1. Adaptation: from genes to traits
“Curiously, the improved understanding of the nature of gene and mutation has not added, so far, to the understanding of evolutionary phenomena.”
E. Mayr Animal Species and Evolution (1963, p. 172)

2. How do new phenotypes evolve?

3. The paper that started it all
Humans and chimps share 99% of protein-coding DNA

4. king & wilson weren’t emphasizing similarity
But rather that protein-coding gene differences do not appear to account for substantial phenotypic differences between humans and chimps

6. The great Cis- vs. Trans- debate
Almost as important as this one…

7. away from the coding region “junk” DNA involve a transcribed product
cis-regulation
trans-regulation
5’ of the coding region
away from the coding region
“junk” DNA
involve a transcribed product

8. Observations favoring a -cis worldview
SEAN Carroll 2008
Observations favoring a -cis worldview
1. Mosaic Pleiotropy
“Most proteins regulating development participate in multiple, independent developmental processes”
2. Ancestral Genetic Complexity
“Morphologically disparate and long-diverged animal taxa share similar toolkits of body-building and body-patterning genes.”
3. Functional Equivalence of Distant Orthologs & Paralogs
“Many animal toolkit proteins, despite over 1 billion years of independent evolution in different lineages, often exhibit functionally equivalent activities in vivo when substituted for one another. These observations indicate that the biochemical properties of these proteins and their interactions with receptors, cofactors, etc. have diverged little over vast expanses of time.”

9. 5. Infrequent Toolkit Gene Duplication
4. Deep Homology
“ The formation and differentiation of many structures such as eyes, limbs, and hearts—so morphologically divergent among different phyla that they were long thought to have evolved completely independently—are governed by similar sets of genes and some deeply conserved genetic regulatory circuits.”
5. Infrequent Toolkit Gene Duplication
“Duplications within several prominent toolkit gene families have been surprisingly rare in the course of animal diversification relative to duplications of other gene families.”
6. Heterotopy
“[It is the] spatial regulation of toolkit genes and the genes they regulate [that] are associated with morphological divergence.”

10. HOEKSTRA and COYNE 2007
Why are -cis responsible for morphology, but not physiology, behavior, etc.
And in fact, metabolic function, which we understand better, is usually dominated by -trans regulation and gene duplication, not -cis regulation
Gene duplication is observable and important

11. Gene duplication can produce novel functions
Promiscuous proteins are especially likely to take on new functions after duplication

12. Gene duplication and snake venoms

13. Venom evolved before snakes themselves

14. While venom evolved before snakes, novel proteins have been added
Through repeated gene recruitment

15. THROWING DOWN THE GAUNTLET….
Genome Biology and Evolution 2014

16. SNAP!

17. Subfunctionalization Neofunctionalization

18. Coda (from Hoestrka and Coyne 2007)