Resolving phylogenetic relationships of the recently radiated carnivorous plant genus Sarracenia using target enrichment.

[1]  T. Mes,et al.  Phylogenetic Relationships , 2021, Systematics of Root-knot Nematodes (Nematoda: Meloidogynidae).

[2]  D. Schnell Infraspecific Variation in Sarracenia rubra Walt.: Some Observations , 2016 .

[3]  J. Leebens-Mack,et al.  Phylogenomic analyses of species relationships in the genus Sabal (Arecaceae) using targeted sequence capture , 2016 .

[4]  J. Wen,et al.  Rapid radiation and dispersal out of the Qinghai-Tibetan Plateau of an alpine plant lineage Rhodiola (Crassulaceae). , 2014, Molecular phylogenetics and evolution.

[5]  A. Ellison,et al.  Pitcher Plants (Sarracenia) Provide a 21st-Century Perspective on Infraspecific Ranks and Interspecific Hybrids: A Modest Proposal* for Appropriate Recognition and Usage , 2014 .

[6]  Paul Medvedev,et al.  Informed and automated k-mer size selection for genome assembly , 2013, Bioinform..

[7]  A. Lemmon,et al.  High-Throughput Genomic Data in Systematics and Phylogenetics , 2013 .

[8]  A. Furches,et al.  Hybridization leads to interspecific gene flow in Sarracenia (Sarraceniaceae). , 2013, American journal of botany.

[9]  Bryan C. Carstens,et al.  The carnivorous plant described as Sarracenia alata contains two cryptic species , 2013 .

[10]  Michael S. Y. Lee,et al.  Multilocus phylogeny and recent rapid radiation of the viviparous sea snakes (Elapidae: Hydrophiinae). , 2013, Molecular phylogenetics and evolution.

[11]  K. Katoh,et al.  MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability , 2013, Molecular biology and evolution.

[12]  Travis C Glenn,et al.  Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales. , 2012, Systematic biology.

[13]  Sen Song,et al.  Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model , 2012, Proceedings of the National Academy of Sciences.

[14]  B. Faircloth,et al.  Not All Sequence Tags Are Created Equal: Designing and Validating Sequence Identification Tags Robust to Indels , 2012, PloS one.

[15]  Ramón Doallo,et al.  CircadiOmics: integrating circadian genomics, transcriptomics, proteomics and metabolomics , 2012, Nature Methods.

[16]  A. Ellison,et al.  Phylogeny and Biogeography of the Carnivorous Plant Family Sarraceniaceae , 2012, PloS one.

[17]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[18]  Nicholas G. Crawford,et al.  LSU Digital Commons LSU Digital Commons Ultraconserved elements are novel phylogenomic markers that Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with resolve placental mammal phylogeny when combined with species-tree analysis species-tr , 2022 .

[19]  S. R. Santos,et al.  Genetic Differentiation, Structure, and a Transition Zone among Populations of the Pitcher Plant Moth Exyra semicrocea: Implications for Conservation , 2011, PloS one.

[20]  N. Friedman,et al.  Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data , 2011, Nature Biotechnology.

[21]  Russell L. Malmberg,et al.  Transcriptome Analysis of Sarracenia, an Insectivorous Plant , 2011, DNA research : an international journal for rapid publication of reports on genes and genomes.

[22]  Emily H Turner,et al.  Target-enrichment strategies for next-generation sequencing , 2010, Nature Methods.

[23]  A. Drummond,et al.  Bayesian Inference of Species Trees from Multilocus Data , 2009, Molecular biology and evolution.

[24]  P. Sheridan Ecological and genetic status of the purple pitcher plant, Sarracenia purpurea L., in Maryland and Virginia , 2010 .

[25]  Scott V Edwards,et al.  A maximum pseudo-likelihood approach for estimating species trees under the coalescent model , 2010, BMC Evolutionary Biology.

[26]  Aakrosh Ratan,et al.  Assembly algorithms for next-generation sequence data , 2009 .

[27]  L Lacey Knowles,et al.  Estimating species trees: methods of phylogenetic analysis when there is incongruence across genes. , 2009, Systematic biology.

[28]  L. Kubatko Identifying hybridization events in the presence of coalescence via model selection. , 2009, Systematic biology.

[29]  D. Pearl,et al.  Estimating species phylogenies using coalescence times among sequences. , 2009, Systematic biology.

[30]  S. Edwards,et al.  Phylogenetic analysis in the anomaly zone. , 2009, Systematic biology.

[31]  G. Bertorelle,et al.  Population Genetics for Animal Conservation , 2009 .

[32]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[33]  Noah A Rosenberg,et al.  Gene tree discordance, phylogenetic inference and the multispecies coalescent. , 2009, Trends in ecology & evolution.

[34]  P. Beerli,et al.  How to use MIGRATE or why are Markov chain Monte Carlo programs difficult to use , 2009 .

[35]  S. Edwards IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING? , 2009, Evolution; international journal of organic evolution.

[36]  A. Ellison,et al.  Energetics and the evolution of carnivorous plants--Darwin's 'most wonderful plants in the world'. , 2009, Journal of experimental botany.

[37]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[38]  Liang Liu,et al.  Estimating Species Trees Using Multiple-Allele DNA Sequence Data , 2008, Evolution; international journal of organic evolution.

[39]  A. Löytynoja,et al.  Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis , 2008, Science.

[40]  E. Birney,et al.  Velvet: algorithms for de novo short read assembly using de Bruijn graphs. , 2008, Genome research.

[41]  L. Kubatko,et al.  Inconsistency of phylogenetic estimates from concatenated data under coalescence. , 2007, Systematic biology.

[42]  H. Shaffer,et al.  Phylogeographic concordance in the southeastern United States: the flatwoods salamander, Ambystoma cingulatum, as a test case , 2006, Molecular ecology.

[43]  G. Ye,et al.  A simple and efficient method for DNA extraction from grapevine cultivars andVitis species , 1994, Plant Molecular Biology Reporter.

[44]  S. McPherson Pitcher Plants of the Americas , 2006 .

[45]  Ashley B. Morris,et al.  Comparative phylogeography of unglaciated eastern North America , 2006, Molecular ecology.

[46]  Alexandros Stamatakis,et al.  RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models , 2006, Bioinform..

[47]  Mark Merchant,et al.  SYSTEMATIC RELATIONSHIPS OF SARRACENIACEAE INFERRED FROM NUCLEAR RIBOSOMAL DNA SEQUENCES , 2006 .

[48]  N. Rosenberg,et al.  Discordance of Species Trees with Their Most Likely Gene Trees , 2006, PLoS genetics.

[49]  W. Maddison,et al.  Inferring phylogeny despite incomplete lineage sorting. , 2006, Systematic biology.

[50]  Andrew J. Alverson,et al.  Phylogenetic analyses of Vitis (Vitaceae) based on complete chloroplast genome sequences: effects of taxon sampling and phylogenetic methods on resolving relationships among rosids , 2006, BMC Evolutionary Biology.

[51]  J. F. Storz,et al.  INVITED REVIEW: Using genome scans of DNA polymorphism to infer adaptive population divergence , 2005, Molecular ecology.

[52]  D. Soltis,et al.  The origin and diversification of angiosperms. , 2004, American journal of botany.

[53]  K. Müller,et al.  Phylogenetics of Utricularia (Lentibulariaceae) and molecular evolution of the trnK intron in a lineage with high substitutional rates , 2004, Plant Systematics and Evolution.

[54]  K. Cameron,et al.  Molecular Phylogenetics of Lentibulariaceae Inferred from Plastid rps16 Intron and trnL-F DNA Sequences: Implications for Character Evolution and Biogeography , 2003 .

[55]  M. Hasebe,et al.  Phylogeny of the sundews, Drosera (Droseraceae), based on chloroplast rbcL and nuclear 18S ribosomal DNA Sequences. , 2003, American journal of botany.

[56]  Ziheng Yang,et al.  Likelihood and Bayes estimation of ancestral population sizes in hominoids using data from multiple loci. , 2002, Genetics.

[57]  K. Shaw Conflict between nuclear and mitochondrial DNA phylogenies of a recent species radiation: What mtDNA reveals and conceals about modes of speciation in Hawaiian crickets , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[58]  Peter Beerli,et al.  Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[59]  P. Dittrich,et al.  Molecular Phylogeny of Nepenthaceae Based on Cladistic Analysis of Plastid trnK Intron Sequence Data , 2001 .

[60]  Bin Ma,et al.  From Gene Trees to Species Trees , 2000, SIAM J. Comput..

[61]  Wei Qian,et al.  Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. , 2000, Molecular biology and evolution.

[62]  A. Paterson,et al.  Construction of plant bacterial artificial chromosome (BAC) libraries: an illustrated guide. , 2000 .

[63]  X. Huang,et al.  CAP3: A DNA sequence assembly program. , 1999, Genome research.

[64]  J. Hamrick,et al.  Genetic Divergence Among Infraspecific Taxa of Sarracenia purpurea , 1998 .

[65]  M. Nei,et al.  Relationships between Gene Trees and Species Trees1 , 1998 .

[66]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[67]  D. Soltis,et al.  Phylogenetic Relationships in Sarraceniaceae Based on rbcL and ITS Sequences , 1996 .

[68]  J. Avise,et al.  Conservation Genetics: Case Histories from Nature , 1996 .

[69]  J. Avise Toward a Regional Conservation Genetics Perspective: Phylogeography of Faunas in the Southeastern United States , 1996 .

[70]  M. Chase,et al.  Carnivorous plants: phylogeny and structural evolution. , 1992, Science.

[71]  E. G. Strauss,et al.  Molecular phylogeny , 1992, Current Biology.

[72]  R. J. Robins,et al.  The Carnivorous Plants , 1989 .

[73]  M. Nei,et al.  Relationships between gene trees and species trees. , 1988, Molecular biology and evolution.

[74]  Wen-Hsiung Li,et al.  Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[75]  G. Folkerts The Gulf Coast Pitcher Plant Bogs , 1982 .

[76]  D. Schnell Carnivorous Plants of the United States and Canada , 1976 .

[77]  M. L. Fernald Local plants of the inner coastal plain of Southeastern Virginia , 1937, Contributions from the Gray Herbarium of Harvard University.

[78]  FRANCISCO GINEZ,et al.  Carnivorous Plants , 1877, Nature.