Australian Journal of Botany Australian Journal of Botany Society
Southern hemisphere botanical ecosystems
RESEARCH ARTICLE

Testing the variability of chloroplast sequences for plant phylogeography

M. Byrne A B and M. Hankinson A
+ Author Affiliations
- Author Affiliations

A Science Division, Department of Environment and Conservation, Locked Bag 104, Bentley Delivery Centre, Bentley, WA 6983, Australia.

B Corresponding author. Email: Margaret.Byrne@dec.wa.gov.au

Australian Journal of Botany 60(7) 569-574 https://doi.org/10.1071/BT12146
Submitted: 3 June 2012  Accepted: 30 July 2012   Published: 12 September 2012

Abstract

Phylogeography in plants is hampered by lack of DNA-sequence regions that detect sufficient variation in intra-specific lineages to reveal historical patterns. We tested 13 putatively highly variable non-coding chloroplast regions in six species complexes, from four different angiosperm families, where phylogeographic patterns have previously been identified using restriction fragment length polymorphism analysis of the chloroplast genome. All regions tested amplified in most of the species. The intergenic spacer regions trnQ–rps16, trnS–trnG, psbA–trnH, psbD–trnT and ndhC–trnV were the five most promising regions for phylogeographic analysis in terms of variability, and petB and rpl16 were variable, given the utility of being amplified in a single reaction. The trnQ–rps16 and psbA–trnH intergenic spacer regions and the rpl16 D4-loop intron showed variation between known lineages in all species. The psbA–trnH intergenic spacer that has been suggested as a suitable barcoding gene for plants, generally showed a level of variation similar to that in other variable regions in the species investigated here, suggesting that some caution is required in the use of this region for barcoding applications. The present analysis identified a set of seven chloroplast regions that are a useful basis for informed selection of sequences for assessment of phylogeographic structure in plants.


References

Angelone S, Hilfiker K, Holderegger R, Bergamini A, Hoebee SE (2007) Regional population dynamics define the local genetic structure in Sorbus torminalis. Molecular Ecology 16, 1291–1301.
Regional population dynamics define the local genetic structure in Sorbus torminalis.CrossRef | 1:CAS:528:DC%2BD2sXkvVKrur0%3D&md5=168135aa8e2adeec899be11686990a91CAS |

Avise J (2009) Phylogeography: retrospect and prospect. Journal of Biogeography 36, 3–15.
Phylogeography: retrospect and prospect.CrossRef |

Beheregaray LB (2008) Twenty years of phylogeography: the state of the field and the challenges for the southern hemisphere. Molecular Ecology 17, 3754–3774.

Byrne M, Hines B (2004) Phylogeographical analysis of cpDNA variation in Eucalyptus loxophleba (Myrtaceae). Australian Journal of Botany 52, 459–470.
Phylogeographical analysis of cpDNA variation in Eucalyptus loxophleba (Myrtaceae).CrossRef | 1:CAS:528:DC%2BD2cXmsVChtLk%3D&md5=e1e5dd8c402bef1a22069c7155f999aeCAS |

Byrne M, Moran GF, Tibbits WN (1993) Restriction map and maternal inheritance of chloroplast DNA in Eucalyptus nitens. The Journal of Heredity 83, 218–220.

Byrne M, Macdonald B, Coates DJ (1999) Divergence in the chloroplast genome and nuclear rDNA of the endangered plant Lambertia orbifolia (Proteaceae). Molecular Ecology 8, 1789–1796.
Divergence in the chloroplast genome and nuclear rDNA of the endangered plant Lambertia orbifolia (Proteaceae).CrossRef | 1:CAS:528:DC%2BD3cXlsVygtQ%3D%3D&md5=800ebe5fab19de1a56f8f6086cbedd42CAS |

Byrne M, Macdonald B, Coates D (2002) Phylogeographic patterns within the Acacia acuminata (Myrtaceae) complex in Western Australia. Journal of Evolutionary Biology 15, 576–587.
Phylogeographic patterns within the Acacia acuminata (Myrtaceae) complex in Western Australia.CrossRef |

Byrne M, Macdonald B, Brand J (2003) Phylogeography and divergence in the chloroplast genome of Western Australian sandalwood (Santalum spicatum). Heredity 91, 389–395.
Phylogeography and divergence in the chloroplast genome of Western Australian sandalwood (Santalum spicatum).CrossRef | 1:CAS:528:DC%2BD3sXnsF2msbY%3D&md5=4ac603dc6300f9a590288f6ec8b13247CAS |

Fady B, Lefèvre F, Vendramin GG, Ambert A, Régnier C, Bariteau M (2008) Genetic consequences of past climate and human impact on eastern Mediterranean Cedrus libani forests. Implications for their conservation Conservation Genetics 9, 85–95.
Genetic consequences of past climate and human impact on eastern Mediterranean Cedrus libani forests. Implications for their conservationCrossRef |

Freeman JS, Jackson HD, Steane DA, McKinnon GE, Dutkowski GW, Potts BM, Vaillancourt RE (2001) Chloroplast DNA phylogeography of Eucalyptus globulus. Australian Journal of Botany 49, 585–596.
Chloroplast DNA phylogeography of Eucalyptus globulus.CrossRef | 1:CAS:528:DC%2BD3MXptVemu7w%3D&md5=93aa5a454daa1c059caab3a257c88892CAS |

Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium 41, 95–98.

Huang X (1992) A contig assembly program based on sensitive detection of fragment overlaps. Genomics 14, 18–25.
A contig assembly program based on sensitive detection of fragment overlaps.CrossRef | 1:CAS:528:DyaK38Xmt1Oksb0%3D&md5=9e279a058bb003e56c282c911dca23e7CAS |

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
A two-locus global DNA barcode for land plants: the coding rbcL gene complements the non-coding trnH–psbA spacer region.CrossRef |

Lahaye R van der Bank M Bogarin D Marner J Pupulin F Gigot G Maurin O Duthoit S Barraclough TG Savolainen V (2008 ) DNA barcoding the floras of biodiversity hotspots. Proceedings of the National Academy of Sciences, USA 105 2923 2928

Larcombe MJ, McKinnon GE, Vaillancourt RE (2011) Genetic evidence for the origins of range disjunctions in the Australian dry sclerophyll plant Hardenbergia violacea. Journal of Biogeography 38, 125–136.
Genetic evidence for the origins of range disjunctions in the Australian dry sclerophyll plant Hardenbergia violacea.CrossRef |

Meister J, Hubaishan MA, Kilian N, Oberprieler C (2005) Chloroplast DNA variation in the shrub Justicia areysiana (Acanthaceae) endemic to the monsoon affected coastal mountains of the southern Arabian Peninsula. Botanical Journal of the Linnean Society 148, 437–444.
Chloroplast DNA variation in the shrub Justicia areysiana (Acanthaceae) endemic to the monsoon affected coastal mountains of the southern Arabian Peninsula.CrossRef |

Miller A, Schaal B (2005) Domestication of a Mesoamerican cultivated fruit tree, Spondias purpurea. Proceedings of the National Academy of Sciences, USA 102, 12 801–12 806.
Domestication of a Mesoamerican cultivated fruit tree, Spondias purpurea.CrossRef | 1:CAS:528:DC%2BD2MXhtVWktLfJ&md5=6e9c9aaa7bcaf2c2cbbc964e6147e245CAS |

Mort ME, Archibald JK, Randle CP, Levsen ND, O’Leary TR, Topalov K, Weigand CM, Crawford DJ (2007) Inferring phylogeny at low taxonomic levels: utility of rapidly evolving cpDNA and nuclear ITS loci American Journal of Botany 94, 173–183.
Inferring phylogeny at low taxonomic levels: utility of rapidly evolving cpDNA and nuclear ITS lociCrossRef |

Naciri Y, Gaudeul M (2007) Phylogeography of the endangered Eryngium alpinum L. (Apiaceae) in the European Alps. Molecular Ecology 16, 2721–2733.
Phylogeography of the endangered Eryngium alpinum L. (Apiaceae) in the European Alps.CrossRef | 1:STN:280:DC%2BD2svktFCksw%3D%3D&md5=b235876f36482995a2f7c8cfb55c7835CAS |

Nevill PG, Bossinger G, Ades PK (2010) Phylogeography of the world’s tallest angiosperm, Eucalyptus regnans: evidence for multiple isolated Quaternary refugia. Journal of Biogeography 37, 179–192.
Phylogeography of the world’s tallest angiosperm, Eucalyptus regnans: evidence for multiple isolated Quaternary refugia.CrossRef |

Parisod C, Besnard G (2007) Glacial in situ survival in the Western Alps and polytopic autopolyploidy in Biscutella laevigata L. (Brassicaceae). Molecular Ecology 16, 2755–2767.
Glacial in situ survival in the Western Alps and polytopic autopolyploidy in Biscutella laevigata L. (Brassicaceae).CrossRef |

Petit RJ, Duminil J, Fineschi S, Hampe A, Salvini D, Vendramin GG (2005) Comparative organization of chloroplast, mitochondrial and nuclear diversity in plant populations. Molecular Ecology 14, 689–701.
Comparative organization of chloroplast, mitochondrial and nuclear diversity in plant populations.CrossRef | 1:CAS:528:DC%2BD2MXjtVGitrw%3D&md5=32992ae63497b67a59398e22a42229e8CAS |

Prentice HC, Andersson S, Mansby E (2011) Mosaic variation in allozyme and plastid DNA markers in the European ranges of Silene vulgaris and its partially sympatric relative S. uniflora (Caryophyllaceae) Botanical Journal of the Linnean Society 166, 127–148.
Mosaic variation in allozyme and plastid DNA markers in the European ranges of Silene vulgaris and its partially sympatric relative S. uniflora (Caryophyllaceae)CrossRef |

Sang T, Crawford DJ, Stuessy TF (1997) Chloroplast phylogeny, reticulate evolution, and biogeography of Paeonia (Paeoniaceae). American Journal of Botany 84, 1120–1136.
Chloroplast phylogeny, reticulate evolution, and biogeography of Paeonia (Paeoniaceae).CrossRef | 1:CAS:528:DyaK2sXlvFejuro%3D&md5=13496d28438605a52d68b15ccca4bc07CAS |

Schaal BA, Haywood DA, Olsen KM, Rauscher JT, Smith WA (1998) Phylogeographic studies in plants, problems and prospects. Molecular Ecology 7, 465–474.
Phylogeographic studies in plants, problems and prospects.CrossRef |

Shaw J, Lickey EB, Beck JT, Farmer SB, Liu W, Miller J, Siripun KC, Winder CT, Schilling EE, Small RL (2005) The tortoise and the hare II: relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis. American Journal of Botany 92, 142–166.
The tortoise and the hare II: relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis.CrossRef | 1:CAS:528:DC%2BD2MXht1Klsbc%3D&md5=b3a3088fe3c6bd2eb55a05e9387d2f7eCAS |

Shaw J, Lickey EB, Schilling EE, Small RL (2007) Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: the tortoise and the hare III. American Journal of Botany 94, 275–288.
Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: the tortoise and the hare III.CrossRef | 1:CAS:528:DC%2BD2sXktFOjsLg%3D&md5=eb08d32a392ba8ca394a3226c0836872CAS |

Tate J, Simpson B (2003) Paraphyly of Tarasa (Malvaceae) and diverse origins of the polyploidy species. Systematic Botany 28, 723–737.

Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research 22, 4673–4680.
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.CrossRef | 1:CAS:528:DyaK2MXitlSgu74%3D&md5=2f018694727a24ead2a7df536bddbcfcCAS |

Vaillancourt RE, Jackson HD (2000) A chloroplast DNA hypervariable region in eucalypts. Theoretical and Applied Genetics 101, 473–477.
A chloroplast DNA hypervariable region in eucalypts.CrossRef | 1:CAS:528:DC%2BD3cXmvVGjsL0%3D&md5=1b6a8885cc63772de9d8b8a6a2a0cd45CAS |

Watts CD, Fisher AE, Shrum CD, Newbold WL, Hansen S, Liu C, Kelchner SA (2008) The D4 set: primers that target highly variable intron loops in plant chloroplast genomes. Molecular Ecology Resources 8, 1344–1347.
The D4 set: primers that target highly variable intron loops in plant chloroplast genomes.CrossRef | 1:CAS:528:DC%2BD1cXhsV2ksL7P&md5=10d4cfe576368cf480a588f1a8c6d8b6CAS |

Wheeler M, Byrne M (2006) Congruence between phylogeographic patterns in cpDNA variation in Eucalyptus marginata (Myrtaceae) and geomorphology of the Darling Plateau. Australian Journal of Botany 54, 17–26.
Congruence between phylogeographic patterns in cpDNA variation in Eucalyptus marginata (Myrtaceae) and geomorphology of the Darling Plateau.CrossRef | 1:CAS:528:DC%2BD28Xhs1ajur0%3D&md5=4eca7ba5fef5dbef3e2a9961e9c86451CAS |

Worth JRP, Jordan GJ, McKinnon GE, Vaillancourt RE (2009) The major Australian cool temperate rainforest tree Nothofagus cunninghamii withstood Pleistocene glacial aridity within multiple regions: evidence from the chloroplast. New Phytologist 182, 519–532.
The major Australian cool temperate rainforest tree Nothofagus cunninghamii withstood Pleistocene glacial aridity within multiple regions: evidence from the chloroplast.CrossRef | 1:CAS:528:DC%2BD1MXltVOhurc%3D&md5=d052ff4c34566a266e653d06a46153b2CAS |

Worth JRP, Jordan GJ, Marthic JR, McKinnon GE, Vaillancourt RE (2010) Chloroplast evidence for geographic stasis of the Australian bird-dispersed shrub Tasmannia lanceolata (Winteraceae). Molecular Ecology 19, 2949–2963.
Chloroplast evidence for geographic stasis of the Australian bird-dispersed shrub Tasmannia lanceolata (Winteraceae).CrossRef | 1:CAS:528:DC%2BC3cXhtVyktb3L&md5=c645cae271982f4c3a09fe108324cec0CAS |

Worth JRP, Marthic JR, Jordan GJ, Vaillancourt RE (2011) Low but structured chloroplast diversity in Atherosperma moschatum (Atherospermataceae) suggests bottlenecks in response to the Pleistocene glacial. Annals of Botany 108, 1247–1256.
Low but structured chloroplast diversity in Atherosperma moschatum (Atherospermataceae) suggests bottlenecks in response to the Pleistocene glacial.CrossRef | 1:CAS:528:DC%2BC3MXhtlGktLrM&md5=bad562a8db7655174e2bf5e8c8a75708CAS |



Rent Article (via Deepdyve) Export Citation Cited By (18)