Selected Readings

General Reviews

Davidson EH. Genomic regulatory systems: development and evolution. San Diego: Academic Press, 2001.

Regulatory Evolution: Early Ideas

Britten RJ, Davidson EH. Repetitive and non-repetitive DNA sequences and a speculation on the origins of evolutionary novelty. Q Rev Biol 1971; 46: 111-138.

Jacob F. Evolution and tinkering. Science 1977; 196: 1161-1166.

Wilson AC. The molecular basis of evolution. Sci Am 1985; 253: 164-173.

Zuckerkandl E, Pauling L. Evolutionary divergence and convergence in proteins. In Bryson V, Vogel JH, eds. Evolving genes and proteins. New York: Academic Press, 1965: 97-166.

Functions of cis -Regulatory Element and Transcription Factor Interactions

Arnone MI, Davidson EH. The hardwiring of development: organization and function of genomic regulatory systems. Development 1997; 124: 1851-1864.

Lin Y-S, Carey M, Ptashne M, Green MR. How different eukaryotic transcriptional activators can cooperate promiscuously. Nature 1990; 345: 359-361.

Ptashne M. A genetic switch: phage lambda and higher organisms, 2nd edn. Cambridge, MA: Blackwell Scientific, 1992.

Ptashne M, Gann A. Genes and signals. Cold Spring Harbor: Cold Spring Harbor Laboratory Press, 2002.

Origins of cis -Regulatory Elements

Jordan IK, Rogozin IB, Glazko GV, Koonin EV. Origin of a substantial fraction of human regulatory sequences from transposable elements. Trend Genet 2003; 19: 68-72.

Lynch M, Conery JS. The evolutionary demography of duplicate genes. J Struct Funct Genomics 2003; 3: 35-44.

Stone JR, Wray GA. Rapid evolution of czs-regulatory sequences via local point mutations. Mol Biol Evol 2001; 18: 1764-1770.

Conservation and Turnover of Binding Sites in cis -Regulatory Elements

Costas J, Casares F, Vieira J. Turnover of binding sites for transcription factors involved in early Drosophila development. Gene 2003; 310: 215-220.

Dermitzakis ET, Clark AG. Evolution of transcription factor binding sites in mammalian gene regulatory regions: conservation and turnover. Mol Biol Evol 2002; 19: 1121-2002.

Ludwig M. Functional evolution of noncoding DNA. Curr Opin Genet Dev 2002; 2002: 634-639.

Ludwig MZ, Bergman C, Patel NH, Kreitman M. Evidence for stabilizing selection in a eukaryotic enhancer element. Nature 2000; 403: 564-567.

Ludwig MZ, Patel NH, Kreitman M. Functional analysis of eve stripe 2 enhancer evolution in Drosophila: rules governing conservation and change. Development 1998; 125: 949-958.

Popperl H, et al. Segmental expression of Hoxb-1 is controlled by a highly conserved autoregulatory loop dependent upon exd/pbx. Cell 1995; 81: 1031-1042.

Romano L, Wray G. Conservation of Endo16 expression in sea urchins despite evolutionary divergence in both cis and trans-acting components of transcriptional regulation. Development 2003; 130: 4187-4199.

Divergence of cis -Regulatory Element Function

Hough RB, Avivi A, Davis J, Joel A, Nevo E, Platigorsky J. Adaptive evolution of small heat shock protein alphaB-crystallin promoter activity of the blind subterranean mole rat, Spalax ehrenbergi. Proc Natl Acad Sci USA 2002; 815: 8145-8150.

Ross JL, Fong PP, Cavener DR. Correlated evolution of the cis-acting regulatory elements and developmental expression of the Drosophila Gld gene in seven species from the subgroup melanogaster. Dev Genet 1994; 15: 38-50.

Wang X, Chamberlin H. Multiple regulatory changes contribute to the evolution of the Caenorhabditis lin-48 ovo gene. Genes Dev 2002; 16: 2345-2349.

Coevolution of Binding Sites and Transcription Factors

McGregor AP, Shaw PJ, Hancock JM, et al. Rapid restructuring of bicoid-dependent hunchback promoters within and between Dipteran species: implications for molecular coevolution. Evol Dev 2001; 3: 397-407.

Shaw PJ, Salameh A, McGregor AP, et al. Coevolution in bicoid-dependent promoters and the inception of regulatory incompatibilities among species of higher Diptera. Evol Dev 2002; 4: 265-277.

Regulatory Variation

Cowles CR, Hirschhorn JN, Altshuler D, Lander ES. Detection of regulatory variation in mouse genes. Nature Genet 2002; 32: 432-437.

Enard W, Khaitovich P, Klose J, et al. Intra- and interspecific variation in primate gene expression patterns. Science 2002; 296: 340-343.

Oleksiak MJ, Churchill GA, Crawford DL. Variation in gene expression within and among natural populations. Nature Genet 2002; 32: 261-266.

Rifkin SA, Kim J, White KP. Evolution of gene expression in the Drosophila melanogaster subgroup. Nature Genet 2003; 33: 138-144.

Rockman MV, Wray GA. Abundant raw material for cis-regulatory evolution in humans. Mol Biol Evol 2002; 19: 1991-2004.

Yan H, Yuan W, Velculescu VE, Vogelstein B, Kinzler KW. Allelic variation in human gene expression. Science 2002; 297: 1143.

Population Genetics of cis -Regulatory Elements

Carter AJR, Wagner GP. Evolution of functionally conserved enhancers can be accelerated in large populations: a population-genetic model. Proc R Soc Lond (Biol) 2002; 269: 953-960.

Gerland U, Hwa T. On the selection and evolution of regulatory DNA motifs. J Mol Evol 2001; 55: 386-400.

Morphological Variation within Species

Anh D-G, Gibson G. Axial variation in the threespine stickleback: genetic and environmental factors. Evol Dev 1999; 1: 100-112.

Arthur W. Variable segment number in centipedes: population genetics meets evolutionary developmental biology. Evol Dev 1999; 1: 62-69.

Shubin N, Wake DB, Crawford AJ. Morphological variation in the limbs of Taricha granulosa (Caudata: Salamandridae): evolutionary and phylogenetic implications. Evolution 1995; 49: 874-884.

Extrapolation from Microevolution to Macroevolution

Akam M. Hox genes, homeosis and the evolution of segment identity: no need for hopeless monsters. Int J Dev Biol 1998; 42: 445-451.

Leroi AM. The scale independence of evolution. Evol Dev 2000; 2: 67-77.

Stern DL. Perspective: evolutionary developmental biology and the problem of variation. Evolution 2000; 54: 1079-1091.

Wallace B. Reflections on the still "hopeful monster." Q Rev Biol 1985; 60: 31-42.

activator A protein that positively regulates transcription of a gene.

Annelida Phylum comprising about 15,000 species of segmented worms; includes polychaetes, earthworms, and leeches.

anterior group Hox genes Hox genes expressed in the anterior region of bilaterians and located toward the 3' end of Hox clusters; include the Hoxl and Hox2 genes in vertebrates.

anural The tailless condition in chordates.

apical ectodermal ridge (AER) A thickening of the ectoderm at the distal extent of developing tetrapod limbs.

artificial selection Selection imposed by humans for one or more traits, usually in a laboratory, captive, or domesticated population.

atavism The evolutionary reversion of a character to an ancestral state.

autopod The distal portion of the vertebrate limb, including the hand/foot and digits.

axes The polarity of animals can be defined in three dimensions. In bilaterians, the two main axes are the anteroposterior (head-to-tail or rostrocaudal) axis and the orthogonal dorsoventral axis. Projections from the body wall, such as appendages, also possess a third proximodistal axis.

basal In phylogenetic terms, a group that branches at the base of a clade.

battery A group of genes regulated by the same transcription factor.

Bilateria The bilaterally symmetrical animals, including all protostomes and deuteros-tomes, but not sponges, cnidarians, or ctenophores.

blastopore An invagination on the surface of embryos into which the mesoderm and endoderm move during early embryogenesis.

Cambrian The geological period from 544 to 490 million years ago, during which the diversity of modern animal phyla expanded.

carapacial ridge A prominent outgrowth of ectoderm and mesoderm that arises on the dorsal flank of the turtle embryo and gives rise to the dorsal carapace (shell).

cell autonomous Genes whose products affect only the differentiation or behavior of cells in which they are expressed. Contrast with genes that encode signaling ligands that act on other cells (i.e., non-cell-autonomously).

central group Hox genes Hox genes expressed in the central region of bilaterians and located in the middle of Hox clusters; include the Hox3 through Hox8 genes in vertebrates.

cephalochordate Phylum composed of only approximately 25 marine species characterized by a notochord and small anterior brain vesicle. Also known as the lancelets, due to their body shape, they constitute the nearest phylogenetic outgroup to the vertebrates.

chromatin The material into which DNA in the cell nucleus is packaged with proteins.

circuit A regulatory pathway that includes particular target genes.

c/s-regulatory element A discrete region of DNA that affects transcription of a gene.

clade A group of species descended from a common ancestral species. Also known as a monophyletic group.

Cnidaria Phylum comprising approximately 8000 living, mostly marine species, all of which possess nematocyst cells. Their diploblas-tic, radially symmetric body organization consists of an outer cell layer (ectoderm) and an inner cell layer (endoderm). Cnidaria includes jellyfish, sea anemones, and corals.

co-activator Protein that interacts with the activator in control of transcription. Some co-activators possess activities that modify local chromatin conformation.

coelom A body cavity formed from the mesoderm that lies between the gut (endoderm) and the body wall (ectoderm) in many triploblast animals.

colinearity The correlation between the order of Hox genes on a chromosome and the anteroposterior order of gene deployment in the embryo.

combinatorial regulation The control of gene transcription by two or more transcription factors. The spatial patterns of gene expression are often delimited by the combined action of transcription factors.

compartment A discrete subdivision of a developing field that contains populations of cells that share a lineage restriction. Cells of one compartment do not intermix with adjacent cells in other compartments.

compensatory mutation A mutation that restores or maintains the function of a gene or cis-regulatory element by counteracting the effects of one or more different mutations.

cooperativity The enhanced binding of a protein to a cis-regulatory DNA sequence due to interaction with other bound proteins.

co-option The recruitment of genes into new developmental or biochemical functions.

corepressor A protein that interacts with a repressor in the control of transcription. Corepres-sors may modify the local conformation of chromatin.

cryptic genetic variation The genetic variation in components of developmental programs that exists in the absence of phenotypic variation. Perturbations to developmental programs may unmask this variation and lead to phenotypic variation.

deuterostomes The group of animals including echinoderms, ascidians, cephalochordates, and vertebrates in which the mouth forms at a site separate from the blastopore.

Devonian The geological period from approximately 409 to 362 million years ago, during which terrestrial forms invaded the land.

diploblasts Animals possessing two cell layers— the outer ectoderm layer and the inner endoderm layer; include cnidarians.

disparity The variety of designs in body plans.

diversity The number of species in a clade; the divergence of morphology.

echinoderm A deuterostome animal with a pen-taradially symmetrical adult body plan.

ectoderm The outer tissue layer of animal embryos that gives rise to the epidermis and the nervous system.

Ediacara The fauna that lived 575-544 million years ago, named for their fossil deposits in the hills of South Australia.

endoderm The inner tissue layer of animal embryos that gives rise to the gut and other associated organs exon shuffling The process through which new genes are generated by recombination of one or more exons of other genes.

extant Living, as opposed to extinct, species.

field-specific selector gene A specific class of selector genes that control the formation and patterning of morphogenetic fields such as the eye, leg, and wing.

focus The developmental organizer at the center of the butterfly eyespot field.

gap genes The genes that subdivide the Droso-phila embryo into several regions encompassing many segments. They encode transcription factors that regulate the expression of other gap genes, pair-rule genes, and homeotic genes.

gene complex A group of adjacent genes related by gene duplication.

gene divergence The process through which two or more genes created by a duplication event(s) acquire distinct functions. Changes in regulatory and/or coding regions lead to differences in gene function.

gene duplication The creation of additional genes from the template of one gene.

gene family Two or more genes with related sequences that are derived from a common ancestral gene. They are not necessarily linked, may be widely dispersed in the genome, and may be greatly diverged in function.

genetic architecture Refers to the number and interactions among genes whose products govern a partcular trait.

genetic redundancy Two genes are redundant when the absence of the function of one gene causes little or no effect because a second gene can operate in its place.

germ layers The regions of early animal embryos that give rise to the different tissue layers. Bilaterians have three germ layers, which form the ectoderm, mesoderm, and endoderm.

gradient Formed when the concentration of a regulatory substance varies with the distance from a source.

haltere The hindwing of two-winged insects such as flies and mosquitoes.

helix-loop-helix A structural motif of a distinct class of transcription factors in which the helical domains of two interacting subunits are interrupted by nonhelical polypeptide loops.

helix-turn-helix A structural motif of a distinct class of transcription factors consists of two alpha-helical domains and a short extended amino acid chain between them, found in homeodomain proteins.

hierarchy The organization of regulatory circuits into two or more tiers. Gene products in one tier control the expression of genes in lower tiers.

holometabolous Insects which develop through larval and pupal stages and undergo complete metamorphosis.

homeobox A 180-bp region of DNA encoding a particular class of DNA-binding domains. Approximately 20 families of homeobox-containing genes exist.

homeodomain The protein domain encoded by the homeobox.

homeotic genes Genes that regulate the identity of body regions. Mutations in homeotic genes cause the transformation of one body region or part into the likeness of another.

homolog When referring to genes, indicates genes that share similarities in their sequence because they evolved from a common ancestral gene. When referring to morphological structures, indicates features that are shared due to common ancestry.

homonomous A body plan or body part composed of repeating, similar parts.

housekeeping genes Genes that encode proteins required for basic functions required in all cells.

Hoxgenes Homeotic, homeobox-containing genes found in linked clusters in all bilaterians.

imaginal disc Small sets of epithelial cells that are set aside during Drosophila embryogenesis, subsequently proliferate in the larva, and give rise to adult structures.

individualization/individuation The process of morphological differentiation of similar body parts.

lateral plate mesoderm Mesoderm in vertebrate embryos that gives rise to the blood, kidneys, and heart tissues.

leucine zipper A common transcription factor motif in which two subunits of the protein interact through leucine-containing repeat sequences.

Lophotrochozoa A great clade of protostomes including the annelids, molluscs, flat-worms, and other phyla; many phyla within this group produce a particular form of larva (trochophore) or feeding structure (lophophore).

maternal effect Genes that are expressed during oogenesis and whose products function in the development of the embryo.

meristic variation Differences in the number of repeating structures.

mesoderm The tissue layer between the ectoderm and the endoderm that gives rise to the musculature of all bilaterians.

Metazoa Multicellular animals, including diploblasts and triploblasts.

modularity The organization of animals into devel-opmentally and anatomically distinct parts. Also, the organization of gene regulatory regions into discrete cis-regulatory elements.

molecular clock Differences in the sequences of RNA, DNA, and protein molecules accumulate as species diverge. In theory, geological information can be used to calibrate the rate of sequence changes between lineages. The relative sequence divergence between species can be used to infer phylogenetic relationships.

morphogen A substance whose concentration varies across a tissue or field and to which cells respond differently at different concentrations.

morphogenetic field A discrete region of an embryo that will give rise to a structure and within which pattern formation is largely independent of other developing structures.

network Two or more regulatory circuits that are linked by regulatory interactions between components of each circuit.

neural crest A population of cells in vertebrates that migrates from the edge of the neural plate to different regions of the body and gives rise to tissues such as the facial skeleton, melanocytes, and peripheral neurons.

notochord A structure that runs from head to tail in chordates and lies beneath the developing central nervous system.

novelty New morphological characters of adaptive value.

onychophora A phylum of soft-bodied animals possessing unjointed appendages; closely related to the arthropods.

oral-aboral axis The axis orthogonal to the pentaradial arms of echinoderms.

Ordovician The geological period from approximately 490 to 439 million years ago, which followed the Cambrian and preceded the Devonian.

organizer A signaling center in a developing embryo or field that induces the development of surrounding tissues. Examples include the Spemann organizer of amphibian embryos and the focus in butterfly imaginal wing discs.

orthologs Homologous genes in different species that arose from a single gene in the last common ancestor of these species.

outgroup A taxon that diverged from a group of other taxa before members of that group subsequently diverged from one another.

pair-rule genes Drosophila genes that are usually expressed in seven transverse stripes across the future segmented region of the early embryo, one stripe for every two segment primordia.

ParaHox genes A small cluster of genes that arose from an early duplication of a primitive Proto-Hox gene cluster. ParaHox genes function in endoderm development and may be involved in the evolution of the through gut in bilaterians.

paralogs Homologous genes that are related by duplication of an ancestral gene.

parasegment Units of the Drosophila embryo composed of the posterior part of one segment and the anterior part of the adjacent segment.

paraxial mesoderm That part of the vertebrate mesoderm that gives rise to the somites.

pathway In cell-cell signaling, the components required for the sending, receiving, and transduction of a signal, including one or more ligands, membrane-associated receptors, intracellular signal transducers, and transcription factors. phenocopy A mimic of a genetic mutant pheno-type, usually caused by environmental changes.

phylogenetic tree A depiction of the evolutionary relationships among species and their order of "branching" from common ancestors. pleiotropic Genes or proteins with multiple functions.

polychaete One class of annelids distinguished by the presence of chaetae, projections from the sides of each body segment. Porifera Phylum containing the sponges, the most primitive animal group that does not contain true germ layers. posterior group Hox genes Hox genes that are expressed in the posterior or caudal region of bilaterians and are found at the 5' end of Hox clusters; include the Abd-B-related and Hox9-13 genes. primordia A discrete field of cells that will give rise to a particular organ, appendage, or tissue type.

proleg The leg-like abdominal appendages found on the larva of certain insects, particularly Lepidoptera. promoter The region of a gene near the start site of transcription to which the general transcriptional machinery binds. proneural cluster A group of cells from which one or more neural precursor cells will segregate, divide, and differentiate. Proterozoic The geological era from approximately 2500 to 544 million years ago. protostomes One of two clades of bilaterians characterized by the origin of the mouth at the blastopore. pseudogene The remnant of a gene that has been rendered nonfunctional through the accumulation of mutations.

quantitative trait A character that exhibits continuous variation in a population.

quantitative trait loci (QTL) Genetic loci that contribute to the variation in a quantitative trait in a population.

radiation The evolutionary divergence of a lineage into a variety of forms; often used to describe rapid diversification.

region-specific selector One class of selector genes that regulates the identity of contiguous body regions (e.g., Hox genes).

regulatory circuit A signaling pathway and one or more of the target genes regulated by the pathway in a given cell, tissue, or field.

regulatory evolution Evolutionary changes in gene regulation.

reporter gene A gene whose expression is used to visualize the activity of a heterologous, linked cis-regulatory element in vivo.

repressor A transcription factor that negatively regulates the expression of a gene, often by binding directly to DNA sequences in a cis-regulatory element.

rhombomere A subdivision of the vertebrate hindbrain.

secondary field Discrete units of development that are specified in the developing embryo after the primary axes are established and that give rise to appendages and organs. Pattern formation within secondary fields occurs independently of other fields.

segment polarity gene Genes that act within developing Drosophila segments to regulate the anteroposterior polarity of each segment.

selector gene A gene that controls cell fate.

serial homologs Repeated structures of a single organism that share a similar developmental origin.

somite A segmented subdivision of the vertebrate mesoderm that gives rise to vertebrae and associated processes, selected muscles, and the dermis.

stabilizing selection Selection that acts to keep a character constant in a population.

stem lineage Generally refers to fossil taxa that possess some, but not all, of the characters that define a later group.

syncytium An embryo or tissue containing nuclei that are not separated by cell membranes.

synteny Similarity in the linkage order of ortholo-gous genes between two or more species.

tetraploidization A process of whole-genome duplication caused by doubling the number of chromosomes per cell from diploid (two copies) to tetraploid (four copies).

tetrapod The four-limbed terrestrial classes of vertebrates, including amphibians, reptiles, birds, and mammals.

trace fossil The impressions left in sediments by the meanderings and burrowing activities of ancient animals.

transcription factor A protein that regulates the transcription of genes, often, but not exclusively, by binding to cis-regulatory elements.

triploblasts Animals composed of three germ layers; includes all bilaterians.

Urbilateria The hypothetical last common ancestor of all bilaterians.

urochordate A marine phylum in which the noto-chord (or urochord) is found only in the larval tail.

urodele The tailed form of chordates.

zinc finger A distinct class of transcription factors in which a DNA-binding polypeptide loop or "finger" forms through a coordination complex of zinc with cysteine and histi-dine residues at the base of the loop.

zone of polarizing activity (ZPA) The organizer at the posterior margin of the developing vertebrate limb that regulates anteroposterior polarity.

zygote The fertilized egg. It contains the genetic contributions of both the male and female parents.

Page numbers in italics refer to figures; those in bold to tables.

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