[1] | Fulton TM, der Hoeven RV, Eannetta NT, Tanksley SD (2002) Identification, analysis, and utilization of conserved ortholog set markers for comparative genomics in higher plants. Plant Cell 14: 1457–1467.
|
[2] | Wu F, Mueller LA, Crouzillat D, Pétiard V, Tanksley SD (2006) Combining bioinformatics and phylogenetics to identify large sets of single-copy orthologous genes (COSII) for comparative, evolutionary and systematic studies: A test case in the Euasterid plant clade. Genetics 174: 1407–1420.
|
[3] | Rokas A, Williams BL, King N, Carrol SB (2003) Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425: 798–804.
|
[4] | Drosophila 12 Genomes Consortium (2007) Evolution of genes and genomes on the Drosophila phylogeny. Nature 450: 203–218.
|
[5] | Foster JT, Beckstrom-Sternberg SM, Pearson T, Beckstrom-Sternberg JS, Chain PSG, et al. (2009) Whole-genome-based phylogeny and divergence of the genus Brucella. J Bacteriol 191: 2864–2870.
|
[6] | Sims GE, Jun SR, Wu GA, Kim SH (2009) Whole-genome phylogeny of mammals: Evolutionary information in genic and nongenic regions. Proc Natl Acad Sci USA 106: 17077–17082.
|
[7] | de Villiers EP, Gallardo C, Arias M, da Silva M, Upton C, et al. (2010) Phylogenomic analysis of 11 complete African swine fever virus genome sequences. Virology 400: 128–136.
|
[8] | Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, et al. (2008) Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS ONE 3: e3376.
|
[9] | Lewis ZA, Shiver AL, Stiffler N, Miller MR, Johnson EA, et al. (2007) High-density detection of restriction-site-associated DNA markers for rapid mapping of mutated loci in neurospora. Genetics 177: 1163–1171.
|
[10] | Miller MR, Atwood TS, Eames BF, Eberhart JK, Yan YL, et al. (2007) RAD marker microarrays enable rapid mapping of zebrafish mutations. Genome Biol 8: R105.
|
[11] | Miller MR, Dunham JP, Amores A, Cresko WA, Johnson EA (2007) Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers. Genome Res 17: 240–248.
|
[12] | Emerson KJ, Merz CR, Catchen JM, Hohenlohe PA, Cresko WA, et al. (2010) Resolving postglacial phylogeography using high-throughput sequencing. Proc Natl Acad Sci USA 107: 16196–16200.
|
[13] | Hohenlohe PA, Bassham S, Etter PD, Stiffler N, Johnson EA, et al. (2010) Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags. PLoS Genet 6: e1000862.
|
[14] | Li H, Ruan J, Durbin R (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 18: 1851–1858.
|
[15] | Catchen J, Amores A, Hohenlohe P, Cresko W, Postlethwait J (2011) Stacks: building and genotyping loci de novo from short-read sequences. G3: Genes, Genomes, Genetics 1: 171–182.
|
[16] | Edgar RC (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26: 2460–2461.
|
[17] | Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792–1797.
|
[18] | Burleigh JG, Driskell AC, Sanderson MJ (2006) Supertree bootstrapping methods for assessing phylogenetic variation among genes in genome-scale data sets. Syst Biol 55: 426–440.
|
[19] | Stamatakis A (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688–2690.
|
[20] | Prasad AB, Allard MW, Green ED, NISC Comparative Sequencing Program (2008) Confirming the phylogeny of mammals by use of large comparative sequence data sets. Mol Biol Evol 25: 1795–1808.
|
[21] | Ané C, Larget B, Baum DA, Smith SD, Rokas A (2006) Bayesian estimation of concordance among gene trees. Mol Biol Evol 24: 412–426.
|
[22] | Drummond A, Rambaut A (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 7: 214.
|
[23] | Kubatko LS, Carstens BC, Knowles LL (2009) STEM: species tree estimation using maximum likelihood for gene trees under coalescence. Bioinformatics 25: 971–973.
|
[24] | Taylor JW, Berbee ML (2006) Dating divergences in the fungal tree of life: review and new analyses. Mycologia 98: 838–849.
|
[25] | Murphy WJ, Pringle TH, Crider TA, Springer MS, Miller W (2007) Using genomic data to unravel the root of the placental mammal phylogeny. Genome Res 17: 413–421.
|
[26] | Russo AMC, Takezaki N, Nei M (1995) Molecular phylogeny and divergence times of Drosophilid species. Mol Biol Evol 12: 391–404.
|
[27] | Tamura K, Subramanian S, Kumar S (2004) Temporal patters of fruit fly (Drosophila) evolution revealed by mutation clocks. Mol Biol Evol 21: 36–44.
|
[28] | Cutter AD (2008) Divergence times in Caenorhabditis and Drosophila inferred from direct estimates of the neutral mutation rate. Mol Biol Evol 25: 778–786.
|
[29] | Glazko GV (2003) Estimation of divergence times for major lineages of primate species. Mol Biol Evol 20: 424–434.
|
[30] | Adkins RM, Walton AH, Honeycutt RL (2003) Higher-level systematics of rodents and divergence time estimates based on two congruent nuclear genes. Mol Phylogenet Evol 3: 409–420.
|
[31] | Steppan S, Adkins R, Anderson J (2004) Phylogeny and divergence-date estimates of rapid radiations in Muroid rodents based on multiple nuclear genes. Syst Biol 53: 533–553.
|
[32] | Pollard DA, Iyer VN, Moses AM, Eisen MB (2006) Widespread discordance of gene trees with species tree in Drosophila: Evidence for incomplete lineage sorting. PLoS Genet 2: e173.
|
[33] | Philippe H, Brinkmann H, Lavrov DV, Littlewood DTJ, Manuel M, et al. (2011) Resolving difficult phylogenetic questions: why more sequences are not enough. PLoS Biol 9: e1000602.
|
[34] | Felsenstein J (1978) Cases in which parsimony or compatibility methods will be positively misleading. Syst Zool 27: 401–410.
|
[35] | Hillis DM, Bull JT (1993) An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Syst Biol 42: 182–192.
|
[36] | Bergsten J (2005) A review of long-branch attraction. Cladistics 21: 163–193.
|
[37] | Weins JJ (2003) Missing data, incomplete taxa, and phylogenetic accuracy. Syst Biol 52: 528–538.
|
[38] | Philippe H, Snell EA, Bapteste E, Lopez P, Holland PWH, et al. (2004) Phylogenomics of eukaryotes: Impact of missing data on large alignments. Mol Biol Evol 21: 1740–1752.
|
[39] | Philippe H, Delsuc F, Brinkmann H, Lartillot N (2005) Phylogenomics. Annu Rev Ecol Evol Syst 36: 541–562.
|
[40] | Weins JJ, Morrill MC (2011) Missing data in phylogenetic analysis: reconciling results from simulations and empirical data. Syst Biol 60: 719–731.
|
[41] | Knowles LL, Carstens BC (2007) Delimiting species without monophyletic gene trees. Syst Biol 56: 887–895.
|
[42] | Rannala B, Yang Z (2008) Phylogenetic inference using whole genomes. Annu Rev Genomics Hum Genet 9: 217–31.
|
[43] | Liu L (2008) BEST: Bayesian estimation of species trees under the coalescent model. Bioinformatics 24: 2542–2543.
|
[44] | Bryant D, Bouckaert R, Rosenberg NA (2009) Inferring species trees directly from SNP and AFLP data: Full coalescent analysis without those pesky gene trees. arXiv: 0910.4193v1 [q-bio.PE].
|
[45] | Metzker ML (2010) Sequencing technologies – the next generation. Nat Rev Genet 11: 31–46.
|