LC–16 LITERATURE CITED
- Charlesworth, J., and A. Eyre-Walker. 2006. The rate of adaptive
evolution in enteric bacteria. Mol. Biol. Evol. 23: 1348–1356. - Chen, S. D., B. H. Krinsky, and M. Y. Long. 2013. New genes as
drivers of phenotypic evolution. Nat. Rev. Genet. 14: 645–660. - Deininger, P. L., and M. A. Batzer. 2002. Mammalian retroelements.
Genome Res. 12: 1455–1465. - de Jong, W. W., W. Hendriks, J. W. M. Mulders, H. Bloemendal.
1989. Evolution of eye lens crystallins: The stress connection. Trends
Biochem. Sci. 14: 365–368.
15a. Demuth, J. P., T. D. Bie, J. E. Stajich, N. Cristianini, and M. W. Hahn. - The evolution of mammalian gene families. PLoS ONE 1: e85.
doi:10.1371/journal.pone.0000085
15b. Dobzhansky, Th., and C. Epling. 1944. Contribution to the genetics,
taxonomy, and ecology of Drosophila pseudoobscura and its relatives.
Carnegie Institution Publication 554: 111–183. - Drosophila 12 Genomes Consortium. 2007. Evolution of genes and
genomes on the Drosophila phylogeny. Nature 450: 203–218. - Eyre-Walker, A., and P. D. Keightley. 2007. The distribution of fitness
effects of new mutations. Nat. Rev. Genet. 8: 610–618. - Friz, C. T. 1968. Biochemical composition of free-living amoebae
Chaos chaos, Chaos dubia, and Chaos proteus. Comp. Biochem. Physiol.
26: 81–90. - Galvani, A. P., and J. Novembre. 2005. The evolutionary history of the
CCR5–Δ32 HIV-resistance mutation. Microb. Infect. 7: 302–309. - Ganley, A. R. D., and T. Kobayashi. 2007. Highly efficient concerted
evolution in the ribosomal DNA repeats: Total rDNA repeat variation
revealed by whole-genome shotgun sequence data. Genome Res. 17:
184–191. - Giovannoni, S. J., and 13 others. 2005. Genome streamlining in a
cosmopolitan oceanic bacterium. Science 309: 1242–1245. - Gregory, T. R. 2001. Coincidence, coevolution, or causation? DNA
content, cell size, and the C-value enigma. Biol. Rev. 76: 65–101. - Gregory, T. R. 2005. Genome size evolution in animals. In T. R.
Gregory (ed.), The Evolution of the Genome (pp. 3–87). Elsevier,
Burlington, MA. - Guerzoni, D., and A. McLysaght. 2015. New genes from non-coding
sequence: the role of de novo protein-coding genes in eukaryotic
evolutionary innovation. Phil. Trans. R. Soc. Lond. B 370: 20140332. - Halligan, D. L., F. Oliver, A. Eyre-Walker, B. Harr, and P. D. Keightley.
2010. Evidence for pervasive adaptive protein evolution in wild mice.
PLoS Genet. 6: e1000825. - Hershberg, R., and D. A. Petrov. 2010. Evidence that mutation is
universally biased towards AT in bacteria. PLoS Genet. 6: e1001115. - Hill, R. W., G. A. Wyse, and M. Anderson. 2016. Animal Physiology.
Sinauer, Sunderland, MA. - Hillier, L. W., A. Coulson, J. I. Murray, Z. Bao, J. E. Sulston, and R. H.
Waterston. 2005. Genomics in C. elegans: So many genes, such a little
worm. Genome Res. 15: 1651–1660. - Hof, A. E. van’t, and 8 others. 2016. The industrial melanism
mutation in British peppered moths is a transposable element.
Nature 534: 102–105. - Huvet, M., and M. Stumpf. 2014. Overlapping genes: A window on
gene evolvability. BMC Genomics 15: 721. - Innan, H., and F. Kondrashov. 2010. The evolution of gene
duplications: Classifying and distinguishing between models. Nat.
Rev. Genet. 11: 97–108. - Jones, F. C., and 28 others. 2012. The genomic basis of adaptive
evolution in threespine sticklebacks. Nature 484: 55–61. - Kasahara, M. 2007. The 2R hypothesis: An update. Curr. Opin.
Immunol. 19: 547–552. - Kasimova, M. A., D. Granata, and V. Carnevale. 2016. Voltage-gated
sodium channels: Evolutionary history and distinctive sequence
features. Curr. Top. Membr. 78: 261–286. - Kawahara, R., and M. Nishida. 2007. Extensive lineage-specific
gene duplication and evolution of the spiggin multi-gene family in
stickleback. BMC Evol. Biol. 7: 209.
36. Kirkpatrick, M. 2010. How and why chromosome inversions evolve.
PLoS Biol. 8: e1000501.
37. Kondrashov, F. A. 2012. Gene duplication as a mechanism of
genomic adaptation to a changing environment. Proc. R. Soc. Lond.,
Ser. B: Biol. Sci. 279: 5048–5057.
38. Lamichhaney, S., and 20 others. 2015. Structural genomic changes
underlie alternative reproductive strategies in the ruff (Philomachus
pugnax). Nat. Genet. 48: 84–88. Epub.
39. Lamichhaney, S., and 20 others. 2016. Structural genomic changes
underlie alternative reproductive strategies in the ruff (Philomachus
pugnax). Nat. Genet. 48: 84–88.
40. Li, X. C., M. A. Schuler, and M. R. Berenbaum. 2007. Molecular
mechanisms of metabolic resistance to synthetic and natural
xenobiotics. Annu. Rev. Entomol. 52: 231–253.
41. Lindblad-Toh, K., and 78 others. 2011. A high-resolution map of
human evolutionary constraint using 29 mammals. Nature 478:
476–482.
42. Long, M., E. Betran, K. Thornton, and W. Wang. 2003. The origin of
new genes: Glimpses from the young and old. Nat. Rev. Genet. 4:
865–875.
43. Lynch, M. 2006. Streamlining and simplification of microbial genome
architecture. Annu. Rev. Microbiol. 60: 327–349.
44. Lynch, M. 2007. The Origins of Genome Architecture. Sinauer,
Sunderland, MA.
45. Lynch, M. 2010. Rate, molecular spectrum, and consequences of
human mutation. Proc. Natl. Acad. Sci. USA 107: 961–968.
46. Lysak, M. A., M. A. Koch, J. M. Beaulieu, A. Meister, and I. J. Leitch.
2009. The dynamic ups and downs of genome size evolution in
Brassicaceae. Mol. Biol. Evol. 26: 85–98.
47. McBride, C. S., and 7 others. 2014. Evolution of mosquito preference
for humans linked to an odorant receptor. Nature 515: 222–227.
48. McCutcheon, J. P., and N. A. Moran. 2012. Extreme genome
reduction in symbiotic bacteria. Nat. Rev. Microbiol. 10: 13–26.
49. Mudge, J. M., and 9 others. 2011. The origins, evolution, and
functional potential of alternative splicing in vertebrates. Mol. Biol.
Evol. 28: 2949–2959.
50. Nachman, M. W., and J. B. Searle. 1995. Why is the house mouse
karyotype so variable? Trends Ecol. Evolut. 10: 397–402.
51. Otto, S. P., and J. Whitton. 2000. Polyploid incidence and evolution.
Annu. Rev. Genet. 34: 401–437.
52. Pääbo, S. 2014. The human condition—A molecular approach. Cell
157: 216–226.
53. Palazzo, A. F., and T. R. Gregory. 2014. The case for junk DNA. PLoS
Genet. 10.
54. Pardo-Manuel de Villena, F., and C. Sapienza. 2001. Female meiosis
drives karyotypic evolution in mammals. Genetics 159: 1179–1189.
55. Perry, G. H., and 12 others. 2007. Diet and the evolution of human
amylase gene copy number variation. Nat. Genet. 39: 1256–1260.
56. Piatigorsky, J. 2007. Gene Sharing and Evolution. Harvard University
Press, Cambridge, MA.
57. Plotkin, J. B., and G. Kudla. 2011. Synonymous but not the same: The
causes and consequences of codon bias. Nat. Rev. Genet. 12: 32–42.
58. Price, M. N., A. P. Arkin, and E. J. Alm. 2006. The life-cycle of operons.
PLoS Genet. 2: 859–873.
59. Reneker, J., and 6 others. 2012. Long identical multispecies elements
in plant and animal genomes. Proc. Natl. Acad. Sci. USA 109: E1183–
E1191.
60. Sadava, D. E., D. M. Hillis, H. C. Heller, and S. D. Hacker. 2017. Life:
The Science of Biology, 11th ed. Sinauer, Sunderland MA.
61. Schlotterer, C. 2015. Genes from scratch—the evolutionary fate of de
novo genes. Trends Genet. 31: 215–219.
62. Storz, J. F., J. C. Opazo, and F. G. Hoffmann. 2013. Gene duplication,
genome duplication, and the functional diversification of vertebrate
globins. Mol. Phylogen. Evol. 66: 469–478.
25_EVOL4E_LIT_CITED.indd 16 3/22/17 1:58 PM