Chalk talk IV

1. PROCESSES OF BODY PLAN EVOLUTION: THE CAUSAL ROLES OF GENE REGULATORY NETWORK (GRN) DEPTH, HIERARCHY, AND DEVELOPMENTAL FUNCTION Chalk talk IV

2. EVOLUTION, DEVELOPMENT, AND GRN’S: A SYLLOGISM GENOMIC CHANGES THAT CAUSE ALTERATIONS IN BODY PLAN IN EVOLUTION have to be THOSE THAT ALTER THE DEVELOPMENTAL PROCESSTHE DEVELOPMENTAL PROCESS IS SPECIFIED BY GRN architectureTHEREFORE, EVOLUTION OF ANIMAL BODY PLAN DEPENDS ON CHANGES IN GRN architectureYOU CAN THINK OF EVOLUTIONARY PROCESS AS THE TIME DERIVATIVE OF THE DEVELOPMENTAL PROGRAM

3. DEVELOPMENTAL GRN HIERARCHY AND EVOLUTION SINCE THE NATURE OF EVOLUTIONARY PROCESS MUST DEPEND DIRECTLY ON THE STRUCTURAL PROPERTIES OF THE GRNS THAT CONTROL DEVELOPMENT OF THE BODY PLAN,AND SINCE THESE GRNS ARE FUNDAMENTALLY HIERARCHICAL,THE NATURE OF EVOLUTIONARY PROCESS MUST DEPEND DIRECTLY ON GRN HIERARCHYThis means that the evolutionary consequences of change at different levels of grn hierarchy will differ, just as do the developmental consequences

4. A DIAGRAM OF GRN HIERARCHY

5. A SECOND GENERAL AND FUNDAMENTAL FEATURE OF GRNS THAT AFFECTS EVOLUTIONARY PROCESS: HOW BODY PARTS ARE POSITIONED THE GENERAL MECHaNISM BY WHICH THE FORMATION OF ADULT BODY PARTS BEGINS: SPECIFICATION OF PROGENITOR FIELD REGULATORY STATE IN A GIVEN PLACE IN THE BODYTHUS WHERE THE PROGENITOR FIELDS ARE SET UP DETERMINES BASIC MORPHOLOGICAL STRUCTURE OF THE BODY PLAN

6. PROGENITOR FIELDS

7. A THIRD FUNDAMENTAL FEATURE OF DEVELOPMENTAL GRNS THAT ULTIMATELY AFFECTS EVOLUTIONARY PROCESS: THEIR REGULATORY STATE OUTPUT IN SPACE IS BOOLEAN

9. THE MEANING OF A CIS-REGULATORY SEQUENCE MUTATION DEPENDS ENTIRELY ON ITS HIERARCHICAL LOCATION IN THE GRN!

10. EVOLUTION AT DIFFERENT LEVELS OF THE GRN HIERARCHY: AT THE PERIPHERY OF THE GRN, AFFECTING EXPRESSION OF DIFFERENTION GENE BATTERIESAt upper levels of THE grn, affecting spatial regulatory state specification earlier in development of the body plan

11. EVOLUTION AT THE LEVEL OF THE DIFFERENTIATION GENE BATTERY -BY CHANGE IN PROTEIN CODING SEQUENCE OF AN EFFECTOR GENE (usually requires homozygosity for phenotype)-BY CHANGE IN CIS-REGULATORY SEQUENCE OF A MODULE CONTROLLING EXPRESSION OF AN EFFECTOR GENETHESE KINDS OF CHANGE ARE CONTINUOUS, AND THEIR FIXATION ISDIRECTLY AFECTED BY ENVIRONMENTAL SELECTION-BY REDEPLOYMENT OF THE WHOLE differentiation gene BATTERY, A HIGHER LEVEL CHANGE

13. EXAMPLES OF CONTINUOUS, SELECTIVE CHANGE IN PHENOTYPE BY CIS-REGULATORY SEQUENCE MUTATION AT THE PERIPHERAL GRN LEVEL The drosophila ebony GENE, which antagonizes pigment formation:A CIS-REG MODULE of the ebony gene CONTROLLING ABDOMINAL PIGMENTATION WHICH IS SELECTIVELY ADVANTAGEOUS AT HOTTER CLIMATESTHE DROSOPHILA YELLOW GENE, WHICH MAKES BLACK PIGMENT:a YELLOW GENE CIS-REGULATORY MODULE CONTROLLING SPECIES SPECIIFIC WING PATTERN FORMATION(SEAN Carroll lab)

14.  Concerted changes in the expression of Yellow and Ebony underlie the evolution of novel wing patterns.

15.  Expression of the Yellow protein prefigures adult wing pigmentation.

16. The spot element evolved through the acquisition of sites for both activators and repressors

17. Cryptic prepatterns and the evolution of novel gene expression patterns through the evolution of cis-regulatory sequences

19. Multiple mutations in the ebony abdominal cis regulatory element contribute to enhancer activity differences. Five mutations decrease ebony expression in the dark allele and show a varied distribution across Africa. (A)

20. GRN EVOLUTION at UPPER HIERARCHICAL LEVELS 1. The basic mechanism of TOPOLOGICAL CHANGE IN GRNS is REGULATORY GENE COOPTION2. COOPTION IS CAUSED BY CIS-REGULATIORY re-DEPLOYMENT OF A REGULATORY GENE TO A NEW DEVELOPMENTAL DOMAIN3. This is a gain of function type of change

21. CO-OPTION

22. EXAMPLE OF COOPTIVE REDEPLOYMENT OF A REGULATORY GENE IN ECHINODERM EVOLUTION: THE T-BRAIN GENE IN SEA URCHINS AND SEA STARS (AND OTHER ECHINODERM CLASSES)

23. Asterina Eucidaris S.purpuratus P/TExtinction end Cambrian

24. In starfish, Tbr is required for archenteron formation

25. Sp Tbr Morpholino 48 Hr

26. COOPTIVE REDEPLOYMENT OF REGULATORY GENE EXPRESSION CAN HAVE DEEP EFFECTS ON DEVELOPMENTAL FUNCTION -CAN ALTER DEPLOYMENT OF DIFFERENTIATION GENE BATTERIES OR OF OTHER WHOLE SUBCIRCUITS-CAN CAUSE SIGNALS TO BE ISSUED IN NEW PLACES-CAN BLOCK OR PERMIT OPERATION OF SUBCIRCUITS THAT DO GIVEN JOBS-CAN CONTRIBUTE NEW FUNCTIONALITIES TO grn SUBCIRCUITSTHIS IS HOW BODY PLANS CHANGE IN EVOLUTION!

27. THINKING ABOUT COOPTION: 1. TOPOLOGICAL CHANGE IN GRNS OCCURS BY REGULATORY GENE COOPTION2. COOPTION IS CAUSED BY GAIN OF FUNCTION CIS-REGULATIORY CHANGE THAT RESULTS IN DEPLOYMENT OF A REGULATORY GENE TO A NEW DEVELOPMENTAL DOMAIN3. a great many lab experiments show that redeployment of regulatory gene expression is dominant and usually haplosufficient4. therefore any animal bearing a cooptive gain of function cis-regulatory change could become the founder of a clone of animals expressing this change

28. SOME (HERETICAL) CONSEQUENCES FOR THEORIES OF BODY PLAN EVOLUTION ALL DESCENDANTS OF ORGANISMS IN WHICH REGULATORY COOPTIONS OCCUR that are not DELETERIOUS WILL transcriptionaly express THEMSome cooptions might affect GRN topology at once; others could remain cryptic AND HARMLESS pending further changeTHE GENERAL RESULT IS THAT EVOLUTIONARY CHANGE IN GRN WIRING AND THUS DEVELOPMENTAL PROGRAM IS BASICALLY LIKELY, NOT UNLIKELY , TO HAPPEN !

29. AN IMPORTANT ASPECT OF REGULATORY GENE REDEPLOYMENT: THE SYSTEM IS PREDICTED TO GENERATE GRN RECONFIGURATIONS FREQUENTLY -CIS-REG MODULES EVOLVE RAPIDLY-THERE IS likely TO BE A PREEXISTING POOL OF REGULATORY GENE DEPLOYMENT VARIANTS ALWAYS PRESENT-AND CONTRARY TO THE TENETS OF CLASSICAL THEORY NEW cis-reg FUNCTIONALITIES DO NOT REQUIRE HOMOZYGOSITY to alter grn structure and functionTHEREFORE network EVOLUTION resulting in execution of new developmental processes IS probably to be EXPECTED TO HAPPEN….

30. BUT THEN WE MUST CONFRONT A MAJOR MYSTERY OF THE PALEONTOLOGICAL RECORD DISCONTINUOUS EVOLUTION:“RAPID” CHANGE FOLLOWED BY VERY LONG PERIODS OF STASISEXAMPLE: ECHINODERM FOSSIL RECORD

32. ALL ECHINODERMS, MODERN AND EXTINCT, MAKE STEREOM SKELETON

35. DEVELOPMENTAL GRNS ARE CHARACTERIZED BY MULTIPLE SUBCIRCUITS BROUGHT TO BEAR ON THE SAME JOB -THEY ALL ACT TO ENSURE THAT GRN WILL RELIABLY PRODUCE THE REGULATORY STATE -TOGETHER THEY ENSURE TREMENDOUS STABILITY OF DEVELOPMENTAL REGULATORY SYSTEM-PERHAPS THIS DESIGN FEATURE IS RESPONSIBLE FOR LONG PERIODS OF STASIS IN CROWN GROUP LINEAGES-IMPLICATION THAT STEM GROUP GRNS MAY HAVE BEEN MORE MALLEABLE AND LESS “OVERWIRED”

36. LARGE SCALE EVOLUTIONARY CONSERVATION OF GRN SUBCIRCUITS: THE KERNELS OF GENE REGULATORY NETWORKS

37. KERNEL THEORY • GRN KERNELS UNDERLIE CLASS, PHYLUM, AND SUPERPHYLUM HOMOLOGIES IN ANIMAL BODY PARTS • THIS PREDICTS THEIR ROLES IN DEVELOPENT OF BODY PARTS CONSERVED AT CLASS, PHYLUM AND SUPERPHYLUM LEVELS • THEREFORE GRN KERNELS ARE OF CAMBRIAN OR PRECAMBRIAN ANTIQUITY • ONLY SOME DIFFERENTIATION GENE BATTERIES, AND THE TERMINAL GRNS THAT SET UP CELL TYPE-SPECIFIC REGULATORY STATES, MAY BE OLDER

41. CANALIZATION OF DEVELOPMENTAL PROCESS KERNELS OPERATE AT INITIAL PATTERN FORMTION LEVEL OF DEVELOPMNTAL PROCESSThus they constrain subsequent spatial subdivision processesThe exclusion of alternatives, and distribution of morphological forms dependent on these pattern formation processes are for this reason phylogenetically distributed

42. ANOTHER VERY IMPORTANT POINT: EVOLUTIONARY CHANGE AT UPPER HIERARCHICAL GRN LEVELS IS DISCONTINUOUS THERE IS NO CONTINUOUS VARIATION BRIDGING BETWEEN DIFFERENT PHYLA OR CLASSES(E.G., EITHER AN ANIMAL HAS LEGS OR IT DOESN’T)WHY IS THIS????????A MAJOR REASON IS THAT BECAUSE OF HIERARCHY IN DEVELOPMENTAL GRNS, ONCE UPPER LEVEL CIRCUITRY GETS INSTALLED (E.G., SETTING UP A PROGENITOR FIELD), SUBSEQUENT CHANGES ALL HAVE TO BE CONSISTENT WITH THAT OUTPUT: CANALIZATION

43. A DIAGRAM OF GRN HIERARCHY

44. HIERARCHICAL UPPER LEVEL GRN DESIGN FEATURES WHICH ACT TO ENSURE CANONICAL OUTPUT: 1. PREVALENT FEEDBACK WIRING, WHICH ERASES PRIOR QUANTITATIVE VARIATION, AND CAN MAGNIFY DELETERIOUS CHANGE INTO GRN COLLAPSE2. Frequent use of Dominant repression subcircuits, WHICH producE all or nothing boundaries and BOOLEAN SPATIAL PATTERNS OF REGULATORY STATE3. “over-wiring”, multiplicity of non-redundant individual subcircuits, WHICH ensure correct spatial output4. relative insensitivity to dynamics of grn operation

45. THE BUFFERING EFFECT OF UPPER LEVEL GRN DESIGN ESSENTIALLY RESULTS IN “BOOLEANIZATION” OF SUBCIRCUIT OUTPUT IN CONTRAST, WHERE VARIATION IN EXPRESION OF A SINGLE GENE (LIKE YELLOW OR EBONY) AFFECTS A DOWNSTREAM PROPERTY OF THE ORGANISM, CONTINUOUS VARIATION MAY OCCURTHEREFORE AT THE GRN PERIPHERY VARIATION IS THE RULE, WHILE IN BODY PLAN EVOLUTION MEDIATED BY MULTIGENE UPSTREAM GRN SUBCIRCUITS, ALL OR NOTHING CHANGE IS THE RULE

46. OVERALL CONSEQUENCES SELECTION OF CONTINUOUS VARIANTS ACTS SPECIFICALLY ON PERIPHERAL GRN FEATURES IN MODERN ANIMALSTHE MAIN ASPECTS OF THE BODY PLAN THAT ARE CONTROLLED BY UPPER LEVEL GRN COMPONENTS EITHER OPERATE TO PRODUCE THE PHYLETIC BODY PLAN OR THE ORGANISM DIESBODY PLAN EVOLUTION HAS OCCURRED IN BURSTS DURING THE PHANEROZOIC, AS PHYLOGENY AND PALEONTOLOGY SHOW, BUT ACCORDING TO THE CONSTRAINTS OF GRN HIERARCHY AND CANALIZATION