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References

Abbott AL, Alvarez-Saavedra E, Miska EA, Lau NC, Bartel DP, Horvitz HR, Ambros V (2005) The let-7 microRNA family members mir-48, mir-84, and mir-241 function together to regulate developmental timing in Caenorhabditis elegans. Dev Cell 9:403–414.

Abzhanov A, Protas M, Grant RB, Grant PR, Tabin CJ (2004) Bmp4 and morphological variation of beaks in Darwin’s finches. Science 305:1462–1465.

Abzhanov A, Kuo WP, Hartmann C, Grant BR, Grant PR, Tabin CJ (2006) The calmodulin pathway and evolution of elongated beak morphology in Darwin’s finches. Nature 442:563–567.

Adachi-Yamada T, O’Connor MB (2002) Morphogenetic apoptosis: A mechanism for correcting discontinuities in morphogen gradients. Dev Biol 251:74–90.

Adami C (1995) Learning and complexity in genetic auto-adaptive systems. Physica D 80:154–170.

Adami C (1998) Introduction to Artificial Life (Springer, New York).

Adami C (2003) Sequence complexity in Darwinian evolution. Complexity 8:49–56.

Ahnelt PK, Kolb H (2000) The mammalian photoreceptor mosaic-adaptive design. Prog Retin Eye Res 19:711–777.

Alberts B, Bray D, Lewis J, Raff M, Roberts K, Watson JD (1989) Molecular Biology of the Cell (Garland, New York).

Albertson RC, Kocher TD (2006) Genetic and developmental basis of cichlid trophic diversity. Heredity 97:211–221.

Aldenderfer MS (2003) Moving up in the world: Archaeologists seek to understand how and when people came to occupy the Andean and Tibetan plateaus. Am Sci 91:542–549.

Alexander RD, Noonan KM, Crespi BJ (1991) The evolution of eusociality. In The Biology of the Naked Mole Rat, eds Sherman PW, Jarvis JUM, Alexander RD (Princeton Univ Press, Princeton), pp 3–44.

Allaby RG, Peterson GW, Merriwether DA, Fu YB (2005) Evidence of the domestication history of flax (Linum usitatissimum L.) from genetic diversity of the sad2 locus. Theor Appl Genet 112:58–65.



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References Abbott Al, Alvarez-saavedra e, Miska eA, lau nC, Bartel DP, horvitz hr, Ambros v (2005) The let-7 micrornA family members mir-48, mir-84, and mir-241 function together to regulate developmental timing in Caenorhabditis elegans. Dev Cell 9:403–414. Abzhanov A, Protas M, Grant rB, Grant Pr, Tabin CJ (2004) Bmp4 and morphological varia- tion of beaks in Darwin’s finches. Science 305:1462–1465. Abzhanov A, Kuo WP, hartmann C, Grant Br, Grant Pr, Tabin CJ (2006) The calmodulin pathway and evolution of elongated beak morphology in Darwin’s finches. Nature 442:563–567. Adachi-yamada T, o’Connor MB (2002) Morphogenetic apoptosis: A mechanism for correct- ing discontinuities in morphogen gradients. Dev Biol 251:74–90. Adami C (1995) learning and complexity in genetic auto-adaptive systems. Physica D 80:154–170. Adami C (1998) Introduction to Artificial Life (springer, new york). Adami C (2003) sequence complexity in Darwinian evolution. Complexity 8:49–56. Ahnelt PK, Kolb h (2000) The mammalian photoreceptor mosaic-adaptive design. Prog Retin Eye Res 19:711–777. Alberts B, Bray D, lewis J, raff M, roberts K, Watson JD (1989) Molecular Biology of the Cell (Garland, new york). Albertson rC, Kocher TD (2006) Genetic and developmental basis of cichlid trophic diver- sity. Heredity 97:211–221. Aldenderfer Ms (2003) Moving up in the world: Archaeologists seek to understand how and when people came to occupy the Andean and Tibetan plateaus. Am Sci 91:542–549. Alexander rD, noonan KM, Crespi BJ (1991) The evolution of eusociality. in The Biology of the Naked Mole Rat, eds sherman PW, Jarvis JUM, Alexander rD (Princeton Univ Press, Princeton), pp 3–44. Allaby rG, Peterson GW, Merriwether DA, Fu yB (2005) evidence of the domestication history of flax (Linum usitatissimum l.) from genetic diversity of the sad2 locus. Theor Appl Genet 112:58–65. 0

OCR for page 305
0 / References Allen C, Bekoff M, lauder G, eds (1998) Nature’s Purposes: Analyses of Function and Design in Biology (MiT Press, Cambridge, MA). Alonso Cr, Wilkins As (2005) The molecular elements that underlie developmental evolu - tion. Nat Rev Genet 6:709–715. Altenberg l (2005) evolvability suppression to stabilize far-sighted adaptations. Artif Life 11:427–443. Andersson Jo, Andersson sG (1999) insights into the evolutionary process of genome deg- radation. Curr Opin Genet Dev 9:664–671. Andersson Jo, hirt rP, Foster PG, roger AJ (2006) evolution of four gene families with patchy phylogenetic distributions: influx of genes into protist genomes. BMC Evol Biol 6:27. Andersson M (1984) The evolution of eusociality. Annu Rev Ecol Syst 15:165–189. Andersson M (1994) Sexual Selection (Princeton Univ Press, Princeton). Andres A, Garriga P, Manyosa J (2003) Altered functionality in rhodopsin point mutations associated with retinitis pigmentosa. Biochem Biophys Res Commun 303:294–301. Anonymous (1981) Unbiased biology textbook planned. Origins Res 4:1. Anonymous (1992) rotary engines. Creation 15:23. Antezana AM, Antezana G, Aparicio o, noriega i, velarde Fl, richalet JP (1998) Pulmonary hypertension in high-altitude chronic hypoxia: response to nifedipine. Eur Respir J 12:1181–1185. Aranzana MJ, Kim s, Zhao K, Bakker e, horton M, Jakob K, lister C, Molitor J, shindo C, Tang C, et al. (2005) Genome-wide association mapping in Arabidopsis identifies previ- ously known flowering time and pathogen resistance genes. PLoS Genet 1:e60. Arendt D (2003) evolution of eyes and photoreceptor cell types. Int J Dev Biol 47:563–571. Armstrong K (2000) The Battle for God (Knopf, new york). Aronson hG, royer We, hendrickson WA (1994) Quantification of tertiary structural conser- vation despite primary sequence drift in the globin fold. Protein Sci 3:1706–1711. Arrow GJ (1951) Horned Beetles (Dr. W. Junk, The hague). Arthur W (2000) The Origin of Animal Body Plans (Cambridge Univ Press, Cambridge, UK), 2nd ed. Asenjo AB, rim J, oprian DD (1994) Molecular determinants of human red/green color discrimination. Neuron 12:1131–1138. Aury JM, Jaillon o, Duret l, noel B, Jubin C, Porcel BM, segurens B, Daubin v, Anthouard v, Aiach n, et al. (2006) Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia. Nature 444:171–178. Averof M, Akam M (1995) hox genes and the diversification of insect and crustacean body plans. Nature 376:420–423. Averof M, Patel nh (1997) Crustacean appendage evolution associated with changes in hox gene expression. Nature 388:682–686. Avery J (2003) Information Theory and Evolution (World scientific, singapore). Avise JC (2006) Evolutionary Pathways in Nature: A Phylogenetic Approach (Cambridge Univ Press, Cambridge, UK). Ayala FJ (1999) Adaptation and novelty: Teleological explanations in evolutionary biology. Hist Philos Life Sci 21:3–33. Bagnold rA (1988) The Physics of Sediment Transport by Wind and Water (Am soc of Civil eng, new york). Baker PT (1976) Work performance of highland natives. in Man in the Andes: A Multidisciplinary Study of High-Altitude Quechua, eds Baker PT, little MA (Dowden, hutchinson, and ross, stroudsburg, PA), pp 300–314.

OCR for page 305
References / 0 Balasubramanian s, sureshkumar s, Agrawal M, Michael TP, Wessinger C, Maloof Jn, Clark r, Warthmann n, Chory J, Weigel D (2006) The PhyToChroMe C photoreceptor gene mediates natural variation in flowering and growth responses of Arabidopsis thaliana. Nat Genet 38:711–715. Baldwin JM (1896) A new factor in evolution. Am Nat 30:441–451. Baldwin JM (1902) Development and Evolution (Macmillan, new york). Balhoff JP, Wray GA (2005) evolutionary analysis of the well characterized endo16 promoter reveals substantial variation within functional sites. Proc Natl Acad Sci USA 102:8591– 8596. Ballerio A (1999) revision of the genus Pterorthochaetes, first contribution (Coleoptera: scarabaeoidea: Ceratocanthidae). Folia Heyrovskiana 7:221–228. Barabasi A-l, Albert r (1999) emergence of scaling in random networks. Science 286:509– 512. Barabasi A-l, oltvai Z (2004) network biology: Understanding the cell’s functional organi- zation. Nat Rev Genet 5:101–113. Barlow n (1958) The Autobiography of Charles Darwin (Collins, london). Bastock M (1956) A gene mutation which changes a behavior pattern. Evolution 10:421– 439. Baumann P (2005) Biology of bacteriocyte-associated endosymbionts of plant sap-sucking insects. Annu Rev Microbiol 59:155–189. Beall CM (2001) Adaptations to altitude: A current assessment. Annu Rev Anthropol 30:423– 446. Beall CM (2002) Biodiversity of human populations in mountain environments. in Mountain Biodiversity; A Global Assessment, eds Korner C, spehn eM (The Parthenon Publishing Group, new york), pp 199–210. Beall CM (2006) Andean, Tibetan, and ethiopian patterns of adaptations to high-altitude hypoxia. Integr Comp Biol 46:18–24. Beall CM, henry J, Worthman C, Goldstein MC (1996) Basal metabolic rate and dietary seasonality among Tibetan nomads. Am J Hum Biol 8:361–370. Beall CM, Brittenham GM, strohl KP, Decker MJ, Goldstein MC, Blangero J, Williams- Blangero s, Almasy l, Worthman CM (1997a) ventilation and hypoxic ventilatory response of Tibetan and Aymara high altitude natives. Am J Phys Anthropol 104:427– 447. Beall CM, strohl K, Blangero J, Williams-Blangero s, Brittenham GM, Goldstein MC (1997b) Quantitative genetic analysis of arterial oxygen saturation in Tibetan highlanders. Hum Biol 69:597–604. Beall CM, Brittenham GM, strohl KP, Blangero J, Williams-Blangero s, Goldstein MC, Decker MJ, vargas e, villena M, soria r, et al. (1998) hemoglobin concentration of high-altitude Tibetans and Bolivian Aymara. Am J Phys Anthropol 106:385–400. Beall CM, Almasy lA, Blangero J, Williams-Blangero s, Brittenham GM, strohl KP, Decker M, vargas e, villena M, soria r, et al. (1999) Percent of oxygen saturation of arterial hemoglobin of Bolivian Aymara at 3900-4000m. Am J Phys Anthropol 108:41–51. Beall CM, laskowski D, strohl KP, soria r, villena M, vargas e, Alarcon AM, Gonzales C, erzurum sD (2001) Pulmonary nitric oxide in mountain dwellers. Nature 414:411–412. Beall CM, song K, elston rC, Goldstein MC (2004) higher offspring survival among Tibetan women with high oxygen saturation genotypes residing at 4,000 m. Proc Natl Acad Sci USA 101:14300–14304. Beavis WD (1994) The power and deceit of QTl experiments: lessons from comparative QTl studies. in Proceedings of the Forty-Ninth Annual Corn and Sorghum Industry Research Conference (Am seed Trade Assoc, Washington, DC), pp 255–266. Beavis WD (1998) QTl analyses: Power, precision, and accuracy. in Molecular Dissection of Complex Traits, ed Paterson Ah (CrC, Boca raton, Fl), pp 145–162.

OCR for page 305
0 / References Behe M (1996) Darwin’s Black Box: The Biochemical Challenge to Evolution (Free Press, new york). Behe MJ (2005a) Design for living. New York Times, Feb. 7, p A21. Behe MJ (2005b) scientific orthodoxies. First Things 15–20. Beig D (1972) The production of males in queenright colonies of Trigona (Scaptotrigona) postica. J Apic Res 11:33–39. Bekker A, holland hD, Wang Pl, rumble D, iii, stein hJ, hannah Jl, Coetzee ll, Beukes nJ (2004) Dating the rise of atmospheric oxygen. Nature 427:117–120. Beldade P, Brakefield PM, long AD (2005) Generating phenotypic variation: Prospects from “evo-devo” research on Bicyclus anynana wing patterns. Evol Dev 7:101–107. Bell C (1833) The Hand: Its Mechanism and Vital Endowments as Evincing Design (William Pickering, london). Bell G (1997) The Basics of Selection (Chapman & hall, new york). Bell G, Mooers Ao (1997) size and complexity among multicellular organisms. Biol J Linnaean Soc 60:345–363. Belting hG, shashikant Cs, ruddle Fh (1998) Modification of expression and cis-regula- tion of hoxc8 in the evolution of diverged axial morphology. Proc Natl Acad Sci USA 95:2355–2360. Benkman CW (1993) Adaptation to single resources and the evolution of crossbill ( Loxia) diversity. Ecol Monogr 63:305–325. Bennett AF (2003) experimental evolution and the Krogh Principle: Generating biological novelty for functional and genetic analyses. Physiol Biochem Zool 76:1–11. Bennett AF, lenski re (1993) evolutionary adaptation to temperature, ii: Thermal niches of experimental lines of Escherichia coli. Evolution 47:1–12. Bennett AF, lenski re (1999) experimental evolution and its role in evolutionary physiol- ogy. Am Zool 39:346–362. Bennett AF, lenski re, Mittler Je (1992) evolutionary adaptation to temperature, i: Fitness responses of Escherichia coli to changes in its thermal environment. Evolution 46:16–30. Benson Ke, stephens DW (1996) interruptions, tradeoffs, and temporal discounting. Am Zool 36:506–517. Berg J, lassig M, Wagner A (2004) structure and evolution of protein interaction networks: A statistical model for link dynamics and gene duplications. BMC Evol Biol 4:51. Bernard GD (1983) Dark-processes following photoconversion of butterfly rhodopsins. Biophys Struct Mech 9:277–286. Bertalanffy l (1968) General System Theory: Foundations, Applications, Development (Braziller, new york). Bigelow J, Pargetter rP (1998) Functions. in Nature’s Purposes: Analyses of Function and Design in Biology, eds Allen C, Bekoff M, lauder G (MiT Press, Cambridge, MA). Bloom JD, labthavikul sT, otey Cr, Arnold Fh (2006) Protein stability promotes evolvability. Proc Natl Acad Sci USA 103:5869–5874. Blows MW, Chenoweth sF, hine e (2004) orientation of the genetic variance-covariance matrix and the fitness surface for multiple male sexually selected traits. Am Nat 163: e329–e340. Bodmer r, venkatesh Tv (1998) heart development in Drosophila and vertebrates: Conserva- tion of molecular mechanisms. Dev Genet 22:181–186. Bomblies K, Doebley JF (2005) Molecular evolution of FloriCAUlA/leAFy orthologs in the Andropogoneae (Poaceae). Mol Biol Evol 22:1082–1094. Bonner JT (1993) Dividing the labor in cells and societies. Curr Sci 64:459–466. Bonner JT (2006) Why Size Matters: From Bacteria to Blue Whales (Princeton Univ Press, Princeton). Boomsma JJ, Grafen A (1990) intraspecific variation in ant sex ratios and the Trivers–hare hypothesis. Evolution 44:1026–1034.

OCR for page 305
References / 0 Boomsma JJ, Grafen A (1991) Colony-level sex ratio selection in the eusocial hymenoptera. J Evol Biol 4:383–407. Bordy eM, Dumby AJ, Catuneanu o, eriksson PG (2004) Advanced early Jurassic termite (insecta:isoptera) nests: evidence from the Clarens formation in the Tuli Basin, south- ern Africa. Palaios 19:68–78. Bottaro A, inlay MA, Matzke nJ (2006) immunology in the spotlight at the Dover “intelligent design” trial. Nat Immunol 7:433–435. Bourke AFG (1994) Worker matricide in social bees and wasps. J Theor Biol 167:283–292. Bourke AFG (2005) Genetic, relatedness and social behaviour in insect societies. in Insect Evolutionary Ecology, eds Fellowes MDe, holloway GJ, rolff J (CABi, Wallingford, UK), pp 1–30. Bourke AFG, Franks nr (1995) Social Evolution in Ants (Princeton Univ Press, Princeton). Bowmaker JK, hunt DM (1999) Molecular biology of photoreceptor spectral sensitivity. in Adaptive Mechanisms in the Ecology of Vision, eds Archer sn, Djamgoz MBA, loew er, Partridge JC, vallerga s (Kluwer, Dordrecht, The netherlands), pp 439–462. Braendle C, Miura T, Bickel r, shingleton AW, Kambhampati s, stern Dl (2003) Develop- mental origin and evolution of bacteriocytes in the aphid-Buchnera symbiosis. PLoS Biol 1:70–76. Brännström Å, Dieckmann U (2005) evolutionary dynamics of altruism and cheating among social amoebas. Proc R Soc London Ser B 272:1609–1616. Breitbart M, salamon P, Andresen B, Mahaffy JM, segall AM, Mead D, Azam F, rohwer F (2002) Genomic analysis of uncultured marine viral communities. Proc Natl Acad Sci USA 99:14250–14255. Breseghello F, sorrells M (2006a) Association analysis as a strategy for improvement of quantitative traits in plants. Crop Sci 46:1323–1330. Breseghello F, sorrells M (2006b) Association mapping of kernel size and milling quality in wheat (Triticum aestivum l.) cultivars. Genetics 172:1165–1177. Briscoe AD (1998) Molecular diversity of visual pigments in the butterfly Papilio glaucus. Naturwissenschaften 85:33–35. Briscoe AD (2000) six opsins from the butterfly Papilio glaucus: Molecular phylogenetic evidence for paralogous origins of red-sensitive visual pigments in insects. J Mol Evol 51:110–121. Briscoe AD (2001) Functional diversification of lepidopteran opsins following gene duplica - tion. Mol Biol Evol 18:2270–2279. Briscoe AD (2002) homology modeling suggests a functional role for parallel amino acid substitutions between bee and butterfly red- and green-sensitive opsins. Mol Biol Evol 19:983–986. Briscoe AD, Bernard GD (2005) eyeshine and spectral tuning of long wavelength-sensitive rhodopsins: no evidence for red-sensitive photoreceptors among five nymphalini butterfly species. J Exp Biol 208:687–696. Briscoe AD, Chittka l (2001) The evolution of color vision in insects. Annu Rev Entomol 46:471–510. Briscoe AD, Bernard GD, szeto As, nagy lM, White rh (2003) not all butterfly eyes are created equal: rhodopsin absorption spectra, molecular identification and localization of ultraviolet-, blue-, and green-sensitive rhodopsin-encoding mrnAs in the retina of Vanessa cardui. J Comp Neurol 458:334–349. Brisson JA, stern Dl (2006) The pea aphid, Acyrthosiphon pisum: An emerging genomic model system for ecological, developmental and evolutionary studies. Bioessays 28:747–755. Britten rh, Davidson eh (1969) Gene regulation for higher cells: A theory. Science 165:349– 357. Britten rh, Davidson eh (1971) repetitive and non-repetitive DnA sequences and a specu- lation on the origins of evolutionary novelty. Q Rev Biol 46:111–138.

OCR for page 305
0 / References Brogiolo W, stocker h, ikeya T, rintelen F, Fernandez r, hafen e (2001) An evolution- arily conserved function of the Drosophila insulin receptor and insulin-like peptides in growth control. Curr Biol 11:213–221. Brookfield JF (2001) evolution: The evolvability enigma. Curr Biol 11:r106–r108. Brower AvZ (1994) rapid morphological radiation and convergence among races of the butterfly Heliconius erato inferred from patterns of mitochondrial DnA evolution. Proc Natl Acad Sci USA 91:6491–6495. Browne DJ, scholtz Ch (1995) Phylogeny of the families of scarabaeoidea (Coleoptera) based on characters of the hindwing articularion, hindwing base and wing veination. Syst Entomol 20:145–173. Browne J, scholtz Ch (1999) A phylogeny of the families of scarabaeoidea (Coleoptera). Syst Entomol 24:51–84. Brundrett MC (2002) Coevolution of roots and mycorrhizas of land plants. New Phytol 154:275–304. Brutsaert TD, spielvogel h, soria r, Caceres e, Buzenet G, haas JD (1999) effect of devel- opmental and ancestral high-altitude exposure to vo2 peak of Andean and european/ north American natives. J Appl Physiol 110:435–455. Brutsaert TD, Parra eJ, shriver MD, Gamboa A, Palacios JA, rivera M, rodriguez i, leon- velarde F (2003) spanish genetic admixture is associated with larger v(o2) max decre- ment from sea level to 4338 m in Peruvian Quechua. J Appl Physiol 95:519–528. Brutsaert TD, Parra e, shriver M, Gamboa A, Palacios JA, rivera M, rodriguez i, leon- velarde F (2004) effects of birthplace and individual genetic admixture on lung volume and exercise phenotypes of Peruvian Quechua. Am J Phys Anthropol 123:390–398. Buchner P (1965) Endosymbiosis of Animals with Plant Microorganisms (Wiley interscience, new york). Buell J (2004) Preface. in The Design of Life, eds Behe MJ, Davis P, Dembski WA, Kenyon Dh, Wells J (Foundation for Thought and ethics, richardson, TX), pp iv–vi. Bulmer MG (1980) The Mathematical Theory of Quantitative Genetics (oxford Univ Press, oxford). Bürger r (2000) The Mathematical Theory of Selection, Recombination, and Mutation (Wiley, new york). Burke AC, nelson Ce, Morgan BA, Tabin C (1995) hox genes and the evolution of vertebrate axial morphology. Development 121:333–346. Burke JM, Tang s, Knapp sJ, rieseberg lh (2002) Genetic analysis of sunflower domestica- tion. Genetics 161:1257–1267. Burt A, Trivers r (2006) Genes in Conflict: The Biology of Selfish Genetic Elements (Belknap Press of harvard Univ Press, Cambridge MA). Busch T, Bartsch P, Pappert D, Grunig e, hildebrandt W, elser h, Falke KJ, swenson er (2001) hypoxia decreases exhaled nitric oxide in mountaineers susceptible to high- altitude pulmonary edema. Am J Respir Crit Care Med 163:368–373. Buskirk er (1976) Work performance of newcomers to Peruvian highlands. in Man in the Andes: A Multidisciplinary Study of High Altitude Quechua, eds Baker PT, little MA (Dowden, hutchinson, and ross, stroudsburg, PA), pp 283–299. Buss lW (1987) The Evolution of Individuality (Princeton Univ Press, Princeton). Bustamante CD, Fledel-Alon A, Williamson s, nielsen r, hubisz MT, Glanowski s, Tanenbaum DM, White TJ, sninsky JJ, hernandez rD, et al. (2005) natural selection on protein-coding genes in the human genome. Nature 437:1153–1157. Butterfield Ge, Gates J, Fleming s, Brooks GA, sutton Jr, reeves JT (1992) increased energy intake minimizes weight loss in men at high altitude. J App Physiol 72:1741–1748. Caine nG, Mundy ni (2000) Demonstration of a foraging advantage for trichromatic marmosets (Callithrix geoffroyi) dependent on food colour. Proc R Soc London Ser B 267:439–444.

OCR for page 305
References /  Caldwell K, russell J, langridge P, Powell W (2006) extreme population-dependent link- age disequilibrium detected in an inbreeding plant species, Hordeum vulgare. Genetics 172:557–567. Camazine s, Deneubourg Jl, Franks nr, sneyd h, Theraulaz G, Bonabeau e (2001) Self- Organization in Biological Systems (Princeton Univ Press, Princeton). Campbell G (2002) Distalization of the Drosophila leg by graded eGF-receptor activity. Nature 418:781–785. Campbell G, Weaver T, Tomlinson A (1993) Axis specification in the developing Drosophila appendage: The role of wingless, decapentaplegic, and the homeobox gene aristaless. Cell 74:1113–1123. Caporale lh (2003) Foresight in genome evolution. Am Sci 91:234–241. Carlberg r (1992) Galaxies, spiral, nature of spiral arms. in The Astronomy and Astrophysics Encyclopedia, ed Maran sP (van nostrand reinhold, new york), pp 268–270. Carlborg o, haley Cs (2004) epistasis: Too often neglected in complex trait studies? Nat Rev Genet 5:618–625. Carothers JM, oestreich so, Davis Jh, szostak JW (2004) informational complexity and functional activity of rnA structures. J Am Chem Soc 126:5130–5137. Carriere y, roff DA (1995) The evolution of offspring size and number: A test of the smith- Fretwell model in 3 species of crickets. Oecologia 102:389–396. Carroll sB (1995) homeotic genes and the evolution of arthropods and chordates. Nature 376:479–485. Carroll sB (2005a) Endless Forms Most Beautiful (norton, new york). Carroll sB (2005b) evolution at two levels: on genes and form. PLoS Biol 3:1160–1166. Carroll sD, Weatherbee sB, langeland JA (1995) homeotic genes and the regulation and evolution of insect wing number. Nature 375:58–61. Carroll sB, Grenier JK, Weatherbee sD (2001) From DNA to Diversity: Molecular Genetics and the Evolution of Animal Design (Blackwell Publishing, Malden, MA). Carroll sB, Grenier JK, Weatherbee sD (2004) From DNA to Diversity: Molecular Genetics and the Evolution of Animal Design (Blackwell Publishing, Malden, MA), 2nd ed. Carter AJ, hermisson J, hansen TF (2005) The role of epistatic gene interactions in the response to selection and the evolution of evolvability. Theor Popul Biol 68:179–196. Cavalier-smith T (1997) Cell and genome coevolution: Facultative anaerobiosis, glycosomes and kinetoplastan rnA editing. Trends Genet 13:6–9. Chapuisat M, Keller l (1999) Testing kin selection theory with sex allocation data in eusocial hymenoptera. Heredity 82:473–478. Chapuisat M, sundström l, Keller l (1997) sex-ratio regulation: The economics of fratricide in ants. Proc R Soc London Ser B 264:1255–1260. Chen B, Zhong DB, Monteiro A (2006) Comparative genomics and evolution of the hsP90 family of genes across all kingdoms of organisms. BMC Genom 7:156. Chen X, li s, Aksoy s (1999) Concordant evolution of a symbiont with its host insect species: Molecular phylogeny of genus Glossina and its bacteriome-associated endosymbiont, Wigglesworthia glossinidia. J Mol Evol 48:49–58. Chia W, howes G, Martin M, Meng yB, Moses K, Tsubota s (1986) Molecular analysis of the yellow locus of Drosophila. EMBO J 5:3597–3605. Ching A, Caldwell Ks, Jung M, Dolan M, smith os, Tingey s, Morgante M, rafalski AJ (2002) snP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines. BMC Genet 8:19–33. Cho e, Feng y, rauskolb C, Maitra s, Fehon r, irvine KD (2006) Delineation of a Fat tumor suppressor pathway. Nat Genet 38:1142–1150. Claeys i, simonet G, Poels J, van loy T, vercammen l, De loof A, vanden Broeck J (2002) insulin-related peptides and their conserved signal transduction pathway. Peptides 23:807–816.

OCR for page 305
2 / References Clark A (2004) The role of haplotypes in candidate gene studies. Genet Epidemiol 27:321– 333. Clark hW (1965) “The plants will teach you.” Creation Res Soc Q 2:3–5. Clark s, hayes P, henson C (2003) effects of single nucleotide polymorphisms in beta- amylase 1 alleles from barley on functional properties of the enzymes. Plant Physiol Biochem 41:798–804. Codoñer FM, Daròs J-A, solé rv, elena sF (2006) The fittest versus the flattest: experi- mental confirmation of the quasispecies effect with subviral pathogens. PLoS Pathogens 2:1187–1193. Cohen J (1988) Statistical Power Analysis for the Behavioral Sciences, 2nd ed (lawrence erlbaum Associates, hillsdale, nJ). Cohn MJ, Tickle C (1999) Developmental basis of limblessness and axial patterning in snakes. Nature 399:474–479. Colombani J, raisin s, Pantalacci s, radimerski T, Montagne J, leopold P (2003) A nutrient sensor mechanism controls Drosophila growth. Cell 114:739–749. Colombani J, Bianchini l, layalle s, Pondeville e, Dauphin-villemont C, Antoniewski C, Carre C, noselli s, leopold P (2005) Antagonistic actions of ecdysone and insulins determine final size in Drosophila. Science 310:667–670. Colosimo PF, Peichel Cl, nereng K, Blackman BK, shapiro MD, schluter D, Kingsley DM (2004) The genetic architecture of parallel armor plate reduction in three-spine stickle - backs. PLoS Biol 2:0635–0641. Colosimo PF, hosemann Ke, Balabhadra s, villarreal G, Jr, Dickson M, Grimwood J, schmutz J, Myers rM, schluter D, Kingsley DM (2005) Widespread parallel evolution in stickle - backs by repeated fixation of ectodysplasin alleles. Science 307:1928–1933. Comeau AM, Krisch hM (2005) War is peace—dispatches from the bacterial and phage kill - ing fields. Curr Opin Microbiol 8:488–494. Cooper TF, rozen De, lenski re (2003) Parallel changes in gene expression after 20,000 generations of evolution in E. coli. Proc Natl Acad Sci USA 100:1072–1077. Cooper vs, lenski re (2000) The population genetics of ecological specialization in evolv- ing E. coli populations. Nature 407:736–739. Cooper vs, Bennett AF, lenski re (2001a) evolution of thermal dependence of growth rate of Escherichia coli populations during 20,000 generations in a constant environment. Evolution 55:889–896. Cooper vs, schneider D, Blot M, lenski re (2001b) Mechanisms causing rapid and parallel losses of ribose catabolism in evolving populations of E. coli B. J Bacteriol 183:2834– 2841. Copley sD (2000) evolution of a metabolic pathway for degradation of a toxic xenobiotic: The patchwork approach. Trends Biochem Sci 25:261–265. Cornell JF (1984) Analogy and technology in Darwin’s vision of nature. J Hist Biol 17:303– 344. Cotton s, Fowler K, Pomiankowski A (2004) Do sexual ornaments demonstrate heightened condition-dependent expression as predicted by the handicap hypothesis? Proc Biol Sci 271:771–783. Coyne J, lande r (1985) The genetic basis of species differences in plants. Am Nat 126:141– 145. Coyne JA, Barton nh, Turelli M (2000) is Wright’s shifting balance process important in evolution? Evolution 54:306–317. Crespi BJ (1994) Three conditions for the evolution of eusociality: Are they sufficient? Insectes Sociaux 41:395–400. Crickmore MA, Mann rs (2006) hox control of organ size by regulation of morphogen production and mobility. Science 313:63–68.

OCR for page 305
References /  Crow JF, Kimura M (1970) An Introduction to Population Genetics Theory (harper & row, new york). Crowson rA (1981) The Biology of Coleoptera (Academic, london). Crozier rh (1970) Coefficients of relationship and the identity of genes by descent in the hymenoptera. Am Nat 104:216–217. Crozier rh, Pamilo P (1996) Evolution of Social Insect Colonies: Sex Allocation and Kin Selection (oxford Univ Press, oxford). Csete M, Doyle J (2002) Bowties, metabolism, and disease. Trends Biotechnol 22:446–450. Curran l, Zhuang J, sun sF, Moore lG (1997) ventilation and hypoxic ventilatory respon- siveness in Chinese-Tibetan residents at 3,658 m. J Appl Physiol 83:2098–2104. Currie Cr, Poulsen M, Mendenhall J, Boomsma JJ, Billen J (2006) Coevolved crypts and exo - crine glands support mutualistic bacteria in fungus-growing ants. Science 311:81–85. Daimon T, hamada K, Mita K, okano K, suzuki MG, Kobayashi M, shimada T (2003) A Bombyx mori gene, BmChi-h, encodes a protein homologous to bacterial and baculovirus chitinases. Insect Biochem Mol Biol 33:749–759. Dale C, Moran nA (2006) Molecular mechanisms underlying symbiosis with heritable bacteria. Cell 126:453–465. Damuth J, heisler il (1988) Alternative formulations of multilevel selection. Biol Philos 3:407–430. Darlington CD (1963) Chromosome Botany and the Origins of Cultivated Plants (hafner, new york). Darwin C (1859a) On the Origin of Species (harvard Univ Press, Cambridge, MA) 1st ed reprint, p 201. Darwin C (1859b) On The Origin of Species by Means of Natural Selection (Murray, london). Darwin C (1862) On the Various Contrivances by Which British and Foreign Orchids Are Fertilised by Insects, and on the Good Effects of Intercrossing (Murray, london). Darwin Cr (1868) The Variation of Animals and Plants Under Domestication (Murray, london). Darwin C (1871) The Descent of Man and Selection in Relation to Sex (random house, Modern library, new york). Darwin CD (1872) On the Origin of Species (John Murray, london), 6th ed. Darwin C (1886) On the Various Contrivances by Which British and Foreign Orchids Are Fertilized by Insects and on the Good Effects of Intercrossing (Murray, london). Darwin Cr (1909) The Foundations of the Origin of Species: Two Essays Written in 1842 and 1844 (Cambridge Univ Press, Cambridge, UK). Darwin Cr (1958) The Autobiography of Charles Darwin 1809–1882 (Collins, london). Darwin Cr, Wallace Ar (1858) on the tendency of species to form varieties; and on the perpetuation of varieties and species by natural means of selection. J Proc Linn Soc London 3:46–50. Darwin F, ed (1887a) Charles Darwin’s Autobiography (Basic Books, new york), 1959 ed, pp 34–35. Darwin F, ed (1887b) The Life and Letters of Charles Darwin: Including an Autobiographical Chapter (Murray, london). Davidson CJ, Tuddenham eG, Mcvey Jh (2003) 450 Million years of hemostasis. J Thromb Haemost 1:1487–1494. Davidson eh (2001) Genomic Regulatory Systems: Development and Evolution (Academic, san Diego). Davidson eh (2006) The Regulatory Genome: Gene Regulatory Networks in Development and Evolution (Academic, san Diego). Davidson eh, erwin Dh (2006) Gene regulatory networks and the evolution of animal body plans. Science 311:796–800.

OCR for page 305
 / References Davidson eh, rast JP, oliveri P, ransick A, Calestani C, yuh Ch, Minokawa T, Amore G, hinman v, Arenas-Mena C, et al. (2002) A genomic regulatory network for develop- ment. Science 295:1669–1678. Davis PW (1965) land-dwelling vertebrates and the origin of the tetrapod limb. Creation Res Soc Q 2:27–31. Davis PW, Kenyon Dh, Thaxton CB (1989) Of Pandas and People: The Central Question of Biological Origins (haughton, Dallas), 1st ed. Davis PW, Kenyon Dh, Thaxton CB (1993) Of Pandas and People: The Central Question of Biological Origins (haughton, Dallas), 2nd ed. Dawkins r (1976) The Selfish Gene (oxford Univ Press, new york). Dawkins r (1986) The Blind Watchmaker (norton, new york). Dawkins r (1996) Climbing Mount Improbable (norton, new york). Dawkins r (2006) The God Delusion (houghton Mifflin, Boston). De Duve C (1995) Vital Dust: Life as a Cosmic Imperative (Basic Books, new york). De robertis eM (2006) spemann’s organizer and self-regulation in amphibian embryos. Nat Rev Mol Cell Biol 7:296–301. De robertis eM, sasai y (1996) A common plan for dorsoventral patterning in Bilateria. Nature 380:37–40. Deamer DW, evans J (2006) The evolution of life on earth and in the universe: numerical analysis of biocomplexity. in Life As We Know It: Cellular Origin, Life in Extreme Habitats and Astrobiology, ed seckbach J (springer, new york), vol 10. Dedeine F, Bouletreau M, vavre F (2005) Wolbachia requirement for oogenesis: occurrence within the genus Asobara (hymenoptera, Braconidae) and evidence for intraspecific variation in A. tabida. Heredity 95:394–400. Degnan Ph, lazarus AB, Wernegreen JJ (2005) Genome sequence of Blochmannia pennsyl- vanicus indicates parallel evolutionary trends among bacterial mutualists of insects. Genome Res 15:1023–1033. Delattre M, Felix MA (2002) Microevolutionary studies in nematodes: A beginning. BioEssays 23:807–819. Dembski WA (1995) What every theologian should know about creation, evolution, and design. Center Interdiscip Stud Trans 3:1–8. Dembski WA (1998) The Design Inference: Eliminating Chance Through Small Probabilities (Cambridge Univ Press, Cambridge, UK). Dembski WA (1999) Intelligent Design: The Bridge Between Science and Theology (intervarsity Press, Downers Grove, il). Dembski WA (2002) No Free Lunch: Why Specified Complexity Cannot Be Purchased Without Intelligence (rowman & littlefield, lanham, MD). Depew DJ, Weber Dh, eds (1985) Evolution at a Crossroads: The New Biology and the New Philosophy Science (MiT Press, Cambridge, MA). Desplanches D, hoppeler h, linossier MT, Denis C, Claassen h, Dormois D, lacour Jr, Geyssant A (1993) effects of training in normobaric hypoxia on human muscle ultra- structure. Pflügers Arch 425:263–267. Desplanches D, hoppeler h, Tushcer l, Mayet Mh, spielvogel h, Ferretti G, Kayser B, leuenberger M, Grunenfelder A, Favier r (1996) Muscle tissue adaptations of high altitude natives to training in chronic hypoxia or acute normoxia. J Appl Physiol 81:1946–1951. Diaz-Benjumea FJ, Cohen B, Cohen sM (1994) Cell interaction between compartments estab- lishes the proximal-distal axis of Drosophila legs. Nature 372:175–179. Dickinson WJ, seger J (1999) Cause and effect in evolution. Nature 399:30. Doebley J (1989) isozymic evidence and the evolution of crop plants. in Isozymes in Plant Biology, eds soltis De, soltis Ps (Chapman and hall, london), pp 165–191.

OCR for page 305
References /  Doebley J, stec A (1991) Genetic-analysis of the morphological differences between maize and teosinte. Genetics 129:285–295. Doebley J, stec A, Wendel J, edwards M (1990) Genetic and morphological analysis of a maize teosinte F2 population—implications for the origin of maize. Proc Natl Acad Sci USA 87:9888–9892. Doebley J, stec A, Gustus C (1995) Teosinte branched1 and the origin of maize: evidence for epistasis and the evolution of dominance. Genetics 141:333–346. Doebley J, Gaut Bs, smith BD (2006) The molecular genetics of crop domestication. Cell 127:1309–1321. Domon e, saito A, Takeda K (2002) Comparison of the waxy locus sequence from a non- waxy strain and two waxy mutants of spontaneous and artificial origins in barley. Genes Genet Syst 77:351–359. Dorogovtsev sn, Mendes JFF (2003) Evolution of Networks: From Biological Nets to the Internet and the WWW (oxford Univ Press, oxford). Dover G (1982) Molecular drive: A cohesive mode of species evolution. Nature 299:111–117. Doyle JC, Alderson Dl, li l, low s, roughan M, shalunov s, Tanaka r, Willinger W (2005) The “robust but fragile” nature of the internet. Proc Natl Acad Sci USA 102:14497– 14502. Drapeau MD, Cyran sA, viering MM, Geyer PK, long AD (2006) A cis-regulatory sequence within the yellow locus of Drosophila melanogaster required for normal male mating suc- cess. Genetics 172:1009–1030. Droma y, hanaoka M, Basnyat B, Ariyal A, neupane P, Pandit A, sharma D, Miwa n, ito M, Katsuyama y, et al. (2006) Genetic contribution of the endothelial nitric oxide synthase gene to high altitude adaptation in sherpas. High Alt Med Biol 7:209–220. Duboule D, Dolle P (1989) The structural and functional organization of the murine hoX gene family resembles that of Drosophila homeotic genes. EMBO J 8:1497–1505. Duboule D, Wilkins As (1998) The evolution of “bricolage.” Trends Genet 14:54–59. Dulai Ks, von Dornum M, Mollon JD, hunt DM (1999) The evolution of trichromatic color vision by opsin gene duplication in new World and old World primates. Genome Res 9:629–638. Duplain h, sartori C, lepori M, egli M, Allemann y, nicod P, scherrer U (2000) exhaled nitric oxide in high-altitude pulmonary edema. Am J Resp Crit Care Med 162:221–224. earl DJ, Deem MW (2004) evolvability is a selectable trait. Proc Natl Acad Sci USA 101:11531– 11536. eberhard WG (1978) Fighting behavior of male Golofa porteri beetles (scarabaeidae: Dynastinae). Psyche 83:292–298. eberhard WG, Gutierrez ee (1991) Male dimorphisms in beetles and earwigs and the ques- tion of developmental constraints. Evolution 45:18–28. ebner M, shackleton M, shipman r (2002) how neural networks influence evolvability. Complexity 7:19–33. edgar BA (2006) how flies get their size: Genetics meets physiology. Nat Rev Genet 7:907– 916. Edwards v. Aguillard, 482 Us 578 (1987). eichinger l, Pachebat JA, Glockner G, rajandream MA, sucgang r, Berriman M, song J, olsen r, szafranski K, Xu Q, et al. (2005) The genome of the social amoeba Dictyostelium discoideum. Nature 435:43–57. eizirik e, yuhki n, Johnson We, Menotti-raymond M, hannah ss, o’Brien sJ (2003) Molecu- lar genetics and evolution of melanism in the cat family. Curr Biol 13:448–453. eldredge n (2005) Darwin (norton, new york), pp 71–138. ellington Ae, szostak JW (1990) in vitro selection of rnA molecules that bind specific ligands. Nature 346:818–822. emanuel K (2006) hurricanes: Tempests in a greenhouse. Phys Today August:74–75.

OCR for page 305
 / References rueffler C, van Dooren TJM, Metz JAJ (2004) Adaptive walks on changing landscapes: levins’ approach extended. Theor Popul Biol 65:165–178. ruiz P, schwarzler C, Gunthert U (1995) CD44 isoforms during differentiation and develop - ment. BioEssays 17:17–24. rusconi JC, hays r, Cagan rl (2000) Programmed cell death and patterning in Drosophila. Cell Death Differ 7:1063–1070. russell JA, Moran nA (2006) Costs and benefits of symbiont infection in aphids: variation among symbionts and across temperatures. Proc Biol Sci 273:603–610. rutherford si, lindquist s (1998) hsp90 as a capacitor for morphological evolution. Nature 396:336–342. ruvinsky i, ruvkun G (2003) Functional tests of enhancer conservation between distantly related species. Development 130:5133–5142. sachs Jl, Mueller UG, Wilcox TP, Bull JJ (2004) The evolution of cooperation. Q Rev Biol 79:135–160. saier Mh (2004) evolution of bacterial type iii protein secretion systems. Trends Microbiol 12:113–115. salamini F, ozkan h, Brandolini A, schafer-Pregl r, Martin W (2002) Genetics and geography of wild cereal domestication in the near east. Nat Rev Genet 3:429–441. salner r (1980) Professor teaches a supernatural creation of world. San Francisco Examiner, December 17, zA9. sameshima s, Miura T, Matsumoto T (2004) Wing disc development during caste differentia- tion in the ant Pheidole megacephala (hymenoptera: Formicidae). Evol Dev 6:336–341. sapp J (2004) The dynamics of symbiosis: An historical overview. Can J Bot 82:1046–1056. sasaki A, nowak MA (2003) Mutation landscapes. J Theor Biol 224:241–247. sato h (2002) invasion of unisexuals in hermaphrodite populations of animal-pollinated plants: effects of pollination ecology and floral size-number trade-offs. Evolution 56:2374–2382. sato M, severinghaus JW, Bickler P (1994) Time course of augmentation and depression of hypoxic ventilatory responses at altitude. J Appl Physiol 77:313–316. sauman i, Briscoe AD, Zhu h, shi D, Froy o, stalleicken J, yuan Q, Casselman A, reppert sM (2005) Connecting the navigational clock to sun compass input in monarch butterfly brain. Neuron 46:457–467. sax K (1923) The association of size differences with seed-coat pattern and pigmentation in Phaseolus vulgaris. Genetics 8:552–560. scarborough Cl, Ferrari J, Godfray hC (2005) Aphid protected from pathogen by endo- symbiont. Science 310:781. schaap P, Winckler T, nelson M, Alvarez-Curto e, elgie B, hagiwara h, Cavender J, Milano- Curto A, rozen De, Dingermann T, et al. (2006) Molecular phylogeny and evolution of morphology in the social amoebas. Science 314:661–663. schaffer WM (1974) selection for optimal life histories: The effects of age structure. Ecology 55:291–303. schardl Cl, leuchtmann A, spiering MJ (2004) symbioses of grasses with seedborne fungal endophytes. Annu Rev Plant Biol 55:315–340. schink B (2002) synergistic interactions in the microbial world. Antonie Van Leeuwenhoek 81:257–261. schlichting CD, Pigliucci M (1998) Phenotypic Evolution: A Reaction Norm Perspective (sinauer, sunderland, MA), p 387. schlosser G, Wagner G, eds (2004) Modularity in Development and Evolution (harvard Univ Press, Cambridge, MA). schmalhausen ii (1986) Factors in Evolution: The Theory of Stabilizing Selection, ed Dobzhansky T (Univ of Chicago Press, Chicago). schmidt TM (2006) The maturing of microbial ecology. Int Microbiol 9:217–223.

OCR for page 305
References /  schneider A, Greene re, Keyl C, Bandinelli G, Passino C, spadacini G, Bonfichi M, Arcaini l, Malcovati l, Boiardi A, et al. (2001) Peripheral arterial vascular function at altitude: sea-level natives versus himalayan high-altitude natives. J Hypertens 19:213–222. schneider TD, stormo GD, Gold l, ehrenfeuch A (1986) The information content of binding sites on nucleotide sequences. J Mol Biol 188:415–431. scholtz Ch, Chown sl (1995) The evolution of habitat use and diet in the scarabaeoidea: A phylogenetic approach. in Biology, Phylogeny, and Classification of the Coleoptera, eds Pakaluk AFJ, slipinski sA (Muzeum i instytut Zoologii PAn, Warsaw, Poland), pp 335–374. schröder D, Deppisch h, obermayer M, Krohne G, stackebrandt e, hölldobler B, Goebel W, Gross r (1996) intracellular endosymbiotic bacteria of Camponotus species (carpen- ter ants): systematics, evolution and ultrastructural characterization. Mol Microbiol 21:479–489. schwede T, Kopp J, Guex n, Peitsch MC (2003) sWiss-MoDel: An automated protein homology server. Nucleic Acids Res 31:3381–3385. scott eC (2001) The big tent and the camel’s nose. Rep Natl Center Sci Education 21:39–41. scott eC (2004) Evolution vs. Creationism: An Introduction (Greenwood Press, Westport, CT). sears Ke, Behringer rr, rasweiler JJ iv, niswander lA (2006) Development of bat flight: Morphologic and molecular evolution of bat wing digits. Proc Natl Acad Sci USA 103:6581–6586. seeley TD (1989) The honey bee colony as a superorganism. Am Sci 77:546–553. seeley TD (1997) honey bee colonies are group-level adaptive units. Am Nat 150:s22–s41. seeley TD, visscher PK (2004) Group decision making in nest-site selection by honey bees. Apidologie 35:101–116. semenza Gl (2000) hiF-i and human disease: one highly involved factor. Genes Dev 14:1983–1991. semenza Gl (2002) signal transduction to hyoxia-inducible factor 1. Biochem Pharmacol 64:993–998. semenza Gl (2004) hydroxylation of hiF-1: oxygen sensing at the molecular level. Physiology 19:176–182. seppä P, Queller DC, strassmann Je (2002) reproduction in foundress associations of the social wasp, Polistes carolina. Behav Ecol 13:531–542. serrano n, o’Farrell Ph (1997) limb morphogenesis: Connections between patterning and growth. Curr Biol 7:r186–r195. shalizi Cr (2006) Methods and techniques of complex systems science: An overview. ArXiv: nlin.AO/0307015. shallit Jo, elsberry Wr (2004) Playing games with probability: Dembski’s complex specified information. in Why Intelligent Design Fails: A Scientific Critique of the New Creationism , eds young M, edis T (rutgers Univ Press, new Brunswick, nJ), pp 121–138. shannon C (1948) A mathematical theory of communication. Bell System Technical J 27:379– 423, 623–656. shapiro MD, Marks Me, Peichel Cl, Blackman BK, nereng Ks, Jonsson B, schluter D, Kingsley DM (2004) Genetic and developmental basis of evolutionary pelvic reduction in three-spine sticklebacks. Nature 428:717–723. shapiro MD, Bell MA, Kingsley DM (2006) Parallel genetic origins of pelvic reduction in vertebrates. Proc Natl Acad Sci USA 103:13753–13758. sharloo W (1991) Canalization: Genetic and developmental aspects. Annu Rev Ecol Syst 22:65–93. sheth U, Parker r (2006) Targeting of aberrant mrnAs to cytoplasmic processing bodies. Cell 125:1095–1109. shigenobu s, Watanabe h, hattori M, sakaki y, ishikawa h (2000) Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APs. Nature 407:81–86.

OCR for page 305
 / References shimkets lJ (1990) social and developmental biology of the myxobacteria. Microbiol Rev 54:473–501. shingleton AW, Das J, vinicius l, stern Dl (2005) The temporal requirements for insulin signaling during development in Drosophila. PLoS Biol 3:1607. shingleton A, Frankino A, Flatt T, nijhout hF, emlen DJ (2007) size and shape: The devel- opmental regulation of static allometry in insects. BioEssays 29:536–548. short MB, solari CA, Ganguly s, Powers Tr, Kessler Jo, Goldstein re (2006) Flows driven by flagella of multicellular organisms enhance long-range molecular transport. Proc Natl Acad Sci USA 103:8315–8319. shute ev (1965a) More extraordinary adaptations. Creation Res Soc Q 2(1):22–26. shute ev (1965b) remarkable adaptations. Creation Res Soc Q 2(3):22–26. sibly rh (2002) life history theory. in Encyclopaedia of Evolution, ed Page lM (oxford Univ Press, new york), vol 2, pp 623–627. simons KJ, Fellers JP, Trick hn, Zhang Z, Tai ys, Gill Bs, Faris JD (2006) Molecular charac- terization of the major wheat domestication gene Q. Genetics 172:547–555. slatkin M, Wiehe T (1998) Genetic hitch-hiking in a subdivided population. Genet Res 71:155–160. smith ABT, hawks DC, heraty JM (2006) An overview of the classification and evolution of the major scarab beetle clades (Coleoptera: scarabaeoidea) based on preliminary molecular analyses. Coleopterists Soc Monogr 5:35–46. smith AC, Buchanan-smith hM, surridge AK, osorio D, Mundy ni (2003) The effect of colour vision status on the detection and selection of fruits by tamarins (Saguinus spp.). J Exp Biol 206:3159–3165. smith KC (2001) Appealing to ignorance behind the cloak of ambiguity. in Intelligent Design Creationism and Its Critics: Philosophical, Theological, and Scientific Perspectives, ed Pennock rT (MiT Press, Cambridge, MA), pp 705–735. sniegowski PD, Murphy hA (2006) evolvability. Curr Biol 16:r831–r834. sober e (2002) intelligent design and probability reasoning. Int J Philos Religion 52:65–80. sokal rr, rohlf FJ (1981) Biometry (Freeman, san Francisco), 2nd ed, pp 217–218. solari CA (2005) A Hydrodynamics Approach to the Evolution of Multicellularity: Flagellar Motility and the Evolution of Germ-Soma Differentiation in Volvocalean Green Algae. PhD thesis (Univ of Arizona, Tucson). solari CA, Ganguly s, Kessler Jo, Michod re, Goldstein re (2006a) Multicellularity and the functional interdependence of motility and molecular transport. Proc Natl Acad Sci USA 103:1353–1358. solari CA, Kessler Jo, Michod re (2006b) A hydrodynamics approach to the evolution of multicellularity: Flagellar motility and germ-soma differentiation in volvocalean green algae. Am Nat 167:537–554. solé r, Goodwin B (2000) Signs of Life: How Complexity Pervades Biology (Basic Books, new york). sommer rJ (1997) evolution and development—the nematode vulva as a case study. BioEssays 19:225–231. sommer U, Giliwicz ZM (1986) long-range vertical migration of volvox in tropical lake Cahora Bassa (Mozambique). Limmol Oceanogr 31:650–653. spady TC, seehausen o, loew er, Jordan rC, Kocher TD, Carleton Kl (2005) Adaptive molecular evolution in the opsin genes of rapidly speciating cichlid species. Mol Biol Evol 22:1412–1422. spemann h, Mangold h (1924) Über induktion von embryonalanlagen durch implantation artfremder organisatoren. Roux’s Arch Entwicklungsmech Org 100:599–638. stanek D, neugebauer KM (2006) The Cajal body: A meeting place for spliceosomal snrnPs in the nuclear maze. Chromosoma 115:343–354.

OCR for page 305
References /  stanhope MJ, lupas A, italia MJ, Koretke KK, volker C, Brown Jr (2001) Phylogenetic analyses do not support horizontal gene transfers from bacteria to vertebrates. Nature 411:940–944. stanley sM (1985) rates of evolution. Paleobiology 11:13–26. stanojevic D, small s, levine M (1991) Genetic and developmental basis of evolutionary pelvic reduction in threespine sticklebacks. Science 254:1385–1387. stathopoulos A, levine M (2005) Genomic regulatory networks and animal development. Dev Cell 9:449–462. stearns sC (1992) The Evolution of Life Histories (oxford Univ Press, oxford). stebbins Gl (1950) Variation and Evolution in Plants (Columbia Univ Press, new york). stern Dl (2000) evolutionary developmental biology and the problem of variation. Evolu- tion 54:1079–1091. stern Dl, emlen DJ (1999) The developmental basis for allometry in insects. Development 126:1091–1101. stoltzfus A (2006a) Mutationism and the dual causation of evolutionary change. Evol Dev 8:304–317. stoltzfus A (2006b) Mutation-biased adaptation in a protein nK model. Mol Biol Evol 23:1852–1862. strassmann Je (1981) Wasp reproduction and kin selection: reproductive competition and dominance hierarchies among Polistes annularis foundresses. Fla Entomol 64:74–88. strassmann Je, Queller DC (1989) ecological determinants of social evolution. in The Genetics of Social Evolution, eds Breed MD, Page re (Westview, Boulder, Co), pp 81–101. strassmann Je, Queller DC (2007) insect societies as divided organisms: The complexities of purpose and cross purpose. Proc Natl Acad Sci USA 104(suppl):8619–8626; this volume, pp. 145–163. strogatz sh (2001) exploring complex networks. Nature 410:268–276. strohm e, linsenmair Ke (2000) Allocation of parental investment among individual off- spring in the european beewolf Philanthus triangulum F. (hymenoptera: sphecidae). Biol J Linn Soc 69:173–192. sucena e, stern Dl (2000) Divergence of larval morphology between Drosophila sechellia and its sibling species caused by cis-regulatory evolution of ovo/shaven-baby. Proc Natl Acad Sci USA 97:4530–4534. sucena e, Delon i, Jones i, Payre F, stern Dl (2003) regulatory evolution of shavenbaby/ovo underlies multiple cases of morphological parallelism. Nature 424:935–938. sundström l, Chapuisat M, Keller l (1996) Conditional manipulation of sex ratios by ant workers: A test of kin selection theory. Nature 274:993–995. sunnucks P, hales DF (1996) numerous transposed sequences of mitochondrial cytochrome oxidase i-ii in aphids of the genus Sitobion (hemiptera: Aphididae). Mol Biol Evol 13:510–524. surridge AK, osorio D, Mundy ni (2003) evolution and selection of trichromatic vision in primates. Trends Ecol Evol 18:198–205. suzuki K, Kizaki T, hitomi y, nukita M, Kimoto K, Miyazawa n, Kobayashi K, ohnuki y, ohno h (2003) Genetic variation in hypoxia-inducible factor 1 alpha and its possible association with high altitude adaptation in sherpas. Med Hypotheses 61:385–389. sweeney MT, Thomson MJ, Pfeil Be, McCouch s (2006) Caught red-handed: rc encodes a basic helix-loop-helix protein conditioning red pericarp in rice. Plant Cell 18:283–294. swenson r, Turvey MT (1991) Thermodynamic reasons for perception-action cycles. Ecol Psychol 3:317–348. szalma sJ, Buckler es, snook Me, McMullen MD (2005) Association analysis of candidate genes for maysin and chlorogenic acid accumulation in maize silks. Theor Appl Genet 110:1324–1333. szostak JW (2003) Molecular messages. Nature 423:689.

OCR for page 305
 / References Tajima F (1989) statistical method for testing the neutral mutation hypothesis by DnA poly- morphism. Genetics 123:585–595. Takada T, nakajima h (1996) The optimal allocation for seed reproduction and vegetative reproduction in perennial plants: An application to the density-dependent transition matrix model. J Theor Biol 182:179–191. Takiya DM, Tran P, Dietrich Ch, Moran nA (2006) Co-cladogenesis spanning three phyla: leafhoppers (insecta: hemiptera: Cicadellidae) and their dual bacterial symbionts. Mol Ecol 15:4175–4191. Tamas i, Klasson l, Canbäc B, naslund AK, eriksson As, Wernegreen JJ, sandström JP, Moran nA, Andersson sG (2002) 50 million years of genomic stasis in endosymbiotic bacteria. Science 296:2376–2379. Tan y, li Wh (1999) Trichromatic vision in prosimians. Nature 402:36. Tan y, yoder AD, yamashita n, li Wh (2005) evidence from opsin genes rejects nocturnality in ancestral primates. Proc Natl Acad Sci USA 102:14712–14716. Taverna DM, Goldstein rA (2000) The distribution of structures in evolving protein popula- tions. Biopolymers 53:1–8. Technau U, rudd s, Maxwell P, Gordon PM, saina M, Grasso lC, hayward DC, sensen CW, saint r, holstein TW, et al. (2005) Maintenance of ancestral complexity and non- metazoan genes in two basal cnidarians. Trends Genet 21:633–639. Teissier G (1935) les procedes d’etude de la croissance relative. Bull Soc Zool Fr 60:292–307. Tenaillon M, sawkins MC, long AD, Gaut rl, Doebley JF, Gaut Bs (2001) Patterns of DnA sequence polymorphism along chromosome 1 of maize (Zea mays ssp. mays l.). Proc Natl Acad Sci USA 98:9161–9166. Tenaillon Mi, U’ren J, Tenaillon o, Gaut Bs (2004) selection versus demography: A multi- locus investigation of the domestication process in maize. Mol Biol Evol 21:1214–1225. Terakita A (2005) The opsins. Genome Biol 6:213. Terakita A, yamashita T, shichida y (2000) highly conserved glutamic acid in the extra- cellular iv-v loop in rhodopsins acts as the counterion in retinochrome, a member of the rhodopsin family. Proc Natl Acad Sci USA 97:14263–14267. Teshima KM, Coop G, Przeworski M (2006) how reliable are empirical genomic scans for selective sweeps? Genome Res 16:702–712. Thaxton CB, Bradley Wl, olsen rl (1984) The Mystery of Life’s Origin: Reassessing Current Theories (Philosophical library, new york). Theron e, hawkins K, Bermingham e, ricklefs re, Mundy ni (2001) The molecular basis of an avian plumage polymorphism in the wild: A melanocortin-1-receptor point muta - tion is perfectly associated with the melanic plumage morph of the bananaquit, Coereba flaveola. Curr Biol 11:550–557. Thornhill rh, Ussery DW (2000) A classification of possible routes of Darwinian evolution. J Theor Biol 203:111–116. Thornsberry JM, Goodman MM, Doebley J, Kresovich s, nielsen D, Buckler es (2001) Dwarf8 polymorphisms associate with variation in flowering time. Nat Genet 28:286–289. Thornton K, Andolfatto P (2006) Approximate Bayesian inference reveals evidence for a recent, severe bottleneck in a netherlands population of Drosophila melanogaster. Genetics 172:1607–1619. Thornton Kr, Jensen JD (2007) Controlling the false positive rate in multilocus genome scans for selection. Genetics 175:737–750. Tomoyasu y, Wheeler sr, Denell re (2005) Ultrabithorax is required for membranous wing identity in the beetle Tribolium castaneum. Nature 433:643–647. Toomajian C, hu TT, Aranzana MJ, lister C, Tang C, Zheng h, Zhao K, Calabrese P, Dean C, nordborg M (2006) A nonparametric test reveals selection for rapid flowering in the Arabidopsis genome. PLoS Biol 4:e137.

OCR for page 305
References /  Torroni A, Miller JA, Moore lG, Zamudio s, Zhuang J, Droma T, Wallace DC (1994) Mito- chondrial DnA analysis in Tibet: implications for the origin of the Tibetan population and its adaptation to high altitude. Am J Phys Anthropol 93:189–199. Tóth e, Queller DC, imperatriz-Fonseca vl, strassmann Je (2002a) Genetic and behavioral conflict over male production between workers and queens in the stingless bee Paratrigona subnuda. Behav Ecol Sociobiol 53:1–8. Tóth e, strassmann Je, nogueira-neto P, imperatriz-Fonseca vl, Queller DC (2002b) Male production in stingless bees: variable outcomes of queen-worker conflict. Mol Ecol 11:2661–2667. Tóth e, Queller DC, Dollin A, strassmann Je (2004) Conflict over male parentage in stingless bees. Insectes Sociaux 51:1–11. Touchstone (2004) The measure of design. Touchstone: J Mere Christianity 17. Travisano M, lenski re (1996) long-term experimental evolution in Escherichia coli, iv: Targets of selection and the specificity of adaptation. Genetics 143:15–26. Travisano M, Mongold JA, Bennett AF, lenski re (1995) experimental tests of the roles of adaptation, chance, and history in evolution. Science 267:87–90. Trinkaus e (2005) early modern humans. Annu Rev Anthropol 34:207–240. Trivers rl, hare h (1976) haplodiploidy and the evolution of the social insects. Science 191:249–263. True hl, lindquist sl (2000) A yeast prion provides a mechanism for genetic variation and phenotypic diversity. Nature 407:477–483. True Jr, Carroll sB (2002) Gene co-option in physiological and morphological evolution. Annu Rev Cell Dev Biol 18:53–80. True Jr, haag es (2001) Developmental system drift and flexibility in evolutionary trajectories. Evol Dev 3:109–119. Truman JW, riddiford lM (2002) endocrine insights into the evolution of metamorphosis in insects. Annu Rev Entomol 47:467–500. Tsong Ae, Miller MG, raisner rM, Johnson AD (2003) evolution of a combinatorial transcriptional circuit: A case study in yeasts. Cell 115:389–399. Tsong Ae, Tuch BB, li h, Johnson AD (2006) evolution of alternative transcriptional circuits with identical logic. Nature 443:415–420. Tu MP, Tatar M (2003) Juvenile diet restriction and the aging and reproduction of adult Drosophila melanogaster. Aging Cell 2:327–333. Turing A (1936) on computable numbers, with an application to the entscheidungs problem. Proc London Math Soc 42:230–265. Uauy C, Distelfeld A, Fahima T, Blechl A, Dubcovsky J (2006) A nAC gene regulating senes- cence improves grain protein, zinc, and iron content in wheat. Science 314:1298–1301. van ham rChJ, Kamerbeek J, Palacios C, rausell C, Abascal F, Bastolla U, Fernandez JM, Jimenez l, Postigo M, silva FJ, et al. (2003) reductive genome evolution in Buchnera aphidicola. Proc Natl Acad Sci USA 100:581–586. van nimwegen e, Crutchfield JP, huymen M (1999) neutral evolution of mutational robust- ness. Proc Natl Acad Sci USA 96:9716–9720. van Zandt Brower J (1958) experimental studies of mimicry in some north American butter- flies, Pt i: The monarch, Danaus plexippus, and viceroy, Limenitis archippus archippus. Evolution 12:32–47. vavilov n (1926) Origin and Geography of Cultivated Plants (Cambridge Univ Press, Cambridge, UK). voight BF, Adams AM, Frisse lA, Qian yD, hudson rr, Di rienzo A (2005) interrogating multiple aspects of variation in a full resequencing data set to infer human population size changes. Proc Natl Acad Sci USA 102:18508–18513. voight BF, Kudaravalli s, Wen X, Pritchard JK (2006) A map of recent positive selection in the human genome. PLoS Biol 4:e72.

OCR for page 305
0 / References von Baeyer hC (2003) Information: The New Language of Science (Weidenfeld & nicolson, london). von Dohlen CD, Kohler s, Alsop sT, McManus Wr (2001) Mealybug beta-proteobacterial endosymbionts contain gamma-proteobacterial symbionts. Nature 412:433–436. Waddington Ch (1940) The genetic control of wing development in Drosophila. J Genet 41:75–139. Waddington Ch (1953) Evolution 7:118–126. Waddington Ch (1957) The Strategy of the Genes (Allen & Unwin, london). Wagner Pl, Waldor MK (2002) Bacteriophage control of bacterial virulence. Infect Immun 70:3985–3993. Wahlberg n, Braby MF, Brower AvZ, de Jong r, lee MM, nylin s, Pierce ne, sperling FAh, vila r, Warren AD, et al. (2005) synergistic effects of combining morphological and molecular data in resolving the phylogeny of butterflies and skippers. Proc R Soc London Ser B 272:1577–1586. Wallace Ar (1858) on the tendency of varieties to depart indefinitely from the original type. J Proc Linn Soc London (Zool) 3:53–62. Wallace Ar (1889) Darwinism: An Exposition of the Theory of Natural Selection (Macmillan, london). Walter MF, Black BC, Afshar G, Kermabon Ay, Wright Tr, Biessmann h (1991) Temporal and spatial expression of the yellow gene in correlation with cuticle formation and dopa decarboxylase activity in Drosophila development. Dev Biol 147:32–45. Wang h, Wagler T, li B, Zhao Q, vigouroux y, Faller M, Bomblies K, lukens l, Doebley J (2005) The origin of the naked grains of maize. Nature 436:714–719. Wang Qs, Unrau PJ (2005) ribozyme motif structure mapping using random recombination and selection. RNA 11:404–411. Wang X, Chamberlin hM (2002) Multiple regulatory changes contribute to the evolution of the Caenorhabditis lin-48 ovo gene. Genes Dev 16:2345–2349. Ward MP, Milledge Js, West JB (2000) High Altitude Medicine and Physiology (oxford Univ Press, london). Warren rW, nagy l, selegue J, Gates J, Carroll s (1994) evolution of homeotic gene regula- tion and function in flies and butterflies. Nature 372:458–461. Waters e, hohn MJ, Ahel i, Graham De, Adams MD, Barnstead M, Beeson Ky, Bibbs l, Bolanos r, Keller M, et al. (2003) The genome of Nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism. Proc Natl Acad Sci USA 100:12984– 12988. Weatherbee sD, halder G, Kim J, hudson A, Carroll s (1998) Ultrabithorax regulates genes at several levels of the wing-patterning hierarchy to shape the development of the Drosophila haltere. Genes Dev 12:1474–1482. Weatherbee sD, nijhout hF, Grunert lW, halder G, Galant r, selegue J, Carroll s (1999) Ultrabithorax function in butterfly wings and the evolution of insect wing patterns. Curr Biol 9:109–115. Weatherbee sD, Behringer rB, rasweiler JJ iv, niswander lA (2006) interdigital webbing retention in bat wings illustrates genetic changes underlying amniote limb diversifica - tion. Proc Natl Acad Sci USA 103:15103–15107. Weigel D, nordborg M (2005) natural variation in Arabidopsis. how do we find the causal genes? Plant Physiol 138:567–568. Weihe U, Milán M, Cohen sM (2005) Drosophila limb development. Comp Mol Insect Sci 1:305–347. Weil Jv, Byrne-Quinn e, sodal ie, Filley GF, Grover rF (1971) Acquired attenuation of chemoreceptor function in chronically hypoxic man at high altitude. J Clin Invest 50:186–195.

OCR for page 305
References /  Weinkove D, leevers sJ (2000) The genetic control of organ growth: insights from Drosophila. Curr Opin Genet Dev 10:75–80. Weiss KM, Clark AG (2002) linkage disequilibrium and the mapping of complex human traits. Trends Genet 18:19–24. Welch JJ, Waxman D (2003) Modularity and the cost of complexity. Evolution 57:1723–1734. Welch rA, Burland v, Plunkett G, 3rd, redford P, roesch P, rasko D, Buckles el, liou sr, Boutin A, hackett J, et al. (2002) extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli. Proc Natl Acad Sci USA 99:17020– 17024. Wenseleers T, ratnieks FlW (2004) Tragedy of the commons in Melipona bees. Biol Lett 271: s310–s312. Wenseleers T, ratnieks FlW (2006) enforced altruism in insect societies. Nature 444:50. Wenseleers T, hart AG, ratnieks FlW, Quezada-euán JJG (2004) Queen execution and caste conflict in the stingless bee, Melipona beecheii. Ethology 110:725–736. Wenseleers T, ratnieks FlW, ribeiro MdF, Alves DdA, imperatriz-Fonseca vl (2005) Working-class royalty: Bees beat the caste system. Biol Lett 1:125–128. Wernegreen JJ (2002) Genome evolution in bacterial endosymbionts of insects. Nat Rev Genet 3:850–861. Werren Jh (1997) Biology of Wolbachia. Annu Rev Entomol 42:587–609. West-eberhard MJ (1969) social biology of Polistine wasps. Misc Publ Mus Zool Univ Mich 140:1–101. West-eberhard MJ (1975) The evolution of social behavior by kin selection. Q Rev Biol 50:1–33. West-eberhard MJ (2003) Developmental Plasticity and Evolution (oxford Univ Press, new york). Wheeler WM (1911) The ant colony as organism. J Morphol 22:307–325. Whitfield J (2005) order out of chaos. Nature 436:905–907. Whitt sr, Wilson lM, Tenaillon Mi, Gaut Bs, Buckler es (2002) Genetic diversity and selec- tion in the maize starch pathway. Proc Natl Acad Sci USA 99:12959–12962. Wiester Jl (1983) The Genesis Connection (nelson, nashville, Tn). Wilkins As (2002) The Evolution of Developmental Pathways (sinauer, sunderland, MA). Wilkins As (2004) Deciphering the swordtail’s tale: A molecular and evolutionary quest. BioEssays 26:116–119. Wilkins As (2005) recasting developmental evolution in terms of genetic pathway and network evolution ... and the implications for comparative biology. Brain Res Bull 66:495–509. Wilkins As (2007a) From the lac operon to gene recruitment: evolving ideas about gene regulation and its evolution. in Biological Regulation, eds hammerstein P, laublichler M (MiT Press, Cambridge, MA). in press. Wilkins As (2007b) Genetic networks as transmitting and amplifying devices for natural genetic tinkering. in Novartis Symposium 284: Tinkering: The Microevolution of Develop- ment (Wiley, Chichester, UK). Wilkins Js, elsberry Wr (2001) The advantages of theft over toil: The design inference and arguing from ignorance. Biol Philos 16:711–724. Wilkins Mr, Aldashev A, Morrell nW (2002) nitric oxide, phosphodiesterase inhibition, and adaptation to hypoxic conditions. Lancet 359:1539–1540. Williams GC (1966) Adaptation and Natural Selection (Princeton Univ Press, Princeton). Wilson Ds, szostak JW (1999) in vitro selection of functional nucleic acids. Annu Rev Biochem 68:611–647. Wilson eo (1971) The Insect Societies (Belknap Press of harvard Univ Press, Cambridge MA). Wilson eo (1975) Sociobiology: The New Synthesis (Belknap, Cambridge, MA).

OCR for page 305
2 / References Wilson eo (1987) Causes of ecological success: The case of the ants. sixth Tansley lecture. J Anim Ecol 56:1–9. Wilson eo (1992) The Diversity of Life (MiT Press, Cambridge, MA). Winslow rM, Monge CC, statham nJ, Gibson CG, Charache s, Whittembury J, Moran o, Berger rl (1981) variability of oxygen affinity of blood: human subjects native to high altitude. J Appl Physiol 51:1411–1416. Winslow rM, Chapman KW, Gibson CC, samaja M, Monge C, Goldwasser e, sherpa M, Blume FD, santolaya r (1989) Different hematologic responses to hypoxia in sherpas and Quechua indians. J Appl Physiol 66:1561–1569. Wittkopp PJ (2006) evolution of cis-regulatory sequence and function in Diptera. Heredity 97:139–147. Wittkopp PJ, True Jr, Carroll sB (2002a) reciprocal functions of the Drosophila yellow and ebony proteins in the development and evolution of pigment patterns. Development 129:1849–1858. Wittkopp PJ, vaccaro K, Carroll sB (2002b) evolution of yellow gene regulation and pigmen- tation in Drosophila. Curr Biol 12:1547–1556. Wittkopp PJ, Carroll sB, Kopp A (2003) evolution in black and white: Genetic control of pigment patterns in Drosophila. Trends Genet 19:495–504. Woese Cr (1987) Bacterial evolution. Microbiol Rev 51:221–271. Woese Cr (2004) A new biology for a new century. Microbiol Mol Biol Rev 68:173–186. Wolf JB, Brodie eD, iii, Wade MJ, eds (2000) Epistasis and the Evolutionary Process (oxford Univ Press, new york). Wolfram s (2002) A New Kind of Science (Wolfram, Champaign, il). Wratten ns, McGregor AP, shaw PJ, Dover GA (2006) evolutionary and functional analy- sis of the tailless enhancer in Musca domestica and Drosophila melanogaster. Evol Dev 8:6–15. Wray GA, hahn MW, Abouheif e, Balhoff JP, Pizer M, rockman Mv, romano lA (2003) The evolution of transcriptional regulation in eukaryotes. Mol Biol Evol 20:1377–1419. Wright s (1931) evolution in Mendelian populations. Genetics 16:97–159. Wright s (1942) statistical genetics and evolution. Bull Am Math Soc 48:223–246. Wright s (1968) Evolution and the Genetics of Populations (Univ of Chicago Press, Chicago), vol 1. Wright s (1980) Genic and organismic selection. Am Nat 34:825–843. Wright si, Gaut Bs (2005) Molecular population genetics and the search for adaptive evolu - tion in plants. Mol Biol Evol 22:506–519. Wright si, Bi iv, schroeder sG, yamasaki M, Doebley JF, McMullen MD, Gaut Bs (2005) The effects of artificial selection of the maize genome. Science 308:1310–1314. Wu D, Daugherty sC, van Aken se, Pai Gh, Watkins Kl, Khouri h, Tallon lJ, Zaborsky JM, Dunbar he, Tran Pl, et al. (2006) Metabolic complementarity and genomics of the dual symbiosis of sharpshooters. PloS Biol 4:1079–1092. Wu M, sun lv, vamathevan J, riegler M, Deboy r, Brownlie JC, McGraw eA, Martin W, esser C, Ahmadinejad n, et al. (2004) Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: A streamlined genome overrun by mobile genetic elements. PLoS Biol 2:327–341. Wu T, Kayser B (2006) high altitude adaptation in Tibetans. High Alt Med Biol 7:193–208. Xie G, Keyhani no, Bonner CA, Jensen rA (2003) Ancient origin of the tryptophan operon and the dynamics of evolutionary change. Microbiol Mol Biol Rev 67:303–342. Xing y, lee C (2006) Alternative splicing and rnA selection pressure—evolutionary conse- quences for eukaryotic genomes. Nat Rev Genet 7:499–505.

OCR for page 305
References /  yamasaki M, Tenaillon Mi, vroh Bi i, schroeder sG, sanchez-villeda h, Doebley JF, Gaut Bs, McMullen MD (2005) A large-scale screen for artificial selection in maize identi - fies candidate agronomic loci for domestication and crop improvement. Plant Cell 17:2859–2872. yampolsky ly, stoltzfus A (2001) Bias in the introduction of variation as an orienting factor in evolution. Evol Dev 3:73–83. yang Z (1997) PAMl: A program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 13:555–556. yang Zh, Bielawski JP (2000) statistical methods for detecting molecular adaptation. Trends Ecol Evol 15:496–503. yang Z, nielsen r (2002) Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol Biol Evol 19:908–917. yang Z, Wong WsW, nielsen r (2005) Bayes empirical Bayes inference of amino acid sites under positive selection. Mol Biol Evol 22:1107–1118. yokoyama s (1997) Molecular genetic basis of adaptive selection: examples from color vision in vertebrates. Annu Rev Genet 31:311–332. yokoyama s, Takenaka n (2005) statistical and molecular analyses of evolutionary sig- nificance of red-green color vision and color blindness in vertebrates. Mol Biol Evol 22:968–975. yu J, Buckler e (2006) Genetic association mapping and genome organization of maize. Curr Opin Biotechnol 17:155–160. Zaccardi G, Kelber A, sison-Mangus MP, Briscoe AD (2006) Color discrimination in the red range with only one long-wavelength sensitive opsin. J Exp Biol 209:1944–1955. Zarowski JC (2004) An Introduction to Numerical Analysis for Electrical and Computer Engineers (Wiley, new york). Zecca M, Basler K, struhl G (1995) sequential organizing activities of engrailed, hedgehog and decapentaplegic in the Drosophila wing. Development 121:2265–2278. Zeven AC (1973) englebrecht’s views on the origin of cultivated plants. Euphytica 22:279– 286. Zhang J (2006) Parallel adaptive origins of digestive rnases in Asian and African leaf mon- keys. Nat Genet 38:819–823. Zhang J, Kumar s (1997) Detection of convergent and parallel evolution at the amino acid sequence level. Mol Biol Evol 14:527–536. Zhang J, nielsen r, yang Z (2005) evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Mol Biol Evol 22:2472–2479. Zhu Q, Zheng X, luo J, Gaut Bs, Ge s (2007) Multilocus analysis of nucleotide variation of Oryza sativa and its wild relatives: severe bottleneck during domestication of rice. Mol Biol Evol 24:875–888. Zhuang J, Droma T, sun s, Janes C, McCullough re, McCullough rG, Cymerman A, huang sy, reeves JT, Moore lG (1993) hypoxic ventilatory responsiveness in Tibetan com- pared with han residents of 3,658 m. J Appl Physiol 74:303–311. Zhuang J, Droma T, sutton Jr, Groves BM, McCullough re, McCullough rG, sun s, Moore lG (1996) smaller alveolar-arterial o2 gradients in Tibetan than han residents in lhasa (3658 m). Respir Physiol 103:75–82. Ziani s (1995) Un interesante caso di teratologia simmetrica in Onthophagus (Paleonthophagus) fracticornis (Coleoptera: scarabaeidae). Boll Assoc Romana Entomol 49:3–4. Zucchi r (1993) ritualized dominance, evolution of queen-worker interactions and related aspects in stingless bees (hymenoptera: Apidae). in Evolution of Insect Societies, eds inoue T, yamane s (hakuhinsha, Tokyo), pp 207–249. Zuzarte-luis v, hurle JM (2002) Programmed cell death in the developing limb. Int J Dev Biol 46:871–876.

OCR for page 305