High-Throughput Genomic Data in Systematics and Phylogenetics

Annual Review of Ecology, Evolution, and Systematics - Tập 44 Số 1 - Trang 99-121 - 2013
Emily Moriarty Lemmon1, Alan R. Lemmon2
1Department of Biological Science, Florida State University, Biomedical Research Facility, Tallahassee, Florida 32306;
2Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, Florida 32306;

Tóm tắt

High-throughput genomic sequencing is rapidly changing the field of phylogenetics by decreasing the cost and increasing the quantity and rate of data collection by several orders of magnitude. This deluge of data is exerting tremendous pressure on downstream data-analysis methods providing new opportunities for method development. In this review, we present (a) recent advances in laboratory methods for collection of high-throughput phylogenetic data and (b) challenges and constraints for phylogenetic analysis of these data. We compare the merits of multiple laboratory approaches, compare methods of data analysis, and offer recommendations for the most promising protocols and data-analysis workflows currently available for phylogenetics. We also discuss several strategies for increasing accuracy, with an emphasis on locus selection and proper model choice.

Từ khóa


Tài liệu tham khảo

10.1038/nmeth1111

10.1038/35035083

10.1093/molbev/msl170

10.1111/mec.12276

10.1371/journal.pone.0003376

10.1093/bioinformatics/btn298

10.1126/science.1098119

10.1186/1471-2164-13-403

10.1146/annurev.ecolsys.33.010802.150511

10.1093/oxfordjournals.molbev.a004175

10.1101/gr.141978.112

10.1126/science.1174462

10.1093/bioinformatics/btn651

10.1080/10635150701546249

10.1038/nrg3054

10.1093/molbev/mss086

10.1126/science.1188046

10.1093/gbe/evr106

10.1093/oxfordjournals.molbev.a026334

10.1093/nar/16.23.11141

10.1038/nmeth.1251

10.3732/ajb.1100356

10.1111/mec.12084

10.1038/nrg3012

10.1371/journal.pgen.0020068

10.1371/journal.pbio.0030314

10.1093/bioinformatics/btq429

Edwards MC, Gibbs RA. 1994. Multiplex PCR: advantages, development, and applications. Genome Res. 3:S65–75

10.1111/j.1558-5646.2008.00549.x

10.1073/pnas.0607004104

10.1073/pnas.1006538107

10.1093/sysbio/sys004

10.2307/2412923

Felsenstein J, 2004, Inferring Phylogenies

10.1186/gb-2008-9-10-235

10.1006/mpev.1993.1015

10.1101/gr.121327.111

10.1038/nbt.1523

10.1080/17550874.2012.745909

Good JM, 2011, Molecular Methods for Evolutionary Genetics, 772

10.1007/s00239-010-9398-z

10.1093/sysbio/syt018

10.1111/1755-0998.12059

10.1038/nbt821

10.1093/molbev/msp274

10.1038/nmeth.1343

10.1111/mec.12239

10.1126/science.1142430

10.1093/bioinformatics/btp452

Knowles LL, 2010, Estimating Species Trees: Practical and Theoretical Aspects

10.1093/bioinformatics/btl474

10.1093/bib/bbr030

10.1093/sysbio/syp055

10.1093/bioinformatics/btp079

10.1080/10635150601146041

10.1093/molbev/msr202

10.1093/molbev/mss020

10.1093/sysbio/syr128

10.1093/sysbio/syq073

10.1093/sysbio/syp017

10.1093/sysbio/sys049

10.1093/sysbio/sys051

10.1080/10635150490423520

10.2144/000114039

10.1093/bib/bbq015

10.1093/sysbio/syr095

10.1093/sysbio/syr027

10.1186/1471-2148-10-302

10.1016/j.ympev.2009.05.033

10.2307/2413694

10.1080/10635150500354928

10.1186/1745-6150-2-33

10.1038/nmeth.1419

10.1371/journal.pone.0014004

10.1002/jcla.2058

10.1038/nrg3068

10.1101/gr.120196.111

10.1016/j.ympev.2011.12.007

10.1016/j.ympev.2011.10.012

10.1093/oxfordjournals.molbev.a025722

10.1186/gb-2007-8-6-r105

10.1093/sysbio/syp006

10.1007/978-0-387-09760-2_7

10.1371/journal.pcbi.0030123

10.1093/molbev/mss216

10.1111/mec.12049

10.1073/pnas.96.6.2896

10.1038/nrg2934

10.1080/10635150490468675

10.1098/rstb.2008.0178

10.1038/nature05295

10.1016/S0168-9525(02)02764-6

10.1371/journal.pone.0037135

10.1371/journal.pbio.1000602

10.1146/annurev.ecolsys.35.112202.130205

10.1093/molbev/msm095

10.1093/bioinformatics/14.9.817

10.1146/annurev.genom.9.081307.164407

10.1101/gr.123901.111

Reid NM, Hird SM, Brown JM, Pelletier TA, McVay JD, et al. 2013. Poor fit to the multispecies coalescent is widely detectable in empirical data. Syst. Biol. In press. doi: 10.1093/sysbio/syt057

10.1111/mec.12228

10.1080/10635150701397643

10.1126/science.281.5375.363

10.1093/bioinformatics/btg180

10.1371/journal.pone.0033394

10.1093/bioinformatics/bti191

10.1086/319501

10.1101/gr.095760.109

10.3732/apps.1200497

10.1146/annurev.ecolsys.36.102003.152633

10.1007/s00239-004-0352-9

Swofford DL, 2000, PAUP*: Phylogenetic Analysis Using Parsimony and Other Methods

Swofford DL, 1996, Molecular Systematics, 407

10.1016/j.molmed.2012.05.001

10.1186/gb-2009-10-10-r116

10.1371/journal.pone.0029696

10.1080/10635150701311362

10.1146/annurev-genom-082908-150112

10.1371/journal.pone.0001172

10.1111/mec.12023

10.1038/nrg2484

10.1093/molbev/mss008

10.1371/journal.pbio.0030007

10.1007/BF02198856

10.1093/sysbio/syq084

10.1093/bioinformatics/bti045

Thông tin
Thông tin xuất bản

Annual Review of Ecology, Evolution, and Systematics

Tập 44 Số 1

99-121

Thông tin tác giả