1. Phylotypic stage
   1. Review (see figures 5.14 )
      1. notochord
      2. neural tube -> brain, spinal cord
      3. neural crest (table 5.2) -> connective tissue of face and pharynx, somatic sensory cranial neurons (CN V), somatic sensory glial cells, visceral motor neurons
      4. neurogenic placodes (Table 5.3) -> visceral sensory cranial neurons (olfactory, otic, lateral lines), somatic sensory cranial neurons
      5. somite (paraxial mesoderm) (Fig. 5.17) - segmented paraxial mesoderm that is largely postcranial (the first few somites are actually at the back of the head.
         1. sclerotome -> vertebral bodies, ribs, arches
         2. dermatome -> skin connective tissue (dermis)
         3. myotome -> body wall muscles, limb muscles, body wall connective tissue
      6. intermediate mesoderm (Fig. 5.17) -> urogenital systems
      7. lateral plate mesoderm (Fig. 5.17)
         1. splanchnic -> gut connective tissue, smooth muscle of gut, smooth muscle and connective tissue of heart and blood vessels, extraembryonic membranes (chorion, amnion)
         2. somatic -> connective tissue of limb buds and parietal peritoneum
      8. coelom (Fig. 5.36)
   2. Segmentation
      1. trunk shows conspicuous segmentation in its organization - that is the repeated pattern of the same (or slight modifications of) organization. The bone (vertebrae, ribs), muscles, and nerves all show this segmentation although the muscle segmentation gets pretty obscured in amniotes (segmented myotome is much easier to see in fishes in amphibians).
      2. Is the head segmented? We will talk about this next week.
   3. Does the phylotypic stage really exist or is it just an illusion due to the conspicuous shared features that one can see externally (pharyngeal pouches, somites, tail)
2. Regulation of Morphology (not much in your text) - a great deal of the differences in morphology at low levels (conspecific, congeneric) and high levels (families, classes) are due to difference in gene regulation. For example:
   1. Hox gene clusters
      1. 4 clusters (a-d) each with 13 subgroups (1-13). Each cluster on a different chromosome.
      2. A hox protein is a transcription factor that regulates gene expression. It has a highly conserved homeobox region that binds to DNA and more variable region that determines where in the DNA it will bind. This more variable region can bind to co-factors.
      3. Hox genes regulate anterior posterior patterning in the animal embryo
      4. Hox genes are spatially and temporally collinear. That is, the order that they are expressed along the axis is the same order that they are arranged on the chromosome. And the timing of their expression is the same as their spatial ordering on the chromosome.
      5. Hox genes regulate the development of the segments along the AP axis
      6. Hox genes and limb growth
         1. the fore and hind limbs are associated with different somites in different vertebrates, a pattern that has always puzzled comparative vertebrate anatomists (and has caused us to expand our definition of homology)
         2. It is now known that HoxC-6 regulates the fore-limb bud and HoxC-8-10 regulate the hind limb bud. So where HoxC-6 is expressed, a forelimb will grow
         3. cervical vertebrate form anterior to expression of HoxC-6 and the forelimb bud grows just anterior to the most anterior expression of HoxC-6
         4. In the python, HoxC-6 is expressed far anteriorly so there is no cervical region and no fore limb buds
      7. Some websites for Hox gene explanations:
         1. http://www.ucalgary.ca/UofC/eduweb/virtualembryo/hox.html (for hox intro in general)
         2. http://biology.uoregon.edu/classes/bi355f02/Topics%2002/topic%2010%2002.html (not as good as an intro but look at the snake story at the end).
3. Sonic Hedgehog (SHH)
   1. SHH regulates AP patterning in the limb bud. There is a recent new study that shows that the duration of its expression in the limb bud of the skink Hemiargis determines how many digits the skin has. Short duration = 2 digits. Intermediate duration = 3-4 digits. Long duration = 5 digits. This is a type of heterochrony. There is more to the story than this too!