Anchored Hybrid Enrichment for Massively High-Throughput Phylogenomics

Alan R. Lemmon; Sandra A. Emme; Emily Moriarty Lemmon

doi:10.1093/sysbio/sys049

journal article Jul 05, 2012

Anchored Hybrid Enrichment for Massively High-Throughput Phylogenomics

Alan R. Lemmon Sandra A. Emme Emily Moriarty Lemmon

Systematic Biology Vol. 61 No. 5 pp. 727-744 · Oxford University Press (OUP)

View at Publisher Save 10.1093/sysbio/sys049

Topics

No keywords indexed for this article. Browse by subject →

References

54

[1]

Albert "Direct selection of human genomic loci by microarray hybridization" Nat. Methods. (2007) 10.1038/nmeth1111

[2]

Ané "Bayesian estimation of concordance among gene trees" Mol. Biol. Evol. (2007) 10.1093/molbev/msl170

[3]

Archer "Effect of probe characteristics on the subtractive hybridization efficiency of human genomic DNA" BMC Res. Notes (2010) 10.1186/1756-0500-3-109

[4]

Bader (2006)

[5]

Bashiardes "Direct genomic selection" Nat. Methods. (2005) 10.1038/nmeth0105-63

[6]

Bejerano "Ultraconserved elements in the human genome" Science (2004) 10.1126/science.1098119

[7]

Cracraft (2004) 10.1093/oso/9780195172348.001.0001

[8]

Donoghue "Immeasurable progress on the tree of life" (2004) 10.1093/oso/9780195172348.003.0034

[9]

Drummond Geneious v5.5.1. (2010)

[10]

MUSCLE: multiple sequence alignment with high accuracy and high throughput

R. C. Edgar

Nucleic Acids Research 2004 10.1093/nar/gkh340

[11]

Edwards "High-resolution species trees without concatenation" Proc. Natl. Acad. Sci. USA. (2007) 10.1073/pnas.0607004104

[12]

Faircloth "Ultraconserved elements anchor thousands of genetic markers for target enrichment spanning multiple evolutionary timescales" Syst. Biol. (2012) 10.1093/sysbio/sys004

[13]

Fu "Repeat subtraction-mediated sequence capture from a complex genome" Plant J. (2010) 10.1111/j.1365-313x.2010.04196.x

[14]

The UCSC Genome Browser database: update 2011

P. A. Fujita, B. Rhead, A. S. Zweig et al.

Nucleic Acids Research 2011 10.1093/nar/gkq963

[15]

[16]

Glazov "Ultraconserved elements in insect genomes: a highly conserved intronic sequence implicated in the constrol of homothorax mRNA splicing" Genome Res. (2005) 10.1101/gr.3545105

[17]

Gnirke "Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing" Nat. Biotechnol. (2009) 10.1038/nbt.1523

[18]

Goin "DNA and amphibian life history" Copeia. (1968) 10.2307/1442021

[19]

Gregory "Eukaryotic genome size databases" Nucleic Acids Res. (2006)

[20]

Hedges "TimeTree: a public knowledge-base of divergence times among organisms" Bioinformatics (2006) 10.1093/bioinformatics/btl505

[21]

Huang "Sources of error inherent in species-tree estimation: impact of muational and coalescent effects on accuracy and implications for choosing among different methods" Syst. Biol. (2010) 10.1093/sysbio/syq047

[22]

Janes "Reptiles and mammals have differentially retained long conserved noncoding sequences from the amniote ancestor" Genome Biol. Evol. (2010) 10.1093/gbe/evq087

[23]

Keeling "The tree of eukaryotes" Trends Ecol. Evol. (2005) 10.1016/j.tree.2005.09.005

[24]

Kircher "Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform" Nucleic Acids Res. (2011)

[25]

Lane "The eukaryotic tree of life: endosymbiosis takes its TOL" Trends Ecol. Evol. (2008) 10.1016/j.tree.2008.02.004

[26]

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

Ben Langmead, Cole Trapnell, Mihai Pop et al.

Genome Biology 2009 10.1186/gb-2009-10-3-r25

[27]

Leaché "The accuracy of species tree estimation under simulation: a comparison of methods" Syst. Biol. (2011) 10.1093/sysbio/syq073

[28]

Liu "BEST: Bayesian estimation of species trees under the coalescent model" Bioinformatics. (2008) 10.1093/bioinformatics/btn484

[29]

Liu "Estimating species trees from unrooted gene trees" Syst. Biol. (2011) 10.1093/sysbio/syr027

[30]

Lutzoni "Assembling the fungal tree of life: progress, classification and evolution of subcellular traits" Amer. J. Bot. (2004) 10.3732/ajb.91.10.1446

[31]

Maddison "Inferring phylogeny despite incomplete lineage sorting" Syst. Biol. (2006) 10.1080/10635150500354928

[32]

Maddison MacClade 4: Analysis of phylogeny and character evolution. (2005)

[33]

Mamanova "Target-enrichment strategies for next-generation sequencing" Nat. Methods. (2010) 10.1038/nmeth.1419

[34]

McCormack "Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species tree analysis" Genome Res. (2012) 10.1101/gr.125864.111

[35]

Illumina Sequencing Library Preparation for Highly Multiplexed Target Capture and Sequencing

Matthias Meyer, Martin Kircher

Cold Spring Harbor Protocols 2010 10.1101/pdb.prot5448

[36]

Nylander (2004)

[37]

Mapping the Tree of Life: Progress and Prospects

Norman R. Pace

Microbiology and Molecular Biology Reviews 2009 10.1128/mmbr.00033-09

[38]

Palmer "The plant tree of life: an overview and some points of view" Amer. J. Bot. (2004) 10.3732/ajb.91.10.1437

[39]

Parfrey "Broadly sampled multigene analyses yield a well-resolved eukaryotic tree of life" Syst. Biol. (2010) 10.1093/sysbio/syq037

[40]

Posada "Selecting the best-fit model of nucleotide substitution" Syst. Biol. (2001) 10.1080/10635150118469

[41]

[42]

Robinson "Creating a buzz about insect genomes" Science. (2011) 10.1126/science.331.6023.1386

[43]

Bushes in the Tree of Life

Antonis Rokas, Sean B Carroll

PLOS Biology 2006 10.1371/journal.pbio.0040352

[44]

Ronquist "MRBAYES 3: Bayesian phylogenetic inference under mixed models" Bioinformatics. (2003) 10.1093/bioinformatics/btg180

[45]

Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes

Adam Siepel, Gill Bejerano, Jakob Skou Pedersen et al.

Genome Research 2005 10.1101/gr.3715005

[46]

Soltis "Assembling the angiosperm tree of life: progress and future prospects" Ann. Missouri Bot. Gard. (2010) 10.3417/2009136

[47]

Stephen "Large-scale appearance of ultraconserved elements in tetrapod genomes and slowdown of the molecular clock" Mol. Biol. Evol. (2008) 10.1093/molbev/msm268

[48]

Thomson "Rapid progress on the vertebrate tree of life" BMC Biol. (2010) 10.1186/1741-7007-8-19

[49]

Townsend "Profiling phylogenetic informativeness" Syst. Biol. (2007) 10.1080/10635150701311362

[50]

Townsend "Taxon sampling and the optimal rates of evolution for phylogenetic inference" Syst. Biol. (2011) 10.1093/sysbio/syq097

Showing 50 of 54 references

Cited By

742

Phylogenomics and the evolution of larval feeding habits in the blow flies (Diptera: Calliphoridae)

Cristian F. Beza‐Beza, John Soghigian · 2025

Systematic Entomology

Inference of Gene Flow between Species from Genomic Data When the Mode, Direction, and Lineages are Misspecified

Yuttapong Thawornwattana, Tomáš Flouri · 2025

Molecular Biology and Evolution

Genome and life-history evolution link bird diversification to the end-Cretaceous mass extinction

Jacob S. Berv, Sonal Singhal · 2024

Science Advances

Phylogenomic insights into Neotropical Magnolia relationships

Fabián A. Aldaba Núñez, Salvador Guzmán-Díaz · 2024

Heliyon

The population genetics of speciation by cascade reinforcement

Carlie B. Anderson, Oscar Ospina · 2023

Ecology and Evolution

Phylogenomics reveals the history of host use in mosquitoes

John Soghigian, Charles Sither · 2023

Nature Communications

A simulation study to examine the impact of recombination on phylogenomic inferences under the multispecies coalescent model

Tianqi Zhu, Tomáš Flouri · 2022

Molecular Ecology

Excluding Loci With Substitution Saturation Improves Inferences From Phylogenomic Data

David A Duchêne, Niklas Mather · 2021

Systematic Biology

Phase Resolution of Heterozygous Sites in Diploid Genomes is Important to Phylogenomic Analysis under the Multispecies Coalescent Model

Jun Huang, Jeremy Bennett · 2021

Systematic Biology

MitoFinder: Efficient automated large‐scale extraction of mitogenomic data in target enrichment phylogenomics

Rémi Allio, Alex Schomaker‐Bastos · 2020

Molecular Ecology Resources

Congruence and Conflict in the Higher-Level Phylogenetics of Squamate Reptiles: An Expanded Phylogenomic Perspective

Sonal Singhal, Timothy J Colston · 2020

Systematic Biology

Phylogenomics Reveals Ancient Gene Tree Discordance in the Amphibian Tree of Life

Paul M Hime, Alan R Lemmon · 2020

Systematic Biology

A Simulation Study to Examine the Information Content in Phylogenomic Data Sets under the Multispecies Coalescent Model

Jun Huang, Tomáš Flouri · 2020

Molecular Biology and Evolution

Phylogenomic analysis on the exceptionally diverse fish clade Gobioidei (Actinopterygii: Gobiiformes) and data-filtering based on molecular clocklikeness

Ting Kuang, Luke Tornabene · 2018

Molecular Phylogenetics and Evoluti...

Tipping the Scales: The Migration–Selection Balance Leans toward Selection in Snake Venoms

Mark J Margres, Austin Patton · 2018

Molecular Biology and Evolution

The impact of GC bias on phylogenetic accuracy using targeted enrichment phylogenomic data

Silas Bossert, Elizabeth A. Murray · 2017

Molecular Phylogenetics and Evoluti...

Genomic Signature of an Avian Lilliput Effect across the K-Pg Extinction

Jacob S. Berv, Daniel J. Field · 2017

Systematic Biology

New insights on the sister lineage of percomorph fishes with an anchored hybrid enrichment dataset

Alex Dornburg, Jeffrey P. Townsend · 2017

Molecular Phylogenetics and Evoluti...

Quantity, Not Quality: Rapid Adaptation in a Polygenic Trait Proceeded Exclusively through Expression Differentiation

Mark J Margres, Kenneth P Wray · 2017

Molecular Biology and Evolution

Reconciling molecular phylogeny, morphological divergence and classification of Madagascan narrow-mouthed frogs (Amphibia: Microhylidae)

MARK D. SCHERZ, MIGUEL VENCES · 2016

Molecular Phylogenetics and Evoluti...

Metrics

742

Citations

54

References

Details

Published: Jul 05, 2012
Vol/Issue: 61(5)
Pages: 727-744

Authors

A

Alan R. Lemmon

Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, FL 32306-4102, USA; and 2 Department of Biological Science, Florida State University, 319 Stadium Drive, PO Box 3064295, Tallahassee, FL, 32306-4295, USA;

S

Sandra A. Emme

Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, FL 32306-4102, USA; and 2 Department of Biological Science, Florida State University, 319 Stadium Drive, PO Box 3064295, Tallahassee, FL, 32306-4295, USA;

E

Emily Moriarty Lemmon

Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, FL 32306-4102, USA; and 2 Department of Biological Science, Florida State University, 319 Stadium Drive, PO Box 3064295, Tallahassee, FL, 32306-4295, USA;

Cite This Article

Alan R. Lemmon, Sandra A. Emme, Emily Moriarty Lemmon (2012). Anchored Hybrid Enrichment for Massively High-Throughput Phylogenomics. Systematic Biology, 61(5), 727-744. https://doi.org/10.1093/sysbio/sys049

Anchored Hybrid Enrichment for Massively High-Throughput Phylogenomics

You May Also Like