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Definitions of Novelty

-morphologically or physiologically new and qualitatively distinct feature
-a key feature that allows the lineage carrying it to enter a new adaptive zone
-new homolog. Evolved from homologous fins, but contain new homologs shared with other limbs
-ex: ancestral globin gene gave rise to new family member myoglobin and hemoglobin family of new gene homologs


Ways of Seeking Novel Features in Evolution

-comparative anatomy
-features of fossil organisms
-features in development
-evolution of genes
-where an organism sits in the phylogenetic tree


Some Major Novelties in Evolution

-origins of animal body plans
-mouth parts of insects
-tetrapod limbs
-body plan of whales
-hominid upright anatomy and walking
-human brain


Organisms Arise From Process of Development

-evolutionary change has to occur through generation by generation of individuals
-development must change for evolution to occur
-gene control of development must evolve for development to evolve-heritable change
-mechanisms of development are under selection and may influence or constrain evolutionary possibilities


Development Itself

-will have features that constrain what evolution can do
-selection doesn't just operate at a single stage in an organism's life
-operates all the way through


Symmetry Breaking

-mostly homogenous sphere egg-->development must produce symmetry breaking to produce body axis and differentiation of cells etc.
-genes and signaling systems exist for all three axes D/V set up first, A/P set up second and L/R set up last
-commonly shared systems-shared by echinoderms, vertebrates, mollusks and likely others


Standard Selection

-phenotypes are the sorting of genes so genes contribute to appearance of phenotypes and there is selection for phenotypes
-if development is included genes-->development (has rules)-->phenotype and there is selection for both development and phenotype


Developmental Constraints

-can selection do anything or is it limited by existing genetics and developmental mechanisms?
-can organisms actually always be moved by variation and selection to optima or are some apparently possible phenotypes unreachable?


All Animal Phyla

-studied share families of regulatory genes used in development
-share similar requirements for development from a basic set up, eggs plus sperm; i.e. development of a multicellular body from a single cell
-share similar gene expression and morphogenetic strategies (i.e. alternate ways of wiring shared gene systems (networks) produces specifically distinct final development outcomes
-distinct phylogenetic pattern among developmental modes -that's what we expect from a common descent from a single animal ancestor


Genes in the Control of Development

-seen in effects of mutations of genes that specifically affect development
-produce phenotypes-are thus targets of natural selection
-can be cloned and their roles and evolution studied


What Embryo's Have to Accomplish

-set up body axes, anterior-posterior, dorsal-ventral, left-right
-turn on an ordered pattern of gene expression
-establish body regions and control cell identities and positions in those regions
-differentiate cells that have specific locations, have defined fates, or talk to each other


Developmental Regulatory Genes and the Evolution of Development

-evo-devo is really only possible if there are relatively few key control genes
-evo-devo only possible if pre-existing genes can be co-opted and used in a new way to construct a new developmental pathway
-kinds of genes involved: all elements of basic gene regulatory machinery


Developmental Regulators

-transcription factors
-growth factors
-membrane-bound signal receptors
-signal cascades
-enzymes that regulate protein functions by protein modification-kinases and phosphatases


Instructions to Build a Fly

-egg born already knowing which end is front and which is back.
-due to Maternal gene in anterior end (14 total)
-start to set up patterns of differentiation in center of embryo
-gap genes (6)-->pair rule genes (8; broad divisions set up)-->segment polarity genes (8; segment facing forward or backward?)-->hox genes (identify body segments)


Hox Genes

-at molecular level each encodes for a protein that binds to DNA
-each has three domains that act together to bind to the wide groove of DNA where they can influence genes and promote transcription of downstream gene
-example of a class of major regulatory genes in development that have played important roles in evolution
-present in animals
-clustered in chromosome organization
-in mammals genome duplication has produced 4 such clusters and gene number up to 13 by amplification of 9-10 group


Function of Hox Proteins

-hydrogen bonds between complementary bases
-the three helix domains of the hbox in the wide groove of the DNA
-the helix that lies across the groove is the recognition helix
-the sequence of amino acids in it determines what DNA binding site the protein binds to



-strategy of development as we saw with limb buds
-one group of cells signals to another
-cell expresses a gene that produces a diffusible ligand
-responding cell has a cell surface receptor for the ligand
-cytoplasmic signal cascade activates transcription factor then turns on transcription in target gene critical for developmental step


Simple Positive Transcription Output

-transcription factor + start site on DNA
-turns gene on


Simple Negative Transcription Output

-transcription factor + block
-turns gene off


Complex Positive Transcription Output

-two negatives result in a positve


Butterflies vs. Flies

-adult: flies have single pair of wings and butterflies have two pairs
-developmental styles: three distinct forms of development in insects. Flies and butterflies share the third with an important distinction
-larva: caterpillars have five pairs of abdominal legs as well as three thoracic pairs


Drosophila Haltere

-pull off and can't stabilize
-can't fly properly
-don't provide power flight but are somehow balance organisms that have evolved from rear wings
-derived from a wing; not a wing but has a function


Paleozoic Primitive Wings Insects

-segment identity not as tightly regulated as in modern insects
-some had legs on abdomen; others had wings on abdominal segments of their larvae
-these identify functions and outcomes are controlled by Hox genes, and their regulation continues to evolve



-re-evolve abdominal legs by trick of double inhibition to get a positive outcome where it was advantageous
-old developmental machinery for growing a leg on an segment was not lost, it was repressed in abdominal segments
-leg outgrowth requires expression of Distal-less gene
-Dll is negatively regulated by Hox AbdA=repression 1
-Drosophila AbdA and AbdB are expressed in abdominal segments, Dll is not


Dll Expression in Young Caterpillar

-holes in AbdA and AbdB expression when Dll will be allowed to be expressed and lead to legs


Two Wings vs. Four

-primitive number of wings among living insects is 4 but flies have 2
-Hox Ubx is expressed in Drosophila T3 segment where it converts rear wing disc into haltere
-wing disc evolved to read Ubx to generate distinct different pattern of development
-wing development was under control of genes controlled by Ubx; in flies the downstream regulation system changed. Ubx still upstream regulator but genes downstream read it differently in terms of developmental path they follow



-jaws express Dll as a key regulator of outgrowth
-thoracic legs express Dll
-in each abdominal segment Dll is being expressed in two dots on each size
-differs from drosophila larva because there is no Dll expression pattern along abdomen--it's repressed in drosophila


Pathway Evolution Summary

-see notes to memorize pathways


Gene Regulatory Network

-regulatory genes act in concert
-genes in a network influence the expression of other genes to produce an outcome of gene expression that affects the behavior or identity of cells in a developing organism
-can be extremely conserved in evolution and still produce different outcomes because of some modification at the end
-networks are flexible at downstream ends especially at what output could be
-upstream less likely to be shifted because would produce larger effects if there's a mutation up there
-thus we see highly conserved roles for Hox genes in laying out animal body axes, but the structures of these bodies can differ