Terms to know: heterochrony, paedomorphosis, terminal addition, ontogeny, "ontogeny recapitulates phylogeny", von Baer's Law, regulatory gene, HOM/Hox gene.

Questions:

1. What is von Baer's Law?  Give an example of von Baer's law.
2. How might mutations that have a strong effect early in embryology and mutations that do not affect the phenotype until the end of embryology differ in: (a) their effect on the phenotype, (b) whether or not they are lethal, (c) the probability that traits derived from such mutations will be commonly observed in living organisms today.  Based on your answers, discuss why ontogeny might recapitulate phylogeny.
3. What does the phrase "ontogeny recapitulates phylogeny" mean.  Does ontogeny always recapitulate phylogeny? Justify your answer.
4. Explain the difference between von Baer's Law and the statement "ontogeny recapitulates phylogeny."  Which of these patterns is more generally observed? Is the other ever observed? Give an explanation for the more generally observed pattern that is based on the likely impact of mutations that affect early development versus mutations that affect late development; explain why these different mutations differ in impact.
5. During embryological development, salamanders start out with few, webbed toes; development in some species proceeds until they have five un-webbed toes per foot, but in other salamanders development stops at a stage where they have three or four webbed toes per foot.  Suppose you are studying five salamander species: two have five un-webbed toes, one has four webbed toes, and two have three webbed toes.  (a) Draw a phylogenetic tree that would suggest that ontogeny recapitulates phylogeny. (b)  Draw a phylogenetic tree that would NOT support a hypothesis that ontogeny recapitulates phylogeny. (c) Which of these trees shows paedomorphosis?  (d) Which of these trees shows terminal addition?
6. It has been argued that snail shell coiling evolves through a process of heterochrony.  Some species have very coiled shells as adults, but developmentally start out with uncoiled shells and go through an intermediate stage with moderately coiled shells.  In other species, the adults have uncoiled shells and still others have adults with moderately coiled shells that developmentally start out uncoiled.  You are going to study the phylogeny of snails to test hypotheses of heterochrony.  (a) What are two possible results of heterochrony?  (b) Which of these (either or both) fit von Baer's Law?  (c)  Which of these (either or both) show ontogeny recapitulating phylogeny? (d) Draw a phylogeny of two species of each shell type (six species total) that would support your first hypothesis.  (c) Draw a phylogeny of two species of each shell type (six species total) that would support your second hypothesis.
7. Fish tails can be one of three shapes, as diagrammed here:


During embryonic development, species with homocercal tails first develop diphycercal tails, then heterocercal tails, and finally homocercal tails.  Species with heterocercal tails as adults start out with diphycercal tails, then develop heterocercal tails.  Species with diphycercal tails do not show either tail shape during development.  (a) Does fish tail shape follow von Baer's Law?  (b)  Draw a phylogeny that would suggest that fish tails have evolved through paedomorphosis.  (c) Draw a phylogeny that suggests that fish tails have evolved through terminal addition.  (d) Based on the fossil record and outgroup comparison, it appears that diphycercal tails evolved first, then heterocercal tails, and finally homocercal tails.  Which hypothesis (paedomorphosis or terminal addition) does this pattern support?  (e)  Does ontogeny recapitulate phylogeny in fish tails?
8. Larval salamanders live in the water and have gills; in most species, adults live on land, and when larvae metamorphose into adults they lose the gills.  Some species have aquatic adults and retain gills throughout life.  (a) Does gill presence/absence follow von Baer's Law?  (b) Draw a phylogeny that suggests that gill presence/absence has evolved through paedomorphosis.  (c) Draw a phylogeny that suggests that gill presence/absence has evolved through terminal addition.  (d) Cladistic analyses of salamanders indicate that the primitive condition in salamanders is to metamorphose into adults and lose the gills; retaining gills throughout life is the derived state.  Does this suggest that gill presence/absence has evolved through paedomorphosis or terminal addition?  (e) Does ontogeny recapitulate phylogeny in salamander gill presence/absence?
9. Humans, chimpanzees, gorillas, and orangutans form a monophyletic group (all evolved from the same ancestor.)  All have head shapes that start out with flat faces and large foreheads.  Humans retain this head shape throughout life, but chimpanzees, gorillas, and orangutans develop elongated snouts and flattened foreheads as adults.  (a) Does von Baer's Law apply to head shape in the humans and great apes?  (b) If head shape evolved through terminal addition, what head shape (like humans or like the other apes) would you expect adults of the outgroup to this group to have?  Draw the appropriate phylogeny, including this outgroup, to support this hypothesis.  (c) If head shape evolved through paedomorphosis, what head shape (like humans or like other apes) would you expect the outgroup to this group to have?  Draw the appropriate phylogeny, including this outgroup, to support this hypothesis. (d)  It turns out that both outgroup comparison and the fossil record suggest that the ape-shaped head is the primitive condition.  Does human head shape appear to have evolved through paedomorphosis or through terminal addition?  (e)  Does human head shape ontogeny recapitulate phylogeny?
10. What are three key traits of HOM/Hox genes? Relate these key traits to: (a) the evolutionary origin of new HOM/Hox genes, and (b) the function of HOM/Hox genes
11. What evidence suggests that HOM/Hox gene duplication and elaboration was a key innovation?
12. Hypotheses of heterochrony were developed before people knew much about the actual developmental mutations that might have occurred.  How does the more recent information on the genetics of development of the tetrapod limb relate to these older hypotheses of heterochrony?  What kinds of mutation could cause heterochrony?  In what kinds of genes would they occur?
13. The initial pattern of development of lobe-finned fish lobes and tetrapod limbs is dependent on the timing of expression of the same genes (including Hox genes).  Late in development, expression of Hox genes in lobe-finned fish stops.  In contrast, Hox genes are expressed late in development in tetrapods; they regulate the development of the hand.  The tetrapod condition is apparently the derived condition.  Relate this description of the genetic regulation of development to hypotheses of heterochrony.  Does this suggest terminal addition or paedomorphosis? Why?
14. What is "deep homology"?  Use the Dll gene described in Chapter 17 of Freeman and Herron (2001) as an example to explain what this means.