Evolution of Darwin’s finches and their beaks revealed by genome sequencing (original) (raw)

• Schluter, D. The Ecology of Adaptive Radiation (Oxford Univ. Press, 2000)
  Google Scholar
• Seehausen, O. African cichlid fish: a model system in adaptive radiation research. Proc. R. Soc. B 273, 1987–1998 (2006)
  Article PubMed PubMed Central Google Scholar
• Lack, D. Darwin’s Finches (Cambridge Univ. Press, 1947)
  Google Scholar
• Grant, P. R. Ecology and Evolution of Darwin’s Finches (Princeton Univ. Press, 1999)
  Google Scholar
• Grant, P. R. & Grant, B. R. How and Why Species Multiply. The Radiation of Darwin’s Finches (Princeton Univ. Press, 2008)
  Google Scholar
• Petren, K., Grant, P. R., Grant, B. R. & Keller, L. F. Comparative landscape genetics and the adaptive radiation of Darwin’s finches: the role of peripheral isolation. Mol. Ecol. 14, 2943–2957 (2005)
  Article CAS PubMed Google Scholar
• Ali, J. R. & Aitchison, J. C. Exploring the combined role of eustasy and oceanic island thermal subsidence in shaping biodiversity on the Galápagos. J. Biogeogr. 41, 1227–1241 (2014)
  Article Google Scholar
• Geist, D., Snell, H., Snell, H., Goddard, C. & Kurz, M. in The Galápagos: A Natural Laboratory for the Earth Sciences (eds Harpp K. S., Mittelstaedt E., d’Ozouville N., & Graham, D. ) 145–166 (American Geophysical Union, 2014)
  Google Scholar
• Farrington, H. L., Lawson, L. P., Clark, C. M. & Petren, K. The evolutionary history of Darwin’s finches: speciation, gene flow, and introgression in a fragmented landscape. Evolution 68, 2932–2944 (2014)
  Article PubMed Google Scholar
• 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)
  Article CAS ADS PubMed Google Scholar
• Abzhanov, A. et al. The calmodulin pathway and evolution of elongated beak morphology in Darwin’s finches. Nature 442, 563–567 (2006)
  Article CAS ADS PubMed Google Scholar
• Mallarino, R. et al. Two developmental modules establish 3D beak-shape variation in Darwin’s finches. Proc. Natl Acad. Sci. USA 198, 4057–4062 (2011)
  Article ADS Google Scholar
• Burns, K. J. et al. Phylogenetics and diversification of tanagers (Passeriformes: Thraupidae), the largest radiation of Neotropical songbirds. Mol. Phylogenet. Evol. 75, 41–77 (2014)
  Article PubMed Google Scholar
• Zhang, G., Parker, P., Li, B., Li, H. & Wang, J. The genome of Darwin’s finch (Geospiza fortis). GigaScience, http://dx.doi.org/10.5524/100040 (3 August 2012)
• Ellegren, H. The evolutionary genomics of birds. Annu. Rev. Ecol. Evol. Syst. 44, 239–259 (2013)
  Article Google Scholar
• Balakrishnan, C. N. & Edwards, S. V. Nucleotide variation, linkage disequilibrium and founder-facilitated speciation in wild populations of the zebra finch (Taeniopygia guttata). Genetics 181, 645–660 (2009)
  Article PubMed PubMed Central Google Scholar
• Swarth, H. S. The avifauna of the Galapagos Islands. Occ. Pap. Calif. Acad. Sci. 18, 1–299 (1931)
  Google Scholar
• Lack, D. The Galapagos finches (Geospizinae): a study in variation. Occ. Pap. Calif. Acad. Sci. 21, 1–159 (1945)
  Google Scholar
• Durand, E. Y., Patterson, N., Reich, D. & Slatkin, M. Testing for ancient admixture between closely related populations. Mol. Biol. Evol. 28, 2239–2252 (2011)
  Article CAS PubMed PubMed Central Google Scholar
• Qvarnstrom, A. & Bailey, R. I. Speciation through evolution of sex-linked genes. Heredity 102, 4–15 (2009)
  Article CAS PubMed Google Scholar
• Li, H. & Durbin, R. Inference of human population history from individual whole-genome sequences. Nature 475, 493–496 (2011)
  Article CAS PubMed PubMed Central Google Scholar
• Rivera-Perez, J. A., Wakamiya, M. & Behringer, R. R. Goosecoid acts cell autonomously in mesenchyme-derived tissues during craniofacial development. Development 126, 3811–3821 (1999)
  CAS PubMed Google Scholar
• Rowe, A., Richman, J. M. & Brickell, P. M. Retinoic acid treatment alters the distribution of retinoic acid receptor-β transcripts in the embryonic chick face. Development 111, 1007–1016 (1991)
  CAS PubMed Google Scholar
• Uz, E. et al. Disruption of ALX1 causes extreme microphthalmia and severe facial clefting: expanding the spectrum of autosomal-recessive ALX-related frontonasal dysplasia. Am. J. Hum. Genet. 86, 789–796 (2010)
  Article CAS PubMed PubMed Central Google Scholar
• Dee, C. T., Szymoniuk, C. R., Mills, P. E. D. & Takahashi, T. Defective neural crest migration revealed by a zebrafish model of Alx1-related frontonasal dysplasia. Hum. Mol. Genet. 22, 239–251 (2013)
  Article CAS PubMed Google Scholar
• 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)
  Article CAS PubMed Google Scholar
• Sommer, P., Napier, H. R., Hogan, B. L. & Kidson, S. H. Identification of Tgfβ1i4 as a downstream target of Foxc1. Dev. Growth Differ. 48, 297–308 (2006)
  Article CAS PubMed Google Scholar
• Wang, J. et al. Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium. Nucleic Acids Res. 41, D171–D176 (2013)
  Article CAS PubMed Google Scholar
• Kumar, P., Henikoff, S. & Ng, P. C. Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nature Protocols 4, 1073–1081 (2009)
  Article CAS PubMed Google Scholar
• Grant, P. R. & Grant, B. R. 40 Years of Evolution. Darwin’s Finches on Daphne Major Island (Princeton Univ. Press, 2014)
  Book Google Scholar
• Boag, P. T. Growth and allometry of external morphology in Darwin’s finches (Geospiza) on Isla Daphne Major, Galápagos. J. Zool. 204, 413–441 (1984)
  Article Google Scholar
• The Heliconius Genome Consortium Butterfly genome reveals promiscuous exchange of mimicry adaptations among species. Nature 487, 94–98 (2012)
  Article ADS CAS PubMed Central Google Scholar
• Andersson, L. Molecular consequences of animal breeding. Curr. Opin. Genet. Dev. 23, 295–301 (2013)
  Article CAS PubMed Google Scholar
• Linnen, C. R. et al. Adaptive evolution of multiple traits through multiple mutations at a single gene. Science 339, 1312–1316 (2013)
  Article CAS ADS PubMed Google Scholar
• Siepel, A. et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 15, 1034–1050 (2005)
  Article CAS PubMed PubMed Central Google Scholar
• Luo, R. et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience 1, 18 (2012)
  Article PubMed PubMed Central Google Scholar
• Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009)
  Article CAS PubMed PubMed Central Google Scholar
• McKenna, A. et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297–1303 (2010)
  Article CAS PubMed PubMed Central Google Scholar
• DePristo, M. A. et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nature Genet. 43, 491–498 (2011)
  Article CAS PubMed Google Scholar
• Van der Auwera, G. A. et al. From FastQ data to high-confidence variant calls: the Genome Analysis Toolkit best practices pipeline. Curr. Protoc. Bioinform. 43, 11.10.1–11.10.33 (2002)
  Google Scholar
• Browning, S. R. & Browning, B. L. Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. Am. J. Hum. Genet. 81, 1084–1097 (2007)
  Article CAS PubMed PubMed Central Google Scholar
• Purcell, S. et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81, 559–575 (2007)
  Article CAS PubMed PubMed Central Google Scholar
• Green, R. E. et al. A draft sequence of the Neandertal genome. Science 328, 710–722 (2010)
  Article CAS ADS PubMed PubMed Central Google Scholar
• Holm, S. A simple sequentially rejective multiple test procedure. Scand. J. Stat. 6, 65–70 (1979)
  MathSciNet MATH Google Scholar
• Rands, C. et al. Insights into the evolution of Darwin’s finches from comparative analysis of the Geospiza magnirostris genome sequence. BMC Genomics 14, 95 (2013)
  Article CAS PubMed PubMed Central Google Scholar
• Weir, J. T. & Schluter, D. Calibrating the avian molecular clock. Mol. Ecol. 17, 2321–2328 (2008)
  Article CAS PubMed Google Scholar
• Watterson, G. A. On the number of segregating sites in genetical models without recombination. Theor. Popul. Biol. 7, 256–276 (1975)
  Article CAS MathSciNet PubMed MATH Google Scholar
• Grant, B. R. & Grant, P. R. Demography and the genetically effective sizes of two populations of Darwin’s finches. Ecology 73, 766–784 (1992)
  Article Google Scholar
• Nei, M. in Molecular Evolutionary Genetics 276–279 (Columbia Univ. Press, 1987)
  Book Google Scholar
• Danecek, P. et al. The variant call format and VCFtools. Bioinformatics 27, 2156–2158 (2011)
  Article CAS PubMed PubMed Central Google Scholar
• Vilella, A. J. et al. EnsemblCompara GeneTrees: complete, duplication-aware phylogenetic trees in vertebrates. Genome Res. 19, 327–335 (2009)
  Article CAS PubMed PubMed Central Google Scholar
• Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792–1797 (2004)
  Article CAS PubMed PubMed Central Google Scholar
• Waterhouse, A. M., Procter, J. B., Martin, D. M. A., Clamp, M. & Barton, G. J. Jalview version 2—a multiple sequence alignment editor and analysis workbench. Bioinformatics 25, 1189–1191 (2009)
  Article CAS PubMed PubMed Central Google Scholar
• Jones, P. et al. InterProScan 5: genome-scale protein function classification. Bioinformatics 30, 1236–1240 (2014)
  Article CAS PubMed PubMed Central Google Scholar
• Cingolani, P. et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w 1118; iso-2; iso-3. Fly (Austin) 6, 80–92 (2012)
  Article CAS Google Scholar
• Grant, B. R., Grant, P. R. & Petren, K. The allopatric phase of speciation: the sharp-beaked ground finch (Geospiza difficilis) on the Galápagos islands. Biol. J. Linn. Soc. 69, 287–317 (2000)
  Article Google Scholar
• Grant, P. R., Abbott, I., Schluter, D., Curry, R. L. & Abbott, L. K. Variation in the size and shape of Darwin’s finches. Biol. J. Linn. Soc. 25, 1–39 (1985)
  Article Google Scholar
• Schluter, D. & Grant, P. R. Ecological correlates of morphological evolution in a Darwin’s finch, Geospiza difficilis. Evolution 38, 856–869 (1984)
  Article PubMed Google Scholar
• Rabosky, D. Diversity-dependence, ecological speciation, and the role of competition in macroevolution. Ann. Rev. Evol. Ecol. Syst. 44, 481–502 (2013)
  Article Google Scholar