Empirical assessment of rad sequencing for interspecific phylogeny

Molecular Biology and Evolution

Volumn 31, Issue 5, 2014, Pages 1272-1274

  Cruaud, Astrid ^a   Gautier, Mathieu ^a,b   Galan, Maxime ^a   Foucaud, Julien ^a   Sauné, Laure ^a   Genson, Gwenaelle ^a   Dubois, Emeric ^c   Nidelet, Sabine ^c   Deuve, Thierry ^d   Rasplus, Jean Yves ^a  

^a CENTRE DE BIOLOGIE ET DE GESTION DES POPULATIONS   (France)

^b LIRMM   (France)

^c INSTITUT DE GÉNOMIQUE FONCTIONNELLE   (France)

^d MUSÉUM NATIONAL D'HISTOIRE NATURELLE   (France)

Author keywords

Carabidae; Empirical data; Insecta; Next generation sequencing; Phylogenomics; Restriction site associated DNA sequencing

Indexed keywords

ARTICLE; BEETLE; BIOINFORMATICS; DNA LIBRARY; DNA SEQUENCE; EUKARYOTE; GENETIC VARIABILITY; NEXT GENERATION SEQUENCING; NONHUMAN; PHYLOGENY; RESTRICTION SITE ASSOCIATED DNA SEQUENCING;

CARABIDAE; EMPIRICAL DATA; INSECTA; NEXT-GENERATION SEQUENCING; PHYLOGENOMICS; RESTRICTION-SITE ASSOCIATED DNA SEQUENCING;

ANIMALS; BEETLES; DNA; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY;

EID: 84899556177     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msu063     Document Type: Article

References (15)

1. Arnold B, Corbett-Detig RB, Hartl D, Bomblies K. 2013. RADseq underestimates diversity and introduces genealogical biases due to nonrandom haplotype sampling. Mol Ecol. 22:3179-3190.
2. Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, Lewis ZA, Selker EU, CreskoWA, Johnson EA. 2008. Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS One 3:e3376.
3. Catchen JM, Amores A, Hohenlohe P, Cresko W, Postlethwait JH. 2011. Stacks: Building and genotyping loci de novo from short-read sequences. G3 1:171-182.
4. Deuve T, Cruaud A, Genson G, Rasplus J-Y. 2012. Molecular systematics and evolutionary history of the genus Carabus (Col. Carabidae). Mol Phylogenet Evol. 65:259-275.
5. Drummond AJ, Ashton B, Buxton S, Cheung M, Cooper A, Heled J, Kearse M, Moir R, Stones-Havas S, Sturrock S, et al. 2010. Geneious v6.1.6. San Francisco (CA): Biomatters Inc. [cited 2014 Feb 17]. Available from: http://www.geneious. com.
6. Etter PD, Bassham S, Hohenlohe PA, Johnson EA, Cresko WA. 2011. SNP discovery and genotyping for evolutionary genetics using RAD sequencing. In: Orgogozo V, Rockman MV, editors. Molecular methods for evolutionary genetics. New York: Humana Press. p. 157-178.
7. Jones JC, Fan SH, Franchini P, Schartl M, Meyer A. 2013. The evolutionary history of Xiphophorus fish and their sexually selected sword: a genome-wide approach using restriction site-associated DNA sequencing. Mol Ecol. 22:2986-3001.
8. Lemmon EM, Lemmon AR. 2013. High-throughput genomic data in systematics and phylogenetics. Annu Rev Ecol. Evol Syst. 44: 99-121.
9. Maddison DR, Maddison WP. 2005. MacClade 4: Analysis of phylogeny and character evolution. Version 4.08a. Sunderland (MA): Sinauer Associates [cited 2014 Feb 17]. Available from: http://mac clade.org.
10. McCormack JE, Hird SM, Zellmer AJ, Carstens BC, Brumfield RT. 2013. Applications of next-generation sequencing to phylogeography and phylogenetics. Mol Phylogenet Evol. 66:526-538.
11. McCormack JE, Maley JM, Hird SM, Derryberry EP, Graves GR, Brumfield RT. 2012. Next-generation sequencing reveals population genetic structure and a species tree for recent bird divergences. Mol Phylogenet Evol. 62:397-406.
12. Nadeau NJ, Martin SH, Kozak KM, Salazar C, Dasmahapatra KK, Davey JW, Baxter SW, Blaxter ML, Mallet J, Jiggins CD. 2013. Genome-wide patterns of divergence and gene flow across a butterfly radiation. Mol Ecol. 22:814-826.
13. Rubin BER, Ree RH, Moreau CS. 2012. Inferring phylogenies from RAD sequence data. PLoS One 7:e33394.
14. Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688-2690.
15. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 28:2731-2739.