Gene expression is a big deal!

1. Evolution of Development Chapter 25 • Gene expression is a big deal! • To explain differences in species, we often need to look at changes in genes that have their effect by altering development and thus phenotype • Phenotypic diversity has resulted not only from changes in genes but from changing patterns of expression (timing, location, frequency).

2. 2 closely related sea urchin species have very different developmental patterns • 2 forms have very similar genes • A dramatic change in gene expression during development (what is it?) • Adult forms nearly the same in both

3. Transcription factor genes are “control genes” critical to the coordination of development • Transcription factors are abundant (2600 in humans); have a “DNA binding motif” that can act to activate or suppress transcription of one or more genes. (We can get mutations in these transcription factors). • About 2 dozen gene families regulate animal and plant development • Hox (homeobox) genes establish the body plan by specifying when and where genes are expressed during development • Hox genes code for proteins that bind to regulatory region of other genes • Plants: shoot growth and leaf development • Animals: establish basic body plans along the anterio-posterior axis of the body. • MADS box genes code for a DNA-binding motif • Establish the body plan of plants, especially flowers • MADS box is highly conserved but we can also expect variation in the coding region sequences that get turned on (or not).

4. Gene duplication and divergence(same gene, new function in paralogues) • Two gene duplications resulted in the AP3 gene in the eudicots that has acquired a role in petal development • Gene duplications of paleoAP3gene family led to flowering-plant flower morphology • MADS box gene duplicated • Gave rise to PI and paleoAP3 genes • In ancestral plant, genes affected stamen development • This function has been retained • paleoAP3 duplicated to produce AP3 • and an AP3 duplicate • AP3 gained a role in petal development 4

5. Heterochrony(different timing) • Alterations in timing of developmental events due to a genetic change • Could affect a gene that controls transition of plant from juvenile to adult, mutation results in small plant that flowers quickly • Most mutations that affect developmental regulatory genes are lethal • If mutation leads to increased fitness, then new phenotype will persist Ambystoma tigrinum

6. Homeosis • Alterations in the spatial pattern of gene expression (where the gene gets expressed) • 4-winged Drosophila requires mutation in 3 genes in Bithorax complex • Drosophila antennapedia has a leg where an antenna should be • Mutations can arise spontaneously or by mutagenesis in the laboratory but bizarre phenotypes would have little survival value in the wild

7. Regulatory region change (where transcription factor binds) may alter time or place (or frequency) of gene expression • Heterochrony or homeosis • Frequency of expression • Downstream targets the same but cells that express target genes or timing of expression could also change (How might the impact of regulatory mutations vary with their timing during development in the two segemented animals shown here ?)

8. Gene Mutationsa minimal mutation could have a major result. Brassica oleracea subspecies have very diverse phenotypes Wild cabbage, kale, tree kale, red cabbage, green cabbage, brussels sprouts, broccoli, and cauliflower • Two genes:CAL and Apetala1havemutations that change regular flowers into masses of arrested flower buds • CAL was cloned from Brassica • Stop codon, TAG, was found in the middle of the sequences for broccoli and cauliflower • Stop codon appeared after ancestors of broccoli and cauliflower diverged but before broccoli and cauliflower diverged from each other

9. Same gene, new function(notochord builder becomes tail builder) • Evolution can be explained in part by the co-option of existing genes for a new functions. Example from vertebrate evolution: • Ascidians (tunicates or sea squirts) have a notochord but no vertebrae • Brachyury gene encodes a transcription factor expressed in developing notochord • Homologues found in invertebrates, specifies anterior – posterior axis. • Region of Brachyury gene encodes protein domain called T box, transcription factor • Transcription factor turns on or off genes that produce a tail • In mice and dogs, Brachyury mutation causes a short tail • Humans have wild-type Brachyury so other genes, that humans lack, must be needed for a tail.

10. Different Genes, Convergent Function • Homoplastic (analogous) structures • Same or similar functions • Arose independently • Phylogenies reveal convergent events • Origin of convergence difficult to understand • Different developmental pathways may have been modified with a similar result (shell in turtles, shell in armadillos) • In other cases not clear whether it is the same or different genes responsible (limb loss in lizards)

11. Flower shapes have converged on a derived condition: • Radially symmetrical flower: two identical parts when cut across center at any point • Daisies, roses, tulips • Bilaterally symmetrical flowers have mirror-image halves • Snapdragons, mints, peas • Shape may be important in their evolutionary success (orchids!)

12. Functional Analysis • Range of experiments designed to test the actual function of a gene in different species • Sequence comparison essential • Need to distinguish paralogues from orthologues • Single base mutation can change active gene into an inactive pseudogene [smelling genes in dolphins] • Therefore, function can be inferred from sequence data but actual function has to be demonstrated experimentally • Functional genomics– experimenting to demonstrate actual function of the gene

13. Diversity of eyes and complexity of genes - case study • Explaining complicated structures was one of Darwin’s greatest challenges • Incremental improvements in function could build a complex structure through natural selection

14. Eyes of organisms are extremely different in many ways • Eyes are often used as an example of convergent evolution • Classically considered to be homoplastic (analogous) structures rather than homologous • Morphological evidence indicates eyes evolved at least twenty times • Most recent common ancestor of all these forms had no ability to detect light

15. Genes discovered that code for transcription factor important in lens development • Pax6 in mice, eyeless in flies • Sequence of genes highly similar – homologues • Walter Gehring inserted mouse Pax6 into genome of a fruit fly • Created transgenic fly • Pax6 gene turned on by regulatory factors in the fly’s leg • Eye formed on leg of fly • Is it a mouse eye or a fly eye??

16. Mouse Pax6 makes an eye on the leg of a fly • Transgenic fly results completely unexpected • Insects and vertebrates diverged more than 500 MYA • Large differences in eye structure • Expected eye development to be controlled by completely different genes

17. Ribbon worms, Lineus sanguineus, also rely on Pax6 for eyespot development • Pax6 homolog has been cloned and has been shown to express at the sites where eyespots develop • In contrast, planarian worms do not rely on Pax6 for eyespot development Ribbon worm Planarian worm

18. Several explanations for Pax6 • Eyes in different types of animals evolved truly independently, as originally believed • Possible Pax6 had role in forehead development and this role has been co-opted time and time again for eye development • Evolutionary biologists think this unlikely since gene sequences and functional roles so similar • Suggests to many that Pax6 acquired its eye development role only a single time in the ancestor to all organisms using Pax6 for eye development