Peregrine and saker falcon genome sequences provide insights into evolution of a predatory lifestyle

Nature Genetics

Volumn 45, Issue 5, 2013, Pages 563-566

  Wang, Jun ^e,f   Bruford, Michael W ^a   Zhan, Xiangjiang ^a   Pan, Shengkai ^b   Wang, Junyi ^b   Dixon, Andrew ^c   He, Jing ^b   Muller, Margit G ^d   Ni, Peixiang ^b   Hu, Li ^b   Liu, Yuan ^b   Hou, Haolong ^b   Chen, Yuanping ^b   Xia, Jinquan ^b   Luo, Qiong ^b   Xu, Pengwei ^b   Chen, Ying ^b   Liao, Shengguang ^b   Cao, Changchang ^b   Gao, Shukun ^b   Wang, Zhaobao ^b   Yue, Zhen ^b   Li, Guoqing ^b   Yin, Ye ^b   Fox, Nick C ^c   more..

^a CARDIFF UNIVERSITY   (United Kingdom)

^b BGI SHENZHEN   (China)

^c International Wildlife Consultants Ltd   (United Kingdom)

^d EAD   (United Arab Emirates)

^e UNIVERSITY OF COPENHAGEN   (Denmark)

^f KING ABDULAZIZ UNIVERSITY   (Saudi Arabia)

Author keywords

[No Author keywords available]

Indexed keywords

ADAPTATION; ARTICLE; CHICKEN; DESERT; EVOLUTION; GALLIFORMES; GENE EXPRESSION; GENE STRUCTURE; GENOME; GENOME SIZE; HEAT STRESS; MITOCHONDRIAL RESPIRATION; NONHUMAN; PHENOTYPE; PHYLOGENY; PREDATION; PREDATOR; PRIORITY JOURNAL; PROTEIN FAMILY; REGULATORY MECHANISM; RNA SEQUENCE; SMELLING; SODIUM ABSORPTION; SODIUM EXCRETION; SWEATING; TAENIOPYGIA GUTTATA; TRANSPOSON; WATER ABSORPTION;

ANIMALS; BIOLOGICAL EVOLUTION; FALCONIFORMES; GENOME; MOLECULAR SEQUENCE DATA; POLYMORPHISM, SINGLE NUCLEOTIDE; PREDATORY BEHAVIOR; RECEPTORS, ODORANT;

ANIMALIA; FALCO CHERRUG; FALCO PEREGRINUS; FALCONIDAE; RAPTORES; TAENIOPYGIA GUTTATA;

EID: 84878588665     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng.2588     Document Type: Article

References (41)

1. Kim, E.B. et al. Genome sequencing reveals insights into physiology and longevity of the naked mole rat. Nature 479, 223-227 (2011).
2. Li, R. et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 20, 265-272 (2010).
3. Li, H. et al. TreeFam: a curated database of phylogenetic trees of animal gene families. Nucleic Acids Res. 34, D572-D580 (2006).
4. Hackett, S.J. et al. A phylogenomic study of birds reveals their evolutionary history. Science 320, 1763-1768 (2008).
5. Roper, T.J. Olfaction in birds. Adv. Stud. Behav. 28, 247-332 (1999).
6. Steiger, S.S., Fidler, A.E., Valcu, M. & Kempenaers, B. Avian olfactory receptor gene repertoires: evidence for a well-developed sense of smell in birds? Proc. R. Soc. Lond. B 275, 2309-2317 (2008).
7. Bang, B.G. Anatomical evidence for olfactory function in some species of birds. Nature 188, 547-549 (1960).
8. Steiger, S.S., Kuryshev, V.Y., Stensmyr, M.C., Kempenaers, B. & Mueller, J.C. A comparison of reptilian and avian olfactory receptor gene repertoires: species-specific expansion of group ? genes in birds. BMC Genomics 10, 446 (2009).
9. Hugall, A.F. & Stuart-Fox, D. Accelerated speciation in colour-polymorphic birds. Nature 485, 631-634 (2012).
10. Ashburner, M. et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25, 25-29 (2000).
11. Hahn, M.W., Demuth, J.P. & Han, S.G. Accelerated rate of gene gain and loss in primates. Genetics 177, 1941-1949 (2007).
12. Dalloul, R.A. et al. Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis. PLoS Biol. 8, e1000475 (2010).
13. Wong, G.K. et al. A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms. Nature 432, 717-722 (2004).
14. Warren, W.C. et al. The genome of a songbird. Nature 464, 757-762 (2010).
15. Li, H. & Durbin, R. Inference of human population history from individual whole-genome sequences. Nature 475, 493-496 (2011).
16. Nittinger, F., Haring, E., Pinsker, W., Wink, M. & Gamauf, A. Out of Africa? Phylogenetic relationships between Falco biarmicus and the other hierofalcons (Aves: Falconidae). J. Zoological Syst. Evol. Res. 43, 321-331 (2005).
17. Kanehisa, M., Goto, S., Furumichi, M., Tanabe, M. & Hirakawa, M. KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res. 38, D355-D360 (2010).
18. Abzhanov, A., Protas, M., Grant, B.R., Grant, P.R. & Tabin, C.J. Bmp4 and morphological variation of beaks in Darwin's finches. Science 305, 1462-1465 (2004).
19. Sorek, R. The birth of new exons: mechanisms and evolutionary consequences. RNA 13, 1603-1608 (2007).
20. Brugmann, S.A. et al. Comparative gene expression analysis of avian embryonic facial structures reveals new candidates for human craniofacial disorders. Hum. Mol. Genet. 19, 920-930 (2010).
21. Menezes, R.X., Boetzer, M., Sieswerda, M., van Ommen, G.B. & Boer, J.M. Integrated analysis of DNA copy number and gene expression microarray data using gene sets. BMC Bioinformatics 10, 203 (2009).
22. Perry, G.H. et al. Diet and evolution of human amylase gene copy number variation. Nat. Genet. 39, 1256-1260 (2007).
23. del Hoyo, J., Elliot, A. & Sargatal, J. Handbook of the Birds of the World, Vol. 2 (Lynx Edicions, Barcelona, Spain, 1994).
24. Tajika, Y. et al. Differential regulation of AQP2 trafficking in endosomes by microtubules and actin filaments. Histochem. Cell Biol. 124, 1-12 (2005).
25. Hays, S.R., Baum, M. & Kokko, J.P. Effects of protein kinase C activation on sodium, potassium, chloride, and total CO2 transport in the rabbit cortical collecting tubule. J. Clin. Invest. 80, 1561-1570 (1987).
26. Sharif-Naeini, R., Ciura, S. & Bourque, C.W. TRPV1 gene required for thermosensory transduction and anticipatory secretion from vasopressin neurons during hyperthermia. Neuron 58, 179-185 (2008).
27. Cade, T.J. & Greenwald, L. Nasal salt secretion in falconiform birds. Condor 68, 338-350 (1966).
28. Abzhanov, A. et al. The calmodulin pathway and evolution of elongated beak morphology in Darwin's finches. Nature 442, 563-567 (2006).
29. Mallarino, R. et al. Two developmental modules establish 3D beak-shape variation in Darwin's finches. Proc. Natl. Acad. Sci. USA 108, 4057-4062 (2011).
30. Tang, H. et al. Synteny and collinearity in plant genomes. Science 320, 486-488 (2008).
31. Guindon, S. & Gascuel, O. A simple, fast and accurate method to estimate large phylogenies by maximum likelihood. Syst. Biol. 52, 696-704 (2003).
32. Posada, D. & Crandall, K.A. Modeltest: testing the model of DNA substitution. Bioinformatics 14, 817-818 (1998).
33. Yang, Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24, 1586-1591 (2007).
34. Bailey, J.A., Yavor, A.M., Massa, H.F., Trask, B.J. & Eichler, E.E. Segmental duplications: organization and impact within the current human genome project assembly. Genome Res. 11, 1005-1017 (2001).
35. Liu, K. et al. SATé-II: very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees. Syst. Biol. 61, 90-106 (2012).
36. Tamura, K. et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28, 2731-2739 (2011).
37. Schneider, A. et al. Estimates of positive Darwinian selection are inflated by errors in sequencing, annotation, and alignment. Genome Biol. Evol. 1, 114-118 (2009).
38. Subramanian, A.R., Kaufmann, M. & Morgenstern, B. DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment. Algorithms Mol. Biol. 3, 6 (2008).
39. Li, R. et al. SNP detection for massively parallel whole-genome resequencing. Genome Res. 19, 1124-1132 (2009).
40. Hammer, Ø., Harper, D.A.T. & Ryan, P.D. PAST: paleontological statistics software package for education and data analysis. Palaeontol. Electronica 4, 9 (2001).
41. Benjamini, Y. & Yekutieli, D. The control of the false discovery rate in multiple testing under dependency. Ann. Stat. 29, 1165-1188 (2001).