Target Capture and Massively Parallel Sequencing of Ultraconserved Elements for Comparative Studies at Shallow Evolutionary Time Scales
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Baird, 2008, Rapid SNP discovery and genetic mapping using sequenced RAD markers, PLoS ONE, 3, e3376, 10.1371/journal.pone.0003376
Beerli, 1999, Maximum-likelihood estimation of migration rates and effective population numbers in two populations using a coalescent approach, Genetics, 152, 763, 10.1093/genetics/152.2.763
Blumenstiel, 2010, Targeted exon sequencing by in-solution hybrid selection, Curr. Protoc. Hum. Genet. Chapter, 18, 10.1002/0471142905.hg1804s66
Bouckaert, 2010, DensiTree: making sense of sets of phylogenetic trees, Bioinformatics, 26, 1372, 10.1093/bioinformatics/btq110
Briggs, 2009, Targeted retrieval and analysis of five Neandertal mtDNA genomes, Science, 325, 318, 10.1126/science.1174462
Broquet, 2009, Molecular estimation of dispersal for ecology and population genetics, Annu. Rev. Ecol. Evol. Syst., 40, 193, 10.1146/annurev.ecolsys.110308.120324
Brumfield, 2012, Inferring the origins of lowland Neotropical birds, Auk, 129, 367, 10.1525/auk.2012.129.3.367
Brumfield, 2003, The utility of single nucleotide polymorphisms in inferences of population history, Trends Ecol. Evol., 18, 249, 10.1016/S0169-5347(03)00018-1
Brumfield, 2007, Evolution into and out of the Andes: a Bayesian analysis of historical diversification in Thamnophilus antshrikes, Evolution, 61, 346, 10.1111/j.1558-5646.2007.00039.x
Bruneaux, 2013, Molecular evolutionary and population genomic analysis of the ninespined stickleback using a modified restriction-site-associated DNA tag approach, Mol. Ecol., 22, 565, 10.1111/j.1365-294X.2012.05749.x
Burney, 2009, Ecology predicts levels of genetic differentiation in Neotropical birds, Am. Nat., 174, 358, 10.1086/603613
Carling, 2007, Gene sampling strategies for multi-locus population estimates of genetic diversity (θ), PLoS ONE, 2, e160, 10.1371/journal.pone.0000160
Crawford, 2012, More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs, Biol. Lett., 8, 783, 10.1098/rsbl.2012.0331
Dickinson, 2003, The Howard and Moore complete checklist of the birds of the World, 3rd ed
Drummond, 2012, Bayesian phylogenetics with BEAUti and the BEAST 1.7, Mol. Biol. Evol., 29, 1969, 10.1093/molbev/mss075
Edwards, 2000, Perspective: gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies, Evolution, 54, 1839
Emerson, 2010, Resolving postglacial phylogeography using high-throughput sequencing, Proc. Natl Acad. Sci. USA, 107, 16196, 10.1073/pnas.1006538107
Faircloth, 2012, Not all sequence tags are created equal: designing and validating sequence identification tags robust to indels, PLoS ONE, 7, e42543, 10.1371/journal.pone.0042543
Faircloth, 2012, Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales, Syst. Biol., 61, 717, 10.1093/sysbio/sys004
Faircloth, 2013, A phylogenomic perspective on the radiation of ray-finned fishes based upon targeted sequencing of ultraconserved elements (UCEs), PLoS ONE., 8, e65923, 10.1371/journal.pone.0065923
Geraldes, 2011, SNP discovery in black cottonwood (Populus trichocarpa) by population transcriptome resequencing, Mol. Ecol. Res., 11, 81, 10.1111/j.1755-0998.2010.02960.x
Gnirke, 2009, Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing, Nat. Biotechnol., 27, 182, 10.1038/nbt.1523
Gompert, 2010, Bayesian analysis of molecular variance in pyrosequences quantifies population genetic structure across the genome of Lycaeides butterflies, Mol. Ecol., 19, 1473
Greenberg, 1981, The abundance and seasonality of forest canopy birds on Barro-Colorado Island, Panama, Biotropica, 13, 241, 10.2307/2387802
Gronau, 2011, Bayesian inference of ancient human demography from individual genome sequences, Nat. Genet., 43, 1031, 10.1038/ng.937
Harris, 2007, Improved pairwise alignment of genomic DNA
Heled, 2010, Bayesian inference of species trees from multilocus data, Mol. Biol. Evol., 27, 570, 10.1093/molbev/msp274
Hird, 2012, lociNGS: a lightweight alternative for assessing suitability of next-generation loci for evolutionary analysis, PLoS ONE, 7, e46847, 10.1371/journal.pone.0046847
Hodgkinson, 2011, Variation in the mutation rate across mammalian genomes, Nat. Rev. Genet., 12, 756, 10.1038/nrg3098
Hoorn, 2010, Amazonia through time: Andean uplift, climate change, landscape evolution, and biodiversity, Science, 330, 927, 10.1126/science.1194585
Hudson, 1990, Gene genealogies and the coalescent process, Oxford surveys in evolutionary biology. Vol. 7, 1
Katoh, 2005, MAFFT version 5: improvement in accuracy of multiple sequence alignment, Nucleic Acids Res., 33, 511, 10.1093/nar/gki198
Kuhner, 1998, Maximum likelihood estimation of population growth rates based on the coalescent, Genetics, 149, 429, 10.1093/genetics/149.1.429
Leaché, 2010, Bayesian species delimitation in West African forest geckos (Hemidactylus fasciatus), Proc. R. Soc. B, 277, 3071, 10.1098/rspb.2010.0662
Leffler, 2012, Revisiting an old riddle: What determines genetic diversity levels within species?, PLoS Biol., 10, e1001388, 10.1371/journal.pbio.1001388
Li, 2009, Fast and accurate short read alignment with Burrows-Wheeler transform, Bioinformatics, 25, 1754, 10.1093/bioinformatics/btp324
Li, 2009, The Sequence Alignment/Map format and SAMtools, Bioinformatics, 25, 2078, 10.1093/bioinformatics/btp352
Loiselle, 1988, Bird abundance and seasonality in a Costa Rican lowland forest canopy, Condor, 90, 761, 10.2307/1368833
McCormack, 2012, Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis, Genome Res., 22, 746, 10.1101/gr.125864.111
McCormack, 2013, A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing, PLoS ONE., 8, e54848, 10.1371/journal.pone.0054848
McCormack, 2012, Applications of next-generation sequencing to phylogeography and phylogenetics, Mol. Phylogenet. Evol., 62, 397, 10.1016/j.ympev.2011.10.012
McCormack, 2012, Next-generation sequencing reveals phylogeographic structure and a species tree for recent bird divergences, Mol. Phylogenet. Evol., 62, 397, 10.1016/j.ympev.2011.10.012
Miller, 2008, Out of Amazonia again and again: episodic crossing of the Andes promotes diversification in a lowland forest flycatcher, Proc. R. Soc. B, 275, 1133, 10.1098/rspb.2008.0015
Morin, 2010, Complete mitochondrial genome phylogeographic analysis of killer whales (Orcinus orca) indicates multiple species, Genome Res., 20, 908, 10.1101/gr.102954.109
Munn, 1985, Permanent canopy and understory flocks in Amazonia: species composition and population density, Neotropical Ornithology. Ornithological Monographs Number 36, 683
Naka, 2012, The role of physical barriers in the location of avian suture zones in the Guiana Shield, northern Amazonia, Am. Nat., 179, E115, 10.1086/664627
O'Neill, 2013, Parallel tagged amplicon sequencing reveals major lineages and phylogenetic structure in the North American tiger salamander (Ambystoma tigrinum) species complex, Mol. Ecol., 10.1111/mec.12049
Peterson, 2012, Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species, PLoS ONE, 7, e37135, 10.1371/journal.pone.0037135
Rambaut, 2010, Tracer v 1.5. Program distributed by the authors
Rannala, 2003, Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci, Genetics, 164, 1645, 10.1093/genetics/164.4.1645
Ribas, 2012, A palaeobiogeographic model for biotic diversification within Amazonia over the past three million years, Proc. R. Soc. B, 279, 681, 10.1098/rspb.2011.1120
Rubin, 2012, Inferring phylogenies from RAD sequence data, PLoS ONE, 7, e33394, 10.1371/journal.pone.0033394
Rull, 2011, Neotropical biodiversity: timing and potential drivers, Trends Ecol. Evol., 26, 508, 10.1016/j.tree.2011.05.011
Ryu, 2012, The evolution of ultraconserved elements with different phylogenetic origins, BMC Evol. Biol., 12, 236, 10.1186/1471-2148-12-236
Smith, 2012, Evaluating the role of contracting and expanding rainforest in initiating cycles of speciation across the Isthmus of Panama, Proc. R. Soc. B, 279, 3520, 10.1098/rspb.2012.0706
Smith, 2012, An asymmetry in niche conservatism contributes to the latitudinal species diversity gradient in New World vertebrates, Ecol. Lett., 15, 1318, 10.1111/j.1461-0248.2012.01855.x
Smith, 2013, Examining the role of effective population size on mitochondrial and multilocus divergence time discordance in a songbird, PLoS ONE, 8, e55161, 10.1371/journal.pone.0055161
Smith, 2013, Identifying biases at different spatial and temporal scales of diversification: a case study using the Neotropical parrotlet genus Forpus, Mol. Ecol., 22, 483, 10.1111/mec.12118
Stephen, 2008, Large-scale appearance of ultraconserved elements in tetrapod genomes and slowdown of the molecular clock, Mol. Biol. Evol., 25, 402, 10.1093/molbev/msm268
Terborgh, 1990, Structure and organization of an Amazonian forest bird community, Ecol. Monogr., 60, 213, 10.2307/1943045
Thornton, 2003, libsequence: a C++ class library for evolutionary genetic analysis, Bioinformatics, 19, 2325, 10.1093/bioinformatics/btg316
Tobias, 2008, Comment on “The latitudinal gradient in recent speciation and extinction rates of birds and mammals”, Science, 901c, 10.1126/science.1150568
Weir, 2008, Calibrating the avian molecular clock, Mol. Ecol., 17, 2321, 10.1111/j.1365-294X.2008.03742.x
Yang, 2002, Likelihood and Bayes estimation of ancestral population sizes in hominoids using data from multiple loci, Genetics, 162, 1811, 10.1093/genetics/162.4.1811
Yang, 2010, Bayesian species delimitation using multilocus sequence data, Proc. Natl Acad. Sci. USA, 107, 9264, 10.1073/pnas.0913022107
Zellmer, 2012, Deep phylogeographical structure and environmental differentiation in the carnivorous plant Serracenia alata, Syst. Biol., 61, 763, 10.1093/sysbio/sys048
Zerbino, 2008, Velvet: algorithms for de novo short read assembly using de Bruijn graphs, Genome Res., 18, 821, 10.1101/gr.074492.107