Erratum: Large-Scale Coding Sequence Change Underlies the Evolution of Postdevelopmental Novelty in Honey Bees (Molecular Biology and Evolution (2015) 32 (334-346) DOI: 10.1093/molbev/msu292);Large-scale coding sequence change underlies the evolution of postdevelopmental novelty in honey bees

Molecular Biology and Evolution

Volumn 32, Issue 2, 2015, Pages 334-346

  Jasper, William Cameron ^a   Linksvayer, Timothy A ^b   Atallah, Joel ^a   Friedman, Daniel ^a   Chiu, Joanna C ^a   Johnson, Brian R ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

bees; evolution of novelty; honey; novel traits; RNA Seq; taxonomically restricted genes

Indexed keywords

RNA;

ADULT; ADULT ANIMAL; ANIMAL TISSUE; ARTICLE; CELL FUNCTION; CODING; GENE EXPRESSION; GENETIC CONSERVATION; HONEYBEE; NONHUMAN; PHENOTYPE; PHYSIOLOGY; PLEIOTROPY; REGULATORY SEQUENCE; RNA SEQUENCE; TISSUES; ANIMAL; BEE; CLASSIFICATION; EVOLUTION; GENETICS;

ANIMALIA; APIS MELLIFERA; APOIDEA;

ANIMALS; BEES; BIOLOGICAL EVOLUTION;

EID: 84925127066     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msw022     Document Type: Erratum

References (83)

1. Andersen SO, Hojrup P, Roepstorff P. 1995. Insect cuticular proteins. Insect Biochem Molec Biol. 25:153-176
2. Arendt J, Reznick D. 2008. Convergence and parallelism reconsidered: what have we learned about the genetics of adaptation?. Trends Ecol Evol. 23:26-32
3. Arthur W. 2002. The emerging conceptual framework of evolutionary developmental biology. Nature 415:757-764
4. Beldade P, Brakefield PM. 2002. The genetics and evo-devo of butterfly wing patterns. Nat Rev Genet. 3:442-452
5. 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
6. Beldade P, Koops K, Brakefield PM. 2002. Modularity, individuality, and evo-devo in butterfly wings. Proc Natl Acad Sci USA. 99: 14262-14267
7. Brockmann A, Robinson GE. 2007. Central projections of sensory systems involved in honey bee dance language communication. Brain Behav Evol. 70:125-136
8. Bulet P, Hetru C, Dimarcq JL, Hoffmann D. 1999. Antimicrobial peptides in insects; structure and function. Dev Comp Immunol. 23:329-344
9. Carroll SB. 1995. Homeotic genes and the evolution of arthropods and chordates. Nature 376:479-485
10. Carroll SB. 2008. Evo-devo and an expanding evolutionary synthesis: a genetic theory of morphological evolution. Cell 134:25-36
11. Carter CS, Devries AC, Getz LL. 1995. Physiological substrates of mammalian monogamy: the prairie vole model. Neurosci Biobehav Rev. 19:303-314
12. Chen SD, Krinsky BH, Long MY. 2013. New genes as drivers of phenotypic evolution. Nat Rev Genet. 14:645-660
13. Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart W, Iyer VN., et al. 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450: 203 218
14. Conant GC,Wolfe KH. 2008. Turning a hobby into a job: how duplicated genes find new functions. Nat Rev Genet. 9:938-950
15. Crailsheim K. 1991. Interadult feeding of jelly in honeybee (Apis mellifera) colonies. J Comp Physiol B. 161:55-60
16. Daltry JC,Wuster W, Thorpe RS. 1996. Diet and snake venom evolution. Nature 379:537-540
17. Ding Y, Zhou Q, Wang W. 2012. Origins of new genes and evolution of their novel functions. Ann Rev Ecol Evol Syst. 43:345-363
18. Domazet-Loso T, Tautz D. 2003. An evolutionary analysis of orphan genes in Drosophila. Genome Res. 13:2213-2219
19. Elsik CG, Worley KC, Bennett AK, Beye M, Camara F, Childers CP, de Graaf DC, Debyser G, Devreese B, Elhaik E., et al. 2014. Finding the missing honey bee genes: lessons learned from a genome upgrade. BMC Genomics 15:86
20. Evans JD, Aronstein K, Chen YP, Hetru C, Imler JL, Jiang H, Kanost M, Thompson GJ, Zou Z, Hultmark D. 2006. Immune pathways and defence mechanisms in honey bees Apis mellifera. Insect Molec Biol. 15:645-656
21. Fitzpatrick MJ, Ben-Shahar Y, Smid HM, Vet LEM, Robinson GE, Sokolowski MB. 2005. Candidate genes for behavioural ecology. Trends Ecol Evol. 20:96-104
22. Fry BG, Wuster W, Kini RM, Brusic V, Khan A, Venkataraman D, Rooney AP. 2003. Molecular evolution and phylogeny of elapid snake venom three-finger toxins. J Mol Evol. 57:110-129
23. Hahn MW, Han MV, Han S-G. 2007. Gene family evolution across 12 Drosophila genomes. PLoS Genet. 3:2135-2146
24. Halligan DL, Kousathanas A, Ness RW, Harr B, Eory L, Keane TM, Adams DJ, Keightley PD. 2013. Contributions of protein-coding and regulatory change to adaptive molecular evolution in Murid Rodents. PLoS Genet. 9:e1003995
25. Harpur BA, Kent CF, Molodtsova D, Lebon JMD, Alqarni AS, Owayss AA, Zayed A. 2014. Population genomics of the honey bee reveals strong signatures of positive selection on worker traits. Proc Natl Acad Sci USA. 111:2614-2619
26. Hoekstra HE. 2006. Genetics, development and evolution of adaptive pigmentation in vertebrates. Heredity 97:222-234
27. Hoekstra HE, Coyne JA. 2007. The locus of evolution: evo devo and the genetics of adaptation. Evolution 61:995-1016
28. Insel TR, Wang ZX, Ferris CF. 1994. Patterns of brain vasopressin receptor distribution associated with social organization in microtine rodents. J Neurosci. 14:5381-5392
29. Johnson BR. 2008. Within-nest temporal polyethism in the honey bee. Behav Ecol Sociobiol. 62:777-784
30. Johnson BR. 2010. Division of labor in honeybees: form, function, and proximate mechanisms. Behav Ecol Sociobiol. 64:305-316
31. Johnson BR, Linksvayer TA. 2010. Deconstructing the superorganism: social physiology, groundplans, and sociogenomics. Q Rev Biol. 85:57-79
32. Johnson BR, Tsutsui ND. 2011. Taxonomically restricted genes are associated with the evolution of sociality in the honey bee. BMC Genomics 12:164
33. Khalturin K, Hemmrich G, Fraune S, Augustin R, Bosch TCG. 2009. More than just orphans: are taxonomically-restricted genes important in evolution?. Trends Genet. 25:404-413
34. King TP, Spangfort MD. 2000. Structure and biology of stinging insect venom allergens. Int Arch Allergy Immunol. 123:99-106
35. Kondrashov FA. 2012. Gene duplication as a mechanism of genomic adaptation to a changing environment. Proc R Soc B-Biol Sci. 279: 5048-5057
36. Kucharski R, Maleszka J, Maleszka R. 2007. Novel cuticular proteins revealed by the honey bee genome. Insect Biochem Molec Biol. 37: 128-134
37. Langfelder P, Horvath S. 2008. WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics 9:559
38. Leal WS. 2013. Odorant reception in insects: roles of receptors, binding proteins, and degrading enzymes. Annu Rev Entomol. 58: 373-391
39. Light S, Basile W, Elofsson A. 2014. Orphans and new gene origination, a structural and evolutionary perspective. Curr Opin Struct Biol. 26: 73-83
40. Lynch M, Conery JS. 2000. The evolutionary fate and consequences of duplicate genes. Science 290:1151-1155
41. Lynch M, Conery JS. 2003. The origins of genome complexity. Science 302:1401-1404
42. Mitchell-Olds T, Willis JH, Goldstein DB. 2007. Which evolutionary processes influence natural genetic variation for phenotypic traits?. Nat Rev Genet. 8:845-856
43. Nadeau NJ, Jiggins CD. 2010. A golden age for evolutionary genetics?. Genomic studies of adaptation in natural populations. Trends Genet. 26:484-492
44. Neme R, Tautz D. 2013. Phylogenetic patterns of emergence of new genes support a model of frequent de novo evolution. BMC Genomics 14:117
45. Owen MD, Bridges AR, Maleszka R. 1976. Aging in venom glands of queen and worker honey bee (Apis mellifera-L)-somemorphological and chemical observations. Toxicon 14:1-5
46. Owen MD, Pfaff LA. 1995. Melittin synthesis in the venom system of the honey bee (Apis mellifera L.). Toxicon 33:1181-1188
47. Page RE, Robinson GE. 1991. The genetics of division of labor in honey bee colonies. Adv Insect Physiol. 23:117-169
48. Parker DJ, Gardiner A, Neville MC, Ritchie MG, Goodwin SF. 2014. The evolution of novelty in conserved genes; evidence of positive selection in the Drosophila fruitless gene is localised to alternatively spliced exons. Heredity 112:300-306
49. Peiren N, de Graaf DC, Vanrobaeys F, Danneels EL, Devreese B, Van Beeurnen FJ, Jacobs J. 2008. Proteomic analysis of the honey bee worker venom gland focusing on the mechanisms of protection against tissue damage. Toxicon 52:72-83
50. Peters L, Zhu-Salzman K, Pankiw T. 2010. Effect of primer pheromones and pollen diet on the food producing glands of worker honey bees (Apis mellifera L.). J Insect Physiol. 56:132-137
51. Ranz JM, Parsch J. 2012. Newly evolved genes: moving from comparative genomics to functional studies in model systems. Bioessays 34: 477-483
52. Reinhardt JA, Wanjiru BM, Brant AT, Saelao P, Begun DJ, Jones CD. 2013. De Novo ORFs in Drosophila are important to organismal fitness and evolved rapidly from previously non-coding sequences. Plos Genet. 9 e1003860
53. Roat TC, Nocelli RCF, de Moraes R, Cruz-Landim C. 2004. Juvenile hormone effect on the venom gland secretory cycle in workers of Apis mellifera (Hymenoptera, apidae). Sociobiology 43:193-199
54. Robinson GE, Grozinger CM, Whitfield CW. 2005. Sociogenomics: social life in molecular terms. Nat Rev Genet. 6:257-270
55. Seeley TD. 1982. Adaptive significance of the age polyethism schedule in honeybee colonies. Behav Ecol Sociobiol. 11:287-293
56. Shigenobu S, Stern DL. 2013. Aphids evolved novel secreted proteins for symbiosis with bacterial endosymbiont. P R Soc B. 280:20121952
57. Smith CR, Toth AL, Suarez AV, Robinson GE. 2008. Genetic and genomic analyses of the division of labour in insect societies. Nat Rev Genet. 9: 735-748
58. Stern DL, Orgogozo V. 2008. The loci of evolution: how predictable is genetic evolution?. Evolution 62:2155-2177
59. 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
60. Sumner S. 2014. The importance of genomic novelty in social evolution. Mol Ecol. 23:26-28
61. Tautz D, Domazet-Loso T. 2011. The evolutionary origin of orphan genes. Nat Rev Genet. 12:692-702
62. Taylor JS, Raes J. 2004. Duplication and divergence: The evolution of new genes and old ideas. Ann Rev Genet. 38:615-643
63. Terra WR, Ferreira C. 1994. Insect digestive enzymes: properties, compartmentalization and function. Comp Biochem Physiol B-Biochem Mol Biol. 109:1-62
64. Toll-Riera M, Bosch N, Bellora N, Castelo R, Armengol L, Estivill X, Mar Alba M. 2009. Origin of primate orphan genes: a comparative genomics approach. Mol Biol Evol. 26:603-612
65. Toth AL, Robinson GE. 2007. Evo-devo and the evolution of social behavior. Trends Genet. 23:334-341
66. Turner LM, Young AR, Roempler H, Schoeneberg T, Phelps SM, Hoekstra HE. 2010. Monogamy evolves through multiple mechanisms: evidence from V1aR in Deer Mice. Mol Biol Evol. 27: 1269-1278
67. Ueno T, Nakaoka T, Takeuchi H, Kubo T. 2009. Differential gene expression in the hypopharyngeal glands of worker honeybees (Apis mellifera L.) Associated with an age-dependent role change. Zool Sci. 26: 557-563
68. Wagner GP, Pavlicev M, Cheverud JM. 2007. The road tomodularity. Nat Rev Genet. 8:921-931
69. Wegener J, Huang ZY, Lorenz MW, Bienefeld K. 2009. Regulation of hypopharyngeal gland activity and oogenesis in honey bee (Apis mellifera) workers. J Insect Physiol. 55:716-725
70. Whitfield CW, Band MR, Bonaldo MF, Kumar CG, Liu L, Pardinas JR, Robertson HM, Soares MB, Robinson GE. 2002. Annotated expressed sequence tags and cDNA microarrays for studies of brain and behavior in the honey bee. Genome Res. 12: 555-566
71. Whitfield CW, Cziko AM, Robinson GE. 2003. Gene expression profiles in the brain predict behavior in individual honey bees. Science 302: 296-299
72. Williams JB, Roberts SP, Elekonich MM. 2008. Age and natural metabolically-intensive behavior affect oxidative stress and antioxidant mechanisms. Exp Gerontol. 43:538-549
73. Wilson GA, Bertrand N, Patel Y, Hughes JB, Feil EJ, Field D. 2005. Orphans as taxonomically restricted and ecologically important genes. Microbiol-Sgm. 151:2499-2501
74. Wilson GA, Feil EJ, Lilley AK, Field D. 2007. Large-scale comparative genomic ranking of taxonomically restricted genes (TRGs) in bacterial and archaeal genomes. PLoS One 2:e324
75. Winslow JT, Hastings N, Carter CS, Harbaugh CR, Insel TR. 1993. A role for central vasopressin in pair bonding in monogamous prairie voles. Nature 365:545-548
76. Wissler L, Gadau J, Simola DF, Helmkampf M, Bornberg-Bauer E. 2013. Mechanisms and Dynamics of Orphan Gene Emergence in Insect Genomes. Genome Biol Evol. 5:439-455
77. Woodard SH, Fischman BJ, Venkat A, Hudson ME, Varala K, Cameron SA, Clark AG, Robinson GE. 2011. Genes involved in convergent evolution of eusociality in bees. Proc Natl Acad Sci USA. 108: 7472-7477
78. 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
79. Yao Z, Shafer OT. 2014. The Drosophila circadian clock is a variably coupled network of multiple peptidergic units. Science 343: 1516-1520
80. Zayed A, Robinson GE. 2012. Understanding the relationship between brain gene expression and social behavior: lessons from the honey bee. Annu Rev Genet. 46:591-615
81. Zhang JZ. 2003. Evolution by gene duplication: an update. Trends Ecol Evol. 18:292-298
82. Zhang G, Wang H, Shi J, Wang X, Zheng H, Wong GKS, ClarkT,Wang W, Wang J, Kang L. 2007. Identification and characterization of insectspecific proteins by genome data analysis. BMC Genomics 8:93
83. Zhao L, Saelao P, Jones CD, Begun DJ. 2014. Origin and spread of de novo genes in Drosophila melanogaster populations. Science 343:769-772