

What gene controls the expression of stickleback spines?

Pitx1

How many different species did Bates collect in the tropics?  How many were new to science?  

14,712. 8,000 were new. Many butterflies.

Describe the scientific interests of Bates and Bateson.  

Bates was very interested in butterfly mimicry. Bateson was interested in individuals with atypical patterns.

What two ways can a scale get its color?   

Chemical pigments or structural colors (reflection)

How do eyespots develop and when during the lifecycle of the butterfly? 

Eyespot development occurs in the wing disc during the caterpillar larval stage/chrysalis. There is an organizer at the center of the developing eyespot responsible for producing the concentric rings.

Describe the deep homologies between butterfly and fruit fly wings.

The location of gene expression in butterfly and fruit fly wings was the same.

What genes control eyespot development?  

Distal-less

What do Engrailed and Spalt do?

Engrailed and Spalt expression produces different colored rings in an eyespot.

How does natural selection for eyespots change between seasons inMalawi?  

During the wet season, the caterpillars sense the environment and produce wings with big spots to deter lizards and birds. During the dry season, the caterpillars sense the environment and produce wings with small spots to blend in well with leaf litter.

Which gene is involved in eyespot formation and HOW does expression change between seasons?  

Distal-less. The switch for distal-less has evolved a hormone-responsive signature sequence that responds to environmental changes. The levels of hormones produced are directly affected by temperature.

Give three “just so” stories for why the zebra has stripes.  

Helps blend in with shadows, hard to spot an individual in a herd, reduces insect bites, aids in mother-young identification

What does the MC1R protein do?  

A receptor on pigment cells that MSH binds to causing eumelanin-synthesizing enzymes.

At a mechanistic level, how does the leopard loose its spots?  

A 5 amino acid deletion and 1 amino acid change makes MC1R continually active. 

What does the gene Agouti do?  

Inhibits MC1R to produce light coloration. It binds to and alters the function of the protein.

Does Carroll think the zebra has black or white stripes?  

Both, Black stripes of cells with melanocytes, and white stripes of cells without melanocytes

How did Charles Lyell date the Neanderthal skull?  

He found fossils of extinct mammoth and wooly rhinoceros in the cave as well

How old are the earliest Homo sapiens?  

Oldest fossils are 160,000 years old.

What is the difference between a hominid and a hominin? 

Hominid – refers to both humans and African apes

Hominin – refers only to humans and our ancestors back to our separation from the apes

Is tool use unique to Homo sapiens in the hominin lineage?  

No, it’s as old as 2.5 million years old with Homo habilis.

What hypothesis does Carroll put forward for why brain size increased in the hominin lineage (sometimes in punctuated steps)?  

The climate changed a lot in the course of about 1 million years. Cooler drier climates reduced the range of primates and Natural Selection might have selected for individuals that could tolerate changes in habitat, food, hunting, etc. Thereby selecting for a bigger brain size.

Explain what “mosaic evolution” means using the brains of tenerec and marmosets as an example.  Also, illustrate the term using hominin traits and developmental features.  

Certain parts of the brain change in concert with another, but independently of other parts. Tenrecs have a non-neocortical brain volume greater than a marmoset, but the marmoset’s neocortex is almost 10x larger.

There is anatomical asymmetry in hominin brain hemispheres. The left hemisphere dominates speech production, right handedness, and gesticulation. Developmentally, timing of teeth formation in H. sapiens is slower,

Were the rates of change in human forms exceptional compared to other vertebrate lineages?  

No

Does Carroll think that changes in protein sequences (think Dn/Ds values) will explain the 98.8% paradox?  

No, it is probably more due to the control of genes. Dn/Ds values do not include switches.

Review the MYH16 and FOXP2 stories.  

Humans have a disrupted protein sequence in MYH16 in the temporalis muscle which helps form muscle fibers (nonfunctional in humans). This occurred between 2.1 and 2.7 mya (w/in Homo).

A European family experience delayed ability to acquire language due to mutation in FOXP2. There is a lot of evidence for a selective sweep (positive selection) for FOXP2 in Homo evolution.

What does FOXP2 do?  

A transcription factor that binds to DNA and regulates the expression of other genes involved in speech.  It is involved in brain development; likely fine scale differences between regions.

 How does Evo-devo help with teaching biology?

It helps to visualize the integration between genetics and development of form via gene expression patterns in embryos. It helps explain macroevolution by understanding changing form.

    What is the difference between micro and macro evolution?

Macroevolution is evolution above the species level, microevolution is variation detectible within species.

About how many species have evolved in the last 500 million years?  

1 billion or more

 What is Carroll’s explanation for novelty and his rationalization of it?  

Innovation is explained by the new modification of existing genes/structures. 

Multifunctionality and redundancy at a genetic and anatomical level.

   What is Carroll’s new slogan for what evolution is?   Not, “Change in gene frequencies” but rather… 

Evolution of form is change in development

What did Darwin regret adding to the Origin of Species?  

“by the Creator”

Who said, “Nothing is worse than active ignorance.”

Johann Wolfgang von Goethe

   Encapsulate the three common arguments against evolution that Carroll presents.  

1)      Evolution is just a theory

2)      Evolution is fraudulent

3)      Evolution is weak b/c scientist disagree

  What does John Haught suggest modern theology must do?

  Have refreshed expression in evolutionary terms.

  What is tragic irony does Carroll see about the more we understand about biology……?

The less species there are available to study due to extinction.