Does complete plastid genome sequencing improve species discrimination and phylogenetic resolution in Araucaria?

Molecular Ecology Resources

Volumn 15, Issue 5, 2015, Pages 1067-1078

  Ruhsam, Markus ^a   Rai, Hardeep S ^b   Mathews, Sarah ^c   Ross, T Gregory ^d   Graham, Sean W ^d   Raubeson, Linda A ^e   Mei, Wenbin ^e,f   Thomas, Philip I ^a   Gardner, Martin F ^a   Ennos, Richard A ^g   Hollingsworth, Peter M ^a  

^a ROYAL BOTANIC GARDEN EDINBURGH   (United Kingdom)

^b UTAH STATE UNIVERSITY   (United States)

^c HARVARD UNIVERSITY   (United States)

^d UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^e CENTRAL WASHINGTON UNIVERSITY   (United States)

^f UNIVERSITY OF FLORIDA   (United States)

^g UNIVERSITY OF EDINBURGH   (United Kingdom)

Author keywords

Araucaria; DNA barcoding; Next generation sequencing; Phylogeny; Plastid genome

Indexed keywords

ARAUCARIA;

CLASSIFICATION; DNA BARCODING; DNA SEQUENCE; GENETICS; HIGH THROUGHPUT SEQUENCING; MOLECULAR GENETICS; PACIFIC ISLANDS; PHYLOGENY; PLASTID; PLASTID GENOME; VASCULAR PLANT;

DNA BARCODING, TAXONOMIC; GENOME, PLASTID; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MOLECULAR SEQUENCE DATA; PACIFIC ISLANDS; PHYLOGENY; PLASTIDS; SEQUENCE ANALYSIS, DNA; TRACHEOBIONTA;

EID: 84938974810     PISSN: 1755098X     EISSN: 17550998     Source Type: Journal    
DOI: 10.1111/1755-0998.12375     Document Type: Article

References (48)

1. Barrabé L, Maggia L, Pillon Y et al. (2013) New Caledonian lineages of Psychotria (Rubiaceae) reveal different evolutionary histories and the largest documented plant radiation for the archipelago. Molecular Phylogenetics and Evolution, 71, 15-35.
2. Cronn R, Liston A, Parks M, Gernandt DS, Shen R, Mockler T (2008) Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology. Nucleic Acids Research, 36, e122.
3. Duangjai S, Samuel R, Munzinger J et al. (2009) A multi-locus plastid phylogenetic analysis of the pantropical genus Diospyros (Ebenaceae), with an emphasis on the radiation and biogeographic origins of the New Caledonian endemic species. Molecular Phylogenetics and Evolution, 52, 602-620.
4. Duarte JM, Wall PK, Edger PP et al. (2010) Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Oryza and their phylogenetic utility across various taxonomic levels. BMC Evolutionary Biology, 10, 61.
5. Egan AN, Schlueter J, Spooner DM (2012) Applications of next-generation sequencing in plant biology. American Journal of Botany, 99, 175-185.
6. Enright NJ, Miller BP, Jaffre T (2009) Ecology and population dynamics of the endemic New Caledonian conifer, Araucaria muelleri (Araucariaceae). In: Araucariaceae (eds Bieleski RD, Wilcox MD), pp. 359-364. International Dendrological Society, Dunedin, New Zealand.
7. Escapa IH, Catalano SA (2013) Phylogenetic analysis of Araucariaceae: integrating molecules, morphology, and fossils. International Journal of Plant Sciences, 174, 1153-1170.
8. Farris JS, Kallersjo M, Kluge AG, Bult C (1994) Testing significance of incongruence. Cladistics, 10, 315-319.
9. Fazekas AJ, Kesanakurti PR, Burgess KS et al. (2009) Are plant species inherently harder to discriminate than animal species using DNA barcoding markers? Molecular Ecology Resources, 9, 130-139.
10. Gaudeul M, Rouhan G, Gardner MF, Hollingsworth PM (2012) AFLP markers provide insights into the evolutionary relationships and diversification of New Caledonian Araucaria species (Araucariaceae). American Journal of Botany, 99, 68-81.
11. Gaudeul M, Gardner MF, Thomas P, Ennos RA, Hollingsworth PM (2014) Evolutionary dynamics of emblematic Araucaria species (Araucariaceae) in New Caledonia: nuclear and chloroplast markers suggest recent diversification, introgression, and a tight link between genetics and geography within species. BMC Evolutionary Biology, 14, 171.
12. Harrison N, Kidner CA (2011) Next-generation sequencing and systematics: what can a billion base pairs of DNA sequence data do for you? Taxon, 60, 1552-1566.
13. Hollingsworth ML, Clark AA, Forrest LL et al. (2009a) Selecting barcoding loci for plants: evaluation of seven candidate loci with species-level sampling in three divergent groups of land plants. Molecular Ecology Resources, 9, 439-457.
14. Hollingsworth PM, Forrest LL, Spouge JL et al. (2009b) A DNA barcode for land plants. Proceedings of the National Academy of Sciences, USA, 106, 12794-12797.
15. Hollingsworth PM, Graham SW, Little DP (2011) Choosing and using a plant DNA barcode. PLoS ONE, 6, e19254.
16. Huelsenbeck JP, Ronquist F (2001) MrBAYES: Bayesian inference of phylogenetic trees. Bioinformatics, 17, 754-755.
17. Kane N, Sveinsson S, Dempewolf H et al. (2012) Ultra-barcoding in cacao (Theobroma spp.; Malvaceae) using whole chloroplast genomes and nuclear ribosomal DNA. American Journal of Botany, 99, 320-329.
18. Kelchner SA (2000) The evolution of non-coding chloroplast DNA and its application in plant systematics. Annals of the Missouri Botanical Garden, 87, 482-498.
19. Kerr KCR, Stoeckle MY, Dove CJ, Weigt LA, Francis CM, Hebert PDN (2007) Comprehensive DNA barcode coverage of North American birds. Molecular Ecology Notes, 7, 535-543.
20. Kranitz M-L (2005) Systematics and evolution of New Caledonian Araucaria. PhD thesis, University of Edinburgh.
21. Kranitz M, Biffin E, Clark A et al. (2014) Evolutionary diversification of New Caledonian Araucaria. PLoS ONE, 9, e110308.
22. Kress WJ, Erickson DL (2007) A two-locus global DNA barcode for land plants: the coding rbcL gene complements the non-coding trnH-psbA spacer region. PLoS ONE, 2, e508.
23. Leslie AB, Beaulieu JM, Rai HS, Crane PR, Donoghue MJ, Mathews S (2012) Hemisphere-scale differences in conifer evolutionary dynamics. Proceedings of the National Academy of Sciences, USA, 109, 16217-16221.
24. Li D-Z, Gao L-M, Li H-T et al. (2011) Comparative analysis of a large dataset indicates that internal transcribed spacer (ITS) should be incorporated into the core barcode for seed plants. Proceedings of the National Academy of Sciences, USA, 108, 19641-19646.
25. Maddison WP (1997) Gene trees in species trees. Systematic Biology, 46, 523-536.
26. Maddison WP, Knowles LL (2006) Inferring phylogeny despite incomplete lineage sorting. Systematic Biology, 55, 21-30.
27. Mei W (2010) A whole plastome approach to inferring relationships in the Araucariaceae. MSc thesis, Central Washington University.
28. Morat P (1993) Our knowledge of the flora of New Caledonia: endemism and diversity in relation to vegetation types and substrates. Biodiversity Letters, 1, 72-81.
29. Myers N, Mittermeier RA, Mittermeier CG, da Fonseca GAB, Kent J (2000) Biodiversity hotspots for conservation priorities. Nature, 403, 853-858.
30. Nock CJ, Waters DLE, Edwards MA et al. (2011) Chloroplast genome sequences from total DNA for plant identification. Plant Biotechnology Journal, 9, 328-333.
31. Nylander JAA (2004) MrModeltest v2. Program distributed by the author. Evolutionary Biology Centre, Uppsala University. Available from http://www.downloadatoz.com/developer-johan-nylander.html.
32. Nylander JAA, Wilgenbusch JC, Warren DL, Swofford DL (2008) AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics. Bioinformatics, 24, 581-583.
33. Parks M, Cronn R, Liston A (2009) Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes. BMC Biology, 7, 84.
34. Rambaut A, Drummond A (2007) Tracer Version 1.5. Available from http://tree.bio.ed.ac.uk/software/tracer/.
35. Rigg LS, Enright NJ, Jaffre T (1998) Stand structure of the emergent conifer Araucaria laubenfelsii, in maquis and rainforest, Mont Do, New Caledonia. Australian Journal of Ecology, 23, 528-538.
36. Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 19, 1572-1574.
37. Rozen S, Skaletsky HJ (2000) Primer3 on the WWW for general users and for biologist programmers. In: Bioinformatics Methods and Protocols: Methods in Molecular Biology (eds Misener S & Krawetz SA). Humana Press, Totowa, NJ.
38. Setoguchi H, Asakawa Osawa T, Pintaud J-C, Jaffré T, Veillon J-M (1998) Phylogenetic relationships within Araucariaceae based on rbcL gene sequences. American Journal of Botany, 85, 1507-1516.
39. Smith MA, Poyarkov NA, Hebert PDN (2008) DNA barcoding: CO1 DNA barcoding amphibians: take the chance, meet the challenge. Molecular Ecology Resources, 8, 235-246.
40. Swofford DL (2003) PAUP*-Phylogenetic Analysis using Parsimony (*and other methods), version 4.0.
41. Van Bel M, Proost S, Wischnitzki E et al. (2012) Dissecting plant genomes with the PLAZA comparative genomics platform. Plant Physiology, 158, 590-600.
42. Ward RD, Zemlak TS, Innes BH, Last PR, Hebert PDN (2005) DNA barcoding Australia's fish species. Philosophical Transactions of the Royal Society B: Biological Sciences, 360, 1847-1857.
43. Weitemier K, Straub SCK, Cronn RC et al. (2014) Hyb-Seq: combining target enrichment and genome skimming for plant phylogenomics. Applications in Plant Sciences, 2, 1400042.
44. Whittall JB, Syring J, Parks M et al. (2010) Finding a (pine) needle in a haystack: chloroplast genome sequence divergence in rare and widespread pines. Molecular Ecology, 19, 100-114.
45. Yang J-B, Tang M, Li H-T, Zhang Z-R, Li D-Z (2013) Complete chloroplast genome of the genus Cymbidium: lights into the species identification, phylogenetic implications and population genetic analyses. BMC Evolutionary Biology, 13, 84.
46. Yao H, Song J, Liu C et al. (2010) Use of ITS2 region as the universal DNA barcode for plants and animals. PLoS ONE, 5, e13102.
47. Zhang Y-J, Ma P-F, Li D-Z (2011) High-throughput sequencing of six bamboo chloroplast genomes: phylogenetic implications for temperate woody bamboos (Poaceae: Bambusoideae). PLoS ONE, 6, e20596.
48. Zuccon A, Zuccon D (2014) MrEnt: an editor for publication-quality phylogenetic tree illustrations. Molecular Ecology Resources, 14, 1090-1094.