Skip to main content
SpringerLink
Log in

Microsatellite diversity and genetic structure of the commercially important tropical tree species Eucalyptus urophylla, endemic to seven islands in eastern Indonesia

  • Original Paper
  • Published:
Tree Genetics & Genomes Aims and scope Submit manuscript

Abstract

Eucalyptus urophylla (Timor mountain gum) is an economically important plantation species that occurs naturally in a series of disjunct populations on the volcanic slopes of seven islands in eastern Indonesia. Twelve microsatellite markers were used to investigate the distribution of nuclear genetic diversity among 19 geographically defined E. urophylla populations. High levels of gene diversity were observed throughout the geographic range (H E = 0.703 to 0.776). The level of genetic differentiation among populations was low (F ST = 0.031), but the amount of differentiation increased with geographic distance. A phenogram produced by a neighbor-joining analysis illustrated that populations clustered according to islands. However, a Bayesian clustering approach revealed a more cryptic population structure comprising two genetically homogeneous groups. Gene flow among the populations is likely responsible for the apparent weak influence of geographic insularity on the genetic diversity and structure of the island species. These findings provide direction for conservation and breeding strategies in E. urophylla.

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

Fig. 1
Fig. 2

Similar content being viewed by others

References

  • Birky Jr CW, Fuerst P, Maruyama T (1989) Organelle gene diversity under migration, mutation, and drift: equilibrium expectations, approach to equilibrium, effects of heteroplasmic cells, and comparison to nuclear genes. Genetics 103:513–527

    Google Scholar 

  • Black WC, Baer CF, Antolin MF, DuTeau NM (2001) Population genomics: genome-wide sampling of insect populations. Annu Rev Entomol 46:441–469

    Article  PubMed  CAS  Google Scholar 

  • Brondani RPV, Brondani C, Tarchini R, Grattapaglia D (1998) Development, characterization and mapping of microsatellite markers in Eucalyptus grandis and E urophylla. Theor Appl Genet 97:816–827

    Article  CAS  Google Scholar 

  • Brondani RPV, Brondani C, Grattapaglia D (2002) Towards a genus wide reference linkage map for Eucalyptus based exclusively on highly informative microsatellite markers. Mol Genet Genomics 267:338–347

    Article  PubMed  CAS  Google Scholar 

  • Brondani RPV, Williams ER, Brondani C, Grattapaglia D (2006) A microsatellite-based consensus linkage map for species of Eucalyptus and a novel set of 230 microsatellite markers for the genus. BMC Plant Biol 6(20):1–16

    Google Scholar 

  • Brooker MIH (2000) A new classification of the genus Eucalyptus L’Hér. (Myrtaceae). Aust Syst Bot 13:79–148

    Article  Google Scholar 

  • Butcher PA, Skinner AK, Gardiner CA (2005) Increased inbreeding and inter-species gene flow in remnant populations of the rare Eucalyptus benthamii. Conservation Genetics 6:213–226

    Article  Google Scholar 

  • Byrne M, Moran GF, Tibbits WN (1993) Restriction map and maternal inheritance of chloroplast DNA in Eucalyptus nitens. J Heredity 84:218–220

    CAS  Google Scholar 

  • Byrne M, Marques-Garcia MI, Uren T, Smith DS, Moran GF (1996) Conservation and genetic diversity of microsatellite loci in the genus Eucalyptus. Aust J Bot 44:331–341

    Article  CAS  Google Scholar 

  • Cornuet JM, Luikart G (1996) Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics 144:2001–2014

    PubMed  CAS  Google Scholar 

  • Corriveau JL, Coleman AW (1988) Rapid screening method to detect potential biparental inheritance of plastid DNA and results for over 200 angiosperm species. Am J Bot 75:1443–1458

    Article  Google Scholar 

  • Cremer KW (1977) Distance of seed dispersal in eucalypts estimated from seed weights. Aust For Res 7:225–228

    Google Scholar 

  • Doran JC, Williams ER, Brophy JJ (1995) Patterns of variation in the seedling leaf oils of Eucalyptus urophylla, E pellita and E scias. Aust J Bot 43:327–336

    Article  Google Scholar 

  • Dvorak WS, Hodge GR, Payn KG (2007) The conservation and breeding of Eucalyptus urophylla: a case study to better protect important populations and improve productivity. In: Eucalypts & diversity: balancing productivity and sustainability. Proc. IUFRO Working Party 2.08.03

  • Eldridge K, Davidson J, Harwood C, Van Wyk G (1993) Eucalypt domestication and breeding. Oxford University Press, Oxford

    Google Scholar 

  • Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620

    Article  PubMed  CAS  Google Scholar 

  • Excoffier L, Smouse PE, Quattro JM (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131:479–491

    PubMed  CAS  Google Scholar 

  • Goudet J (1995) FSTAT: a computer program to calculate F-statistics. J Heredity 86:485–486

    Google Scholar 

  • Goudet J, Raymond M, Demeeus T, Rousset F (1996) Testing differentiation in diploid populations. Genetics 144:1933–1940

    PubMed  CAS  Google Scholar 

  • Gunn BV, McDonald MW (1991) Eucalyptus urophylla seed collections. For Genet Resour 19:34–37 FAO, Rome

    Google Scholar 

  • Heaney LR (1991) A synopsis of climatic and vegetational change in Southeast Asia. Clim Change 19:53–61

    Article  Google Scholar 

  • Hodge GR, Pepe B, Wijoyo FS, Dvorak WS (2001) Early results of Eucalyptus urophylla provenance/progeny trials in Colombia and Venezuela. In: Developing the eucalypts of the future. Proc. IUFRO Working Party 2.08.03

  • House APN, Bell JC (1994) Isozyme variation and mating system in Eucalyptus urophylla ST Blake. Silvae Genet 43:167–176

    Google Scholar 

  • Jaccoud D, Peng K, Feinstein D, Kilian A (2001) Diversity arrays: a solid state technology for sequence information independent genotyping. Nucleic Acids Res 29:25–31

    Article  Google Scholar 

  • Jones RC, Steane DA, Potts BM, Vaillancourt RE (2002) Microsatellite and morphological analysis of Eucalyptus globulus populations. Can J For Res 32:59–66

    Article  Google Scholar 

  • Jones RC, McKinnon GE, Potts MB, Vaillancourt RE (2005) Genetic diversity and mating system of an endangered tree Eucalyptus morrisbyi. Aust J Bot 53:367–377

    Article  Google Scholar 

  • Kalisz S, Nason JD, Hanzawa FM, Tonsor SJ (2001) Spatial population genetic structure in Trillium grandiflorum: the roles of dispersal, mating, history, and selection. Evolution 55:150–1568

    Google Scholar 

  • Kumar S, Tamura K, Nei M (1993) MEGA version 10: molecular evolutionary genetic analysis. Pennsylvania State University, Pennsylvania

    Google Scholar 

  • Lewis PO, Zaykin D (2001) Genetic data analysis: computer program for the analysis of allelic data Version 11. Free program distributed by the authors over the Internet from http://hydrodictyoneebuconnedu/people/plewis/softwarephp

  • Liu K, Muse S (2005) PowerMarker: new genetic data analysis software Version 323. Free program distributed by the author over the internet from http://wwwpowermarkernet

  • Magnuson VL, Ally DS, Nylund SJ, Karanjawala ZE, Rayman JB, Knapp JI, Lowe AL, Ghosh S, Collins FS (1996) Substrate nucleotide-determined non-templated addition of adenine by Taq DNA polymerase: implications for PCR-based genotyping and cloning. Biotechniques 21:700–709

    PubMed  CAS  Google Scholar 

  • Mantel N (1967) The detection of disease clustering and generalized regression approach. Cancer Res 27:209–220

    PubMed  CAS  Google Scholar 

  • Martin B, Cossalter C (1975) Les eucalyptus des iles de la Sonde. Bois For Trop 163:3–25

    Google Scholar 

  • Martin B, Cossalter C (1976) Les eucalyptus des iles de la Sonde. Bois For Trop 164:3–14

    Google Scholar 

  • McGowen MH, Wiltshire RJE, Potts BM, Vaillancourt RE (2001) The origin of Eucalyptus vernicosa, a unique shrub Eucalypt. Biol J Linn Soc 74:397–405

    Article  Google Scholar 

  • McKinnon GE, Vaillancourt RE, Tilyard PA, Potts BM (2001) Maternal inheritance of the chloroplast genome in Eucalyptus globulus and interspecific hybrids. Genome 44:831–835

    Article  PubMed  CAS  Google Scholar 

  • Moura VPG (1983) Resultados de pesquisa com várias procêdencias de Eucalyptys urophylla ST Blake, no centro-leste do Brasil. Silvicultura (São Paulo) 31:474–480

    Google Scholar 

  • Nei M, Tajima F, Tateno Y (1983) Accuracy of genetic distances and phylogenetic trees from molecular data. J Mol Evol 19:153–170

    Article  PubMed  CAS  Google Scholar 

  • Payn KG, Dvorak WS, Myburg AA (2007) Chloroplast DNA phylogeography reveals the island colonisation route of Eucalyptus urophylla (Myrtaceae). Aust J Bot 55:673–683

    Google Scholar 

  • Pepe B, Surata K, Suhartono F, Sipayung M, Purwanto A, Dvorak WS (2004) Conservation status of natural populations of Eucalyptus urophylla in Indonesia and international efforts to protect dwindling gene pools. For Genet Resour 31:62–64 FAO, Rome

    Google Scholar 

  • Pinyopusarerk K, Gunn BV, Williams ER, Pryor LD (1993) Comparative geographical variation in seedling morphology of three closely related red mahoganies, Eucalyptus urophylla, E pellita and E scias. Aust J Bot 41:23–34

    Google Scholar 

  • Piry S, Luikart G, Cornuet JM (1999) BOTTLENECK: a computer programme for detecting recent reductions in the effective population size using allele frequency data. J Heredity 90:502–503

    Article  Google Scholar 

  • Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959

    PubMed  CAS  Google Scholar 

  • Pryor LD, Williams ER, Gunn BV (1995) A morphometric analysis of Eucalyptus urophylla and some related taxa with descriptions of two new species. Aust Syst Bot 8:57–70

    Article  Google Scholar 

  • Raymond M, Rousset F (1995) GENEPOP (version 12): population genetics software for exact tests and ecumenicism. J Heredity 86:248–249

    Google Scholar 

  • Rice WR (1989) Analyzing tables of statistical tests. Evolution 43:223–225

    Article  Google Scholar 

  • Schneider S, Roessli D, Excoffier L (2000) Arlequin ver 2000: a software for population genetics data analysis. Genetics and Biometry Laboratory, University of Geneva, , Switzerland

    Google Scholar 

  • Slatkin M (1985) Rare alleles as indicators of gene flow. Evolution 39:53–65

    Article  Google Scholar 

  • Tripiana V, Bourgeois M, Verhaegen D, Vigneron P, Bouvet JM (2007) Combining microsatellites, growth, and adaptive traits for managing in situ genetic resources of Eucalyptus urophylla. Can J For Res 37:773–785

    Article  Google Scholar 

  • Turnbull JW, Brooker MIH (1978) Timor mountain gum, Eucalyptus urophylla ST Blake. Forest Tree Leaflet 214 CSIRO, Melbourne

    Google Scholar 

  • Van Der Nest MA, Steenkamp ET, Wingfield BD, Wingfield MJ (2000) Development of simple sequence repeat (SSR) markers in Eucalyptus from amplified inter-simple sequence repeats (ISSR). Plant Breed 119:433–436

    Article  Google Scholar 

  • Voris HK (2000) Maps of Pleistocene sea levels in Southeast Asia: shorelines, river systems and time durations. J Biogeogr 27:1153–1167

    Article  Google Scholar 

  • Weir BS (1996) Genetic data analysis II. Sinauer, Sunderland, USA

    Google Scholar 

  • Weir BS, Cockerham C (1984) Estimating F-statistics for the analysis of population structure. Evolution 38:1358–1370

    Article  Google Scholar 

  • Wencelius F (1983) Eucalyptus urophylla en Côte d’Ivoire. Silvicultura (São Paulo) 31:515–518

    Google Scholar 

  • Wright S (1931) Evolution in Mendelian populations. Genetics 28:114–138

    Google Scholar 

Download references

Acknowledgements

We are grateful to PT Sumalindo Lestari Jaya for the seed collections, Camcore for locality and reference information, and Mondi Business Paper South Africa for maintenance of the plant materials. Financial support for this work was provided by Mondi Business Paper South Africa through the Wood and Fiber Molecular Genetics Programme and by Camcore, Raleigh, NC, USA. Additional funding was provided by the Technology and Human Resources for Industry Programme (THRIP) in South Africa.

Author information

Authors and Affiliations

  1. Camcore, North Carolina State University, P.O. Box 7626, Raleigh, NC, 27695, USA

    Kitt G. Payn & William S. Dvorak

  2. Mondi Business Paper South Africa, P.O. Box 31024, Merebank, 4059, South Africa

    Kitt G. Payn & Bernard J. H. Janse

  3. Forest Molecular Genetics Programme, Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa

    Kitt G. Payn & Alexander A. Myburg

Authors
  1. Kitt G. Payn
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. William S. Dvorak
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Bernard J. H. Janse
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Alexander A. Myburg
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Kitt G. Payn.

Additional information

Communicated by Y. Tsumura

Electronic supplementary material

Below is the link to the electronic supplementary material.

Table 1

(DOC 28 kb)

Table 2

(DOC 40 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Payn, K.G., Dvorak, W.S., Janse, B.J.H. et al. Microsatellite diversity and genetic structure of the commercially important tropical tree species Eucalyptus urophylla, endemic to seven islands in eastern Indonesia. Tree Genetics & Genomes 4, 519–530 (2008). https://doi.org/10.1007/s11295-007-0128-7

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11295-007-0128-7

Keywords

Search

Navigation