A Beginner's Guide to Phylogenetics

Overview

Journal Microb Ecol

Specialties Environmental Health
Microbiology

Date 2013 Apr 30

PMID 23624570

Citations 6

Authors

Roy D Sleator

Affiliations

Soon will be listed here.

Abstract

Metagenomics and the development of high throughput next generation sequencing capabilities have forced significant development in the field of phylogenetics: the study of the evolutionary relatedness of the planet's inhabitants. Herein, I review the major tree-building strategies, challenges and opportunities which exist in this rapidly expanding field of evolutionary biology.

Citing Articles

Cyanobacterial phylogenetic analysis based on phylogenomics approaches render evolutionary diversification and adaptation: an overview of representative orders.

Prabha R, Singh D 3 Biotech. 2019; 9(3):87.

PMID: 30800598 PMC: 6385064. DOI: 10.1007/s13205-019-1635-6.

Functional metagenomics identifies novel genes ABCTPP, TMSRP1 and TLSRP1 among human gut enterotypes.

Verma M, Ahmed V, Gupta S, Kumar J, Pandey R, Mandhan V Sci Rep. 2018; 8(1):1397.

PMID: 29362424 PMC: 5780487. DOI: 10.1038/s41598-018-19862-5.

TRAPPIST-1: The dawning of the age of Aquarius.

Sleator R, Smith N Bioengineered. 2017; 8(3):194-195.

PMID: 28324663 PMC: 5470511. DOI: 10.1080/21655979.2017.1306998.

Under the microscope: From pathogens to probiotics and back.

Sleator R Bioengineered. 2015; 6(5):275-82.

PMID: 26339986 PMC: 4825842. DOI: 10.1080/21655979.2015.1089368.

Metagenomic identification of a novel salt tolerance gene from the human gut microbiome which encodes a membrane protein with homology to a brp/blh-family β-carotene 15,15'-monooxygenase.

Culligan E, Sleator R, Marchesi J, Hill C PLoS One. 2014; 9(7):e103318.

PMID: 25058308 PMC: 4110020. DOI: 10.1371/journal.pone.0103318.

References

Brocchieri L . Phylogenetic inferences from molecular sequences: review and critique. Theor Popul Biol. 2001; 59(1):27-40. DOI: 10.1006/tpbi.2000.1485. View

Soltis D, Soltis P . The role of phylogenetics in comparative genetics. Plant Physiol. 2003; 132(4):1790-800. PMC: 526274. DOI: 10.1104/pp.103.022509. View

Sleator R . Proteins: form and function. Bioeng Bugs. 2011; 3(2):80-5. PMC: 3357337. DOI: 10.4161/bbug.18303. View

Dagan T . Phylogenomic networks. Trends Microbiol. 2011; 19(10):483-91. DOI: 10.1016/j.tim.2011.07.001. View

Sleator R . An overview of the processes shaping protein evolution. Sci Prog. 2010; 93(Pt 1):1-6. PMC: 10365403. DOI: 10.3184/003685009X12605492662844. View

Hernandez Fernandez M, Vrba E . A complete estimate of the phylogenetic relationships in Ruminantia: a dated species-level supertree of the extant ruminants. Biol Rev Camb Philos Soc. 2005; 80(2):269-302. DOI: 10.1017/s1464793104006670. View

Dorrell N, Hinchliffe S, Wren B . Comparative phylogenomics of pathogenic bacteria by microarray analysis. Curr Opin Microbiol. 2005; 8(5):620-6. PMC: 7108221. DOI: 10.1016/j.mib.2005.08.012. View

Pallen M, Wren B . Bacterial pathogenomics. Nature. 2007; 449(7164):835-42. DOI: 10.1038/nature06248. View

Yang Z, Rannala B . Molecular phylogenetics: principles and practice. Nat Rev Genet. 2012; 13(5):303-14. DOI: 10.1038/nrg3186. View

10.

Forterre P, Gadelle D . Phylogenomics of DNA topoisomerases: their origin and putative roles in the emergence of modern organisms. Nucleic Acids Res. 2009; 37(3):679-92. PMC: 2647321. DOI: 10.1093/nar/gkp032. View

11.

Lopez P, Bapteste E . Molecular phylogeny: reconstructing the forest. C R Biol. 2009; 332(2-3):171-82. DOI: 10.1016/j.crvi.2008.07.003. View

12.

Naidoo N, Pawitan Y, Soong R, Cooper D, Ku C . Human genetics and genomics a decade after the release of the draft sequence of the human genome. Hum Genomics. 2011; 5(6):577-622. PMC: 3525251. DOI: 10.1186/1479-7364-5-6-577. View

13.

Manning T, Sleator R, Walsh P . Naturally selecting solutions: the use of genetic algorithms in bioinformatics. Bioengineered. 2012; 4(5):266-78. PMC: 3813526. DOI: 10.4161/bioe.23041. View

14.

Bullman S, Lucey B, Sleator R . Molecular diagnostics: the changing culture of medical microbiology. Bioeng Bugs. 2011; 3(1):1-7. DOI: 10.4161/bbug.3.1.19011. View

15.

Takahashi K, Nei M . Efficiencies of fast algorithms of phylogenetic inference under the criteria of maximum parsimony, minimum evolution, and maximum likelihood when a large number of sequences are used. Mol Biol Evol. 2000; 17(8):1251-8. DOI: 10.1093/oxfordjournals.molbev.a026408. View

16.

Karlin S . Global dinucleotide signatures and analysis of genomic heterogeneity. Curr Opin Microbiol. 1999; 1(5):598-610. DOI: 10.1016/s1369-5274(98)80095-7. View

17.

Sleator R . Phylogenetics. Arch Microbiol. 2011; 193(4):235-9. DOI: 10.1007/s00203-011-0677-x. View

18.

Puigbo P, Wolf Y, Koonin E . Search for a 'Tree of Life' in the thicket of the phylogenetic forest. J Biol. 2009; 8(6):59. PMC: 2737373. DOI: 10.1186/jbiol159. View

19.

Lawrence J . Gene transfer in bacteria: speciation without species?. Theor Popul Biol. 2002; 61(4):449-60. DOI: 10.1006/tpbi.2002.1587. View

20.

Delsuc F, Brinkmann H, Philippe H . Phylogenomics and the reconstruction of the tree of life. Nat Rev Genet. 2005; 6(5):361-75. DOI: 10.1038/nrg1603. View