Skip to main content
SpringerLink
Log in

Phylogenetic relationships and divergence times of the family Araucariaceae based on the DNA sequences of eight genes

  • Articles/Molecular Revolution
  • Published:
Chinese Science Bulletin

Abstract

Araucariaceae is one of the most primitive families of the living conifers, and its phylogenetic relationships and divergence times are critically important issues. The DNA sequences of 8 genes, i.e., nuclear ribosomal 18S and 26S rRNA, chloroplast 16S rRNA, rbcL, matK and rps4, and mitochondrial coxI and atp1, obtained from this study and GenBank were used for constructing the molecular phylogenetic trees of Araucariaceae, indicating that the phylogenetic relationships among the three genera of this family should be ((Wollemia, Agathis), Araucaria). On the basis of the fossil calibrations of Wollemia and the two tribes Araucaria and Eutacta of the genus Araucaria, the divergence time of Araucariaceae was estimated to be (308 ± 53) million years ago, that is, the origin of the family was in the Late Carboniferous rather than Triassic as a traditional view. With the same gene combination, the divergence times of the genera Araucaria and Agathis were (246 ± 47) and (61 ± 15) Ma, respectively. Statistical analyses on the phylogenetic trees generated by using different genes and comparisons of the divergence times estimated by using those genes suggested that the chloroplast matK and rps4 genes are most suitable for investigating the phylogenetic relationships and divergence times of the family Araucariaceae.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  1. Farjon A. World Checklist and Bibliography of Conifers. 2nd. Richmond: Royal Botanic Gardens, 2001

    Google Scholar 

  2. Anonymous “Australia Hails a Prehistoric Pine” and “’Fossil Tree’ Reveals Full Splendour.” Nature, 1994, 372: 712, 719

    Google Scholar 

  3. Anderson I. Pine “dinosaur” Lurks in Gorge. New Scientist, 1994, 144: 5

    Google Scholar 

  4. Andrew S. Wollemia nobilis: A Living Fossil and Evolutionary Enigma. Institute for Creation Research, 2006, http://www.icr.org/article/2707/

  5. Jones W G., K D Hill and J M Allen Wollemia nobilis, a new living Australian genus and species in the Araucariaceae. Telopea, 1995, 6: 173–176

    Google Scholar 

  6. Chambers T C, Drinnan A N, McLoughlin S. Some morphological features of wollemi pine (Wollemia nobilis: Araucariaceae) and their comparison to Cretaceous plant fossils. Int J Plant Sci, 1998, 159: 160–171

    Article  Google Scholar 

  7. Setoguchi H, Ohsawa T A, Pintaud J C, et al. Phylogenetic relationships within Araucariaceae based on rbcL gene sequences. Am J Bot, 1998, 85: 1507–1516

    Article  Google Scholar 

  8. Kershaw P, Wagstaff B. The southern conifer family Araucariaceae: History, status, and value for palaeoenvironmental reconstruction. Ann Rev Ecol Syst, 2001, 32: 397–414

    Article  Google Scholar 

  9. Cantrill D J, Raine J I. Wairarapaia mildenhallii gen. et spec. nov., a new Araucarian cone related to Wollemia from the Cretaceous (Albian-Cenomanian) of New Zealand. Int J Plant Sci, 2006, 167: 1259–1269

    Article  Google Scholar 

  10. Gilmore S, Hill K D. Relationships of the Wollemi Pine (Wollemia nobilis) and a molecular phylogeny of the Araucariaceae. Telopea, 1997, 7: 275–291

    Google Scholar 

  11. Stefanovi S, Jager M, Deutsch J, et al. Phylogenetic relationships of conifers inferred from partial 28S rRNA gene sequences. Am J Bot, 1998, 85: 688–697

    Article  Google Scholar 

  12. Rydin C, Kallersjo M, Friis E M. Seed plant relationships and the systematic position of Gnetales based on nuclear and chloroplast DNA: Conflicting data, rooting problems and the monophyly of conifers. Int J Plant Sci, 2002, 163: 197–214

    Article  Google Scholar 

  13. Chaw S M, Parkinson C L, Cheng Y, et al. Seed plant phylogeny inferred from all three-plant genomes: Monophyly of extant gymnosperms and origin of Gnetales from conifers. Proc Natl Acad Sci USA, 2000, 97: 4086–4091

    Article  Google Scholar 

  14. Bowe M, Coat G, Claude W D. Phylogeny of seed plants based on all three genomic compartments: extant gymnosperms are monophyletic and Gnetales closest relatives are conifer. Proc Natl Acad Sci USA, 2000, 97: 4092–4097

    Article  Google Scholar 

  15. Hart J A. A cladistic analysis of conifers: Preliminary results. J Arnold Arboretum, 1987, 68: 269–307

    Google Scholar 

  16. Price R A, Thomas J, Strauss S, et al. Familial relationships of the conifers from rbcL sequence data. Am J Bot, 1993, 80: 172

    Article  Google Scholar 

  17. Miller C N. The origin of modern conifer families. In: Beck C B, ed. Origin and Evolution of Gymnosperms. New York: Columbia University Press, 1988. 448–486

    Google Scholar 

  18. Nixon K C, Crepet W L, Stevenson D, et al. A reevaluation of seed plant phylogeny. Ann Missouri Bot Gard, 1994, 81: 484–533

    Article  Google Scholar 

  19. Doyle J J, Doyle J L. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull, 1987, 19: 11–15

    Google Scholar 

  20. Rydin C, Pedersen K R, Friis E M. On the evolutionary history of Ephedra: Cretaceous fossils and extant molecules. Proc Natl Acad Sci USA, 2004, 101: 16571–16576

    Article  Google Scholar 

  21. Ickert-Bond S M, Wojciechowski M E. Phylogenetic relationships in Ephedra (Gnetales): Evidence from nuclear and chloroplast DNA sequence data. Syst Bot, 2004, 29: 834–849

    Article  Google Scholar 

  22. Gernano J, Klein A S. Species-specific nuclear and chloroplast single nucleotide polymorphisms to distinguish Picea glauca, P. mariana and P. rubens. Theor Appl Genet, 1999, 99: 37–49

    Article  Google Scholar 

  23. Thompson J D, Gibson T J, Plewniak F, et al. The ClustaX windows interface: Flexible strategies for multiple sequences alignment aided by quality analysis tools. Nucleic Acids Res, 1997, 24: 4876–4882

    Article  Google Scholar 

  24. Posada D, Crandall K A. Modeltest: Testing the model of DNA substitution. Bioinformatics, 1998, 14: 817–818

    Article  Google Scholar 

  25. Guindon S, Lethiec F, Duroux P, et al. PHYML Online — a web server for fast maximum likelihood-based phylogenetic inference. Nucleic Acids Res, 2005, 33(Suppl): W557–W559

    Article  Google Scholar 

  26. Swofford D L. PAUP*: Phylogenetic anlysis using parsimony (* and other methods), Version 4. Sinauer Associates, Sunderland, Massachusetts, 2003

    Google Scholar 

  27. Shimodaira H, Hasegawa M. CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics, 2001, 17: 1246–1247

    Article  Google Scholar 

  28. Hill R S, Brodribb T J. Southern conifers in time and space. Austr J Bot, 1999, 47: 639–696

    Article  Google Scholar 

  29. Yang Z. PAML 4: A program package for phylogenetic analysis by maximum likelihood. Mol Biol Evol, 2007, 24: 1586–1591

    Article  Google Scholar 

  30. de Jersey N. Triassic spores and pollen grains from the Clematis Sanstone. Geol Surv Queensland Austr Publ, 1968, 338(Palaeont): 14: 1–44

    Google Scholar 

  31. Bamford M K, Philippe M. Jurassic-Early Cretaceous Gondwanan homoxylous woods: A nomenclatural revision of the genera with taxonomic notes. Rev Palaeobot Palynol, 2001, 113: 287–297

    Article  Google Scholar 

  32. Pires E F, Guerra-Sommer M. Sommerxylon spiralosus from the Upper Triassic in southernmost Parana Basin (Brazil): A new taxon with taxacean affinity. Anais Acad Bras Cien, 2004, 76: 595–609

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200433, China

    Nian Liu, Yong Zhu, Jie Chen, QingBiao Wang, Jing Shi & Yang Zhong

  2. Lushan Botanical Garden, Chinese Academy of Sciences, Lushan, 332900, China

    ZongXian Wei

  3. Shanghai Center for Bioinformation Technology, Shanghai, 200235, China

    Yang Zhong

  4. South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China

    ShuGuang Jian

  5. Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810001, China

    DangWei Zhou

  6. Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China

    Yong Yang

Authors
  1. Nian Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yong Zhu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. ZongXian Wei
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Jie Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. QingBiao Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. ShuGuang Jian
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. DangWei Zhou
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Jing Shi
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Yong Yang
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Yang Zhong
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Yang Zhong.

Additional information

Supported by the National Infrastructure of Natural Resources for Science and Technology (Grant No. 2005DKA21403), MOST Basic Science and Technology (Grant No. 2007FY110100), Shanghai Leading Academic Discipline Project (Grant No. B111), Shanghai Science and Technology Committee (Grant No. 07XD14025), the Graduate Students Innovation Foundation of Fudan University (Grant No. EYH1322098) and National Science Fund for Fostering Talents in Basic Science (Grant No. J0630643)

About this article

Cite this article

Liu, N., Zhu, Y., Wei, Z. et al. Phylogenetic relationships and divergence times of the family Araucariaceae based on the DNA sequences of eight genes. Chin. Sci. Bull. 54, 2648–2655 (2009). https://doi.org/10.1007/s11434-009-0373-2

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11434-009-0373-2

Keywords

Search

Navigation