LITERATURE CITED LC–19
- Young, N. M., G. P. Wagner, and B. Hallgrimsson. 2010. Development
and the evolvability of human limbs. Proc. Natl. Acad. Sci. USA 107:
3400–3405.
CHAPTER 16
- Barrett, R. D. H., and D. Schluter. 2008. Adaptation from standing
genetic variation. Trends Ecol. Evol. 23: 38–44. - Barrett, R. D. H., S. M. Rogers, and D. Schluter. 2008. Natural
selection on a major armor gene in threespine stickleback. Science
322: 255–257. - Brusatte, S. L., G. T. Lloyd, S. C. Wang, and M. A. Norell. 2014.
Gradual assembly of avian body plan culminated in rapid rates of
evolution across the dinosaur-bird transition. Curr. Biol. 24: 2386–
2392. - Carstens, B. C., and L. L. Knowles. 2007. Estimating species
phylogeny from gene-tree probabilities despite incomplete lineage
sorting: An example from Melanoplus grasshoppers. Syst. Biol. 56:
400–411. - Chatterjee, S. 1985. Postosuchus, a new thecodontian reptile from the
Triassic of Texas and the origin of tyrannosaurs. Phil. Trans. R. Soc,. B
309: 395–460. - Colosimo, P. F., and 9 others. 2005. Widespread parallel evolution in
sticklebacks by repeated fixation of Ectodysplasin alleles. Science 307:
1928–1933. - Crawford, N. G., B. C. Faircloth, J. E. McCormack, R. T. Brumfield,
K. Winker, and T. G. Glenn. 2012. More than 1000 ultraconserved
elements provide evidence that turtles are the sister group of
archosaurs. Biol. Lett. 8: 783–786. - Cunningham, C. W., H. Zhu, and D. M. Hillis. 1998. Best-fit
maximum-likelihood mdels for phylogenetic inference: Empirical
tests with known phylogenies. Evolution 52: 978–987. - Currie, T. E., S. J. Greenhill, R. D. Gray, T. Hasegawa, and R. Mace.
2010. Rise and fall of political complexity in island South-East Asia
and the Pacific. Nature 467: 801–804. - dos Reis, M., P. C. J. Donoghue, and Z. Yang. 2013. Neither
phylogenomic nor palaeontological data support a Palaeocene origin
of placental mammals. Biol. Lett. 10: 20131003. (Cited in Springer
and Gatesy 2015.) - Fitch, W. M. 1976. Molecular evolutionary clocks. In F. J. Ayala (ed.),
Molecular Evolution, pp. 160–178. Sinauer, Sunderland, MA. - Fontaine, M. C., and 18 others. 2015. Extensive introgression in a
malaria vector species complex revealed by phylogenomics. Science
347: 1258524. - Gaut, B., L. Yang. S. Takuno, and L. E. Eguiarte. 2011. The patterns
and causes of variation in plant nucleotide substitution rates. Annu.
Rev. Ecol. Evol. Syst. 42: 245–266. - Gire, S. K., and 57 others. 2014. Genomic surveillance elucidates
Ebola virus origin and transmission during the 2014 outbreak. Science
345: 1369–1372. - Graur, D. 2016. Molecular and Genome Evolution. Sinauer, Sunderland,
MA. - Harms, M. J., and J. W. Thornton. 2010. Analyzing protein structure
and function using ancestral gene reconstruction. Curr. Opin. Struct.
Biol. 20: 360–366. - Harvey, P. H., and A. H. Harcourt. 1984. Sperm competition, testes
size, and breeding system in primates. In R. L. Smith (ed.), Sperm
Competition and the Evolution of Animal Breeding Systems, pp. 589–600.
Academic Press, New York. - Hillis, D. M., J. J. Bull, M. E. White, M. R. Badgett, and I. J. Molineaux.
- Experimental phylogenetics: Generation of a known
phylogeny. Science 255: 589–592. - Jarvis, E. D., and 104 others. 2014. Whole-genome analyses resolve
early branches in the tree of life of modern birds. Science 346: 1320–
- Jones, F. C., and 28 others. 2012. The genomic basis of adaptive
evolution in threespine sticklebacks. Nature 484: 55–61. - Kumar, S. 2005. Molecular clocks: Four decades of evolution. Nat.
Rev. Genet. 6: 654–662. - Li, Q., and 9 others. 2012. Reconstruction of Microraptor and the
evolution of iridescent plumage. Science 335: 1215–1219. - Mace, R., and F. M. Jordan. 2011. Macro-evolutionary studies
of cultural diversity: A review of empirical studies of cultural
transmission and cultural adaptation. Phil. Trans. R. Soc,. B 366:
402–411. - Meyer, A., and R. Zardoya. 2003. Recent advances in the (molecular)
phylogeny of vertebrates. Annu. Rev. Ecol. Evol. Syst. 34: 311–338. - Mindell, D. F., and C. E. Thacker. 1996. Rates of molecular evolution:
Phylogenetic issues and applications. Annu. Rev. Ecol. Syst. 27:
279–303. - Pipoly, I., V. Bókony, M. Kirkpatrick, P. F. Donald, T. Székely, and A.
Liker. 2015. The genetic sex-determination system predicts adult sex
ratios in tetrapods. Nature 527: 91–94. - Prum, R. O. 2002. Why ornithologists should care about the theropod
origin of birds. The Auk 119: 1–17. - Prum, R. O., and 6 others. 2015. A comprehensive phylogeny of birds
(Aves) using targeted next-generation DNA sequencing. Nature 526:
569–573. - Przeworski, M., G. Coop, and J. D. Wall. 2005. The signature of
positive selection on standing genetic variation. Evolution 59: 2312–
- Scally, A., and 70 others. 2012. Insights into hominid evolution from
the gorilla genome sequence. Nature 483: 169–175. - Sites, J. W., Jr., T. W. Reeder, and J. J. Wiens. 2011. Phylogenetic
insights on evolutioanry novelties in lizards andd snakes: sex, birth,
bodies, niches, and venom. Annu. Rev. Ecol. Evol. Syst. 42: 227–244. - Springer, M. S., and J. Gatesy. 2015. The gene tree delusion. Mol.
Phyl. Evol. 94: 1–33. - Steiper, M. E., and N. M. Young. 2006. Primate molecular divergence
dates. Mol. Phyl. Evol. 41: 384–394. - Van Rheede, T., T. Bastiaans, D. S. Boone, S. B, Hedges, W. W. deJong,
and O. Madsen. 2006. The platypus is in its place: Nuclear genes and
indels confirm the sister-group relation of monotremes and theirans.
Mol. Biol. Evol. 23: 587–597. - Wagner, G. P., and J. A. Gauthier. 1999. 1, 2, 3 = 2, 3, 4: A solution to
the problem of the homology of the digits in the avialn hand. Proc.
Natl. Acad. Sci. USA 96: 5111–5116. - Wagner, C. E., and 7 others. 2013. Genome-wide RAD sequence
data provide unprecedented resolution of species boundaries and
relationships in the Lake Victoria cichlid adaptive radiation. Mol. Ecol.
22: 787–798. - Yokoyama, S. 2008. Evolution of dim-light and color vision pigments.
Annu. Rev. Genomics Hum. Genet. 9: 259–282. - Yokoyama, S. 2012. Synthesis of experimental molecular biology
and evolutionary biology: An example from the world of vision.
BioScience 62: 939–948. - Yokoyama, S., T. Tada, H. Zhang, and L. Britt. 2008. Elucidation of
phenotypic adaptations: molecular analyses of dim-light vision
proteins in vertebrates. Proc. Natl. Acad. Sci. USA 105: 13480–13485.
CHAPTER 17
- Ahlberg, P. E., and J. A. Clack. 2006. A firm step from water to land.
Nature 440: 747–749. - Ahlberg, P. E., J. A. Clack, E. Lukševicˇ s, H. Blom, and I. Zupins. 2008.
Ventastega curonica and the origin of tetrapod morphology. Nature
453: 1199–1204. - Algeo, T. J., and S. F. Scheckler. 2010. Land plant evolution and
weathering rate changes in the Devonian. J. Earth Sci. 21 (Special
Issue): 75–78.
25_EVOL4E_LIT_CITED.indd 19 3/22/17 1:58 PM