Tree Genetics & Genomes

, Volume 9, Issue 2, pp 511–524 | Cite as

Structure and genetic diversity of Ixora margaretae an endangered species

A baseline study for conservation and restoration of natural dry forest of New Caledonia
  • D. Verhaegen
  • A. Assoumane
  • J. Serret
  • S. Noe
  • B. Favreau
  • A. Vaillant
  • G. Gâteblé
  • A. Pain
  • C. Papineau
  • L. Maggia
  • J. Tassin
  • J.-M. Bouvet
Original Paper

Abstract

The dry forests of New Caledonia are an exceptional ecosystem because of their numerous endemic botanical species and their highly diversified fauna of insects, mollusks, reptiles and birds. Unfortunately, the area of the dry forests has been significantly reduced, mainly by human activities. Ecological, phenological and genetic analysis of Ixora margaretae, a symbolic species of the sclerophyll forest, has revealed contrasting traits among natural stands. The division of the natural range and then the separation of forest islands has greatly reduced the existing genetic variability of this species. The genetic diversity is strongly structured in genetic clusters which correspond well to specific ecotypes according to the environmental conditions and the forest types. Furthermore, genetic analysis of the reproductive and non-reproductive trees as well the half-sib families obtained by complete protection of mother trees has revealed substantial genetic drift which has resulted in increased loss of allelic variability. The total consumption of seeds by mainly rats confirms the observed absence of natural regeneration. All these results show that measures taken to protect the stands of dry forests will not be enough to maintain sufficient genetic variability of I. margaretae populations in the long term. Assisted regeneration with control of the increase in variability will be necessary to maintain the biodiversity of the species. The results obtained for I. margaretae must be confirmed with other symbolic species in order to take the necessary measures for the effective preservation of the dry forests in New Caledonia.

Keywords

Biodiversity hotspot Sclerophyll forests Endemism Ecology SSR Gene flow Genetic drift 

Supplementary material

11295_2012_575_MOESM1_ESM.doc (31 kb)
ESM 1(DOC 31 kb)

References

  1. Aldrich PR, Hamrick JL, Chavarriaga P, Kochert G (1998) Microsatellite analysis of demographic genetic structure in fragmented populations of the tropical tree Symphonia globulifera. Mol Ecol 7(8):933–944PubMedCrossRefGoogle Scholar
  2. Ariyarathna HACK, Gunasekare MTK, Kottawa-Arachchige JD, Paskarathevan R, Ranaweera KK, Ratnayake M, Kumara JBDAP (2011) Morpho-physiological and phenological attributes of reproductive biology of tea (Camellia sinensis (L.) O. Kuntze) in Sri Lanka. Euphytica 181(2):203–215. doi:10.1007/s10681-011-0399-9 CrossRefGoogle Scholar
  3. Assoumane AA (2006) Etude génétique et écologique d'une espèce menacée de forêt sèche en Nouvelle Calédonie: Captaincookia margaretae. Implications pour sa conservation. Université Pierre et Marie Curie Paris. Master Pro II Parcours Génétique et Gestion de la Biodiversité, 1–40Google Scholar
  4. Assoumane AA, Vaillant A, Mayaki AZ, Verhaegen D (2009) Isolation and characterization of microsatellite markers for Acacia senegal (L.) Willd., a multipurpose arid and semi-arid tree. Mol Ecol Resour 9(5):1380–1383PubMedCrossRefGoogle Scholar
  5. Ayelea TB, Gailinga O, Finkeldey R (2011) Assessment and integration of genetic, morphological and demographic variation in Hagenia abyssinica (Bruce) J.F. Gmel to guide its conservation. J Nat Conserv 19(1):8–17. doi:10.1016/j.jnc2010.03.001 CrossRefGoogle Scholar
  6. Barré N, Gay D, Desmoulins F, Selmaoui N (2008) Fragmentation of New-Caledonian dry forests reduces bird diversity. Programme de Conservation des Forêts Sèches, 1–30Google Scholar
  7. Belkhir K, Borsa P, Chikhi L, Raufaste N, Bonhomme F (1996–2004) GENETIX 4.05, logiciel sous Windows TM pour la génétique des populations. Laboratoire Génome, Populations, Interactions, CNRS UMR 5171, Université de Montpellier II, Montpellier (France). Available at http://www.genetix.univ-montp2.fr/genetix/genetix.htm
  8. Billotte N, Lagoda PJL, Risterucci AM, Baurens FC (1999) Microsatellite-enriched librairies: applied methodology for the development of SSR markers in tropical crops. Fruits 54:277–288Google Scholar
  9. Bouchet P, Jaffré T, Veillon J-M (1995) Plant extinction in New Caledonia: protection of sclerophyll forests urgently needed. Biodivers Conserv 4(4):415–428CrossRefGoogle Scholar
  10. Callen DF, Thompson AD, Shen Y, Phillips HA, Richards RI, Mulley JC, Sutherland GR (1993) Incidence and origin of "null" alleles in the (AC)n microsatellite markers. Am J Hum Genet 52(5):922–927PubMedGoogle Scholar
  11. Collectif (2002) Le programme Forêt sèche. Available at http://www.foretsechenc/index.htm
  12. Copyright Addinsoft (1995–2007) XLSTAT Version 2007.8.04. Available at http://www.xlstat.com
  13. Corander J, Marttinen P (2006) Bayesian identification of admixture events using multilocus molecular markers. Mol Ecol 15(10):2833–2843PubMedCrossRefGoogle Scholar
  14. Crandall KA, Bininda-Emonds ORP, Mace GM, Wayne RK (2000) Considering evolutionary processes in conservation biology. Trends Ecol Evol 15(7):290–295PubMedCrossRefGoogle Scholar
  15. Dutech C, Joly HI, Jarne P (2004) Gene flow, historical population dynamics and genetic diversity within French Guianan populations of a rainforest tree species, Vouacapoua americana. Heredity 92(2):69–77. doi:10.1038/sj.hdy.6800384 PubMedCrossRefGoogle Scholar
  16. El Mousadik A, Petit RJ (1996) High level of genetic differentiation for allelic richness among populations of the argan tree [Argania spinosa (L.) Skeels] endemic to Morocco. Theor Appl Genet 92(7):832–839CrossRefGoogle Scholar
  17. England PR, Usher AV, Whelan RJ, Ayre DJ (2002) Microsatellite diversity and genetic structure of fragmented populations of the rare, fire-dependent shrub Grevillea macleayana. Mol Ecol 11(6):967–977PubMedCrossRefGoogle Scholar
  18. Excoffier L, Laval G, Schneider S (2007) Arlequin ver 3.11: an integrated software package for population genetics data analysis. Computanional and Molecular Population Genetics Lab, Institute of Zoology University of Berne Switzerland, distributed by the authors at http://lgb.unige.ch/arlequin/
  19. Favreau B, Andrianoelina O, Nunez P, Vaillant A, Ramamonjisoa L, Danthu P, Bouvet J-M (2007) Characterization of microsatellite markers in the rosewood (Dalbergia monticola Bosser & R. Rabev.). Mol Ecol Notes 7(5):774–776CrossRefGoogle Scholar
  20. Fofana IJ, Ofori D, Poitel M, Verhaegen D (2009) Diversity and genetic structure of teak (Tectona grandis L.f) in its natural range using DNA microsatellite markers. New For 37(2):175–195. doi:10.1007/s11056-008-9116-5 CrossRefGoogle Scholar
  21. Gillespie TW, Jaffré T (2003) Tropical dry forests in New Caledonia. Biodivers Conserv 12(8):1687–1697CrossRefGoogle Scholar
  22. Goudet J (2001) FSTAT, a program to estimate and test gene diversities and fixation indices. Version 2.9.3. Department of Ecology & Evolution, Biology Building, UNIL, CH-1015 Lausanne, Switzerland, distributed by the authors at http://www2.unil.ch/popgen/softwares/fstat.htm
  23. Guillot G, Mortier F, Estoup A (2005) Geneland: a computer package for landscape genetics. Mol Ecol Notes 5(3):712–715CrossRefGoogle Scholar
  24. Hallé N (1973) Captaincookia, a new monotypic New Caledonian genus of Rubiaceae, Ixoreae. Adansonia Sér 2(13):195–202Google Scholar
  25. Hardy OJ, Vekemans X (2002) SPAGeDi: a versatile computer program to analyse spatial genetic structure at the individual or population levels. Mol Ecol Notes 2(4):618–620CrossRefGoogle Scholar
  26. Hequet V (2010) Ixora margaretae. In: IUCN 2011 IUCN Red List of Threatened SpeciesGoogle Scholar
  27. Hurlbert SH (1971) The nonconcept of species diversity: a critique and alternative parameters. Ecology 52(4):577–586CrossRefGoogle Scholar
  28. Jaffré T (2003) Les groupements végétaux de la forêt sèche. Available at http://www.foretsechenc/index.htm
  29. Jaffré T, Veillon J-M (eds) (1994) Les principales formations végétales autochtones en Nouvelle-Calédonie: caractéristiques, vulnérabilité, mesures de sauvegarde, vol 2. Rapports de Synthèses. Sciences de la Vie. Biodiversité, ORSTOM edn. ORSTOM, Centre de NouméaGoogle Scholar
  30. Jaffré T, Morat P, Veillon J-M (1994) La Flore Caractéristiques et composition floristique des principales formations végétales. Bois For Trop 242:7–30Google Scholar
  31. Jaffré T, Morat P, Veillon J-M, Rigault F, Dagostini G (2001) Composition and characteristics of the native flora of New Caledonia. Doc Sci Tech II4:1–138Google Scholar
  32. Kalinowski ST, Taper ML, Marshall TC (2007) Revising how the computer program CERVUS accomodates genotyping error increase sucess in paternity assigment. Mol Ecol 16(5):1099–1106PubMedCrossRefGoogle Scholar
  33. Kier G, Kreft H, Lee TM, Jetz W, Ibisch PL, Nowicki C, Mutke J, Barthlott W (2009) A global assessment of endemism and species richness across island and mainland regions. Proc Natl Acad Sci USA 106(23):9322–9327. doi:10.1073/pnas.0810306106 PubMedCrossRefGoogle Scholar
  34. Kurata K, Jaffré T, Setoguchi H (2008) Genetic diversity and geographical structure of the pitcher plant Nepenthes vieillardii in New Caledonia: a chloroplast DNA haplotype analysis. Am J Bot 95(12):1632–1644PubMedCrossRefGoogle Scholar
  35. Lacy RC (1997) Importance of genetic variation to the viability of mammalian populations. J Mammal 78(2):320–335CrossRefGoogle Scholar
  36. Loiselle BA, Sork VL, Nason J, Graham C (1995) Spatial genetic structure of a tropical understory shrub, Psychotria officinalis (Rubiaceae). Am J Bot 82(11):1420–1425CrossRefGoogle Scholar
  37. Morand M-E, Brachet S, Rossignol P, Dufour J, Frascaria-Lacoste N (2002) A generalized heterozygote deficiency assessed with microsatellites in French common ash populations. Mol Ecol 11(3):377–385PubMedCrossRefGoogle Scholar
  38. Mouly A, Razafimandimbison SG, Florence J, Jérémie J, Bremer B (2009a) Paraphyly of Ixora and new tribal delimitation of Ixoreae (Rubiaceae): inference from combined chloroplast (rps16, rbcL, and trnT-F) sequence data. Ann Mo Bot Gard 96(1):146–160CrossRefGoogle Scholar
  39. Mouly A, Razafimandimbison SG, Khodabandeh A, Bremer B (2009b) Phylogeny and classification of the species-rich pantropical showy genus Ixora (Rubiaceae-Ixoreae) with indications of geographical monophyletic units and hybrids. Am J Bot 96(3):686–706. doi:10.3732/ajb.0800235 PubMedCrossRefGoogle Scholar
  40. Myers N (2003) Biodiversity hotspots revisited. Biosci 53(10):916–917CrossRefGoogle Scholar
  41. Myers N, Mittermeier RA, Mittermeier CG, da Fonseca GAB, Kent J (2000) Biodiversity hotspots for conservation priorities. Nature 403:853–858PubMedCrossRefGoogle Scholar
  42. Ndiade-Bourobou D, Vaillant A, Favreau B, Gayrin E, Bouvet J-M (2009) Isolation and characterization of 15 nuclear microsatellite markers for Baillonella toxisperma Pierre (Sapotaceae), a low-density tree species of Central Africa. Mol Ecol Resour 9(4):1135–1272PubMedCrossRefGoogle Scholar
  43. Nei M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genet 89(3):583–590Google Scholar
  44. Newton AC, Allnutt TR, Gillies ACM, Lowe AJ, Ennos RA (1999) Molecular phylogeography, intraspecific variation and the conservation of tree species. Trends Ecol Evol 14(4):140–145. doi:10.1016/S0169-5347(98)01555-9 PubMedCrossRefGoogle Scholar
  45. Noe S (2009) Etude des flux de gènes chez Captaincookia margaretae. Implications pour sa conservation. Master II Biologie Fonctionnelle des Plantes, Université Montpellier 2, 1–19Google Scholar
  46. Perrier X, Jacquemoud-Collet JP (2006) DARwin software. Cirad-Bios UPR Genetic Improvement of Vegetatively Propagated Crops, distributed by the authors at (http://darwin.cirad.fr/darwin)
  47. Pinto CA, Henriques MO, Figueiredo JP, David JS, Abreu FG, Pereira JS, Correia I, David TS (2011) Phenology and growth dynamics in Mediterranean evergreen oaks: effects of environmental conditions and water relations. For Ecol Manag 262(3):500–508. doi:10.1016/j.foreco.2011.04.018 CrossRefGoogle Scholar
  48. Read J, Sanson GD, de Garine-Wichatitsky M, Jaffré T (2006) Sclerophylly in two contrasting tropical environments: low nutrients vs. low rainfall. Am J Bot 93(11):1601–1614PubMedCrossRefGoogle Scholar
  49. Read J, Sanson GD, Caldwell E, Clissold FJ, Chatain A, Peeters P, Lamont BB, De Garine-Wichatitsky M, Jaffré T, Kerr S (2009) Correlations between leaf toughness and phenolics among species in contrasting environments of Australia and New Caledonia. Ann Bot 103(5):757–767PubMedCrossRefGoogle Scholar
  50. Rice WR (1989) Analysing tables of statistical tests. Evolution 43(1):223–225CrossRefGoogle Scholar
  51. Rigault F, Dagostini G (2004) Caractérisation floristique et physionomique de la forêt sèche de Nékoro. Programme de Conservation des Forêts Sèches, 1–27Google Scholar
  52. Ritland K (1996) Estimators for pairwise relatedness and individual inbreeding coefficients. Genet Res 67(2):175–185CrossRefGoogle Scholar
  53. Rossetto M, Slade RW, Baverstock PR, Henry RJ, Lee LS (1999) Microsatellite variation and assessment of genetic structure in tea tree (Melaleuca alternifolia – Myrtaceae). Mol Ecol 8(4):633–643PubMedCrossRefGoogle Scholar
  54. Saghai-Maroof MA, Soliman KM, Jorgensen RA, Allard RW (1984) Ribosomal DNA spacer length polymorphisms in barley: Mendelian inheritance, chromosomal location, and population dynamics. Proc Natl Acad Sci USA 81:8014–8018PubMedCrossRefGoogle Scholar
  55. Serret J (2007) Etude de la diversité génétique de Captaincookia margaretae, espèce endémique des forêts sèches de Nouvelle Calédonie. Licence Professionnelle "Génie des Biotechnologies Végétales", Université Paul Sabatier Toulouse III, 1–28Google Scholar
  56. Thioulouse J, Chessel D, Dolédec S, Olivier JM (1997) ADE-4: a multivariate analysis and graphical display software. Stat Comput 7:75–83CrossRefGoogle Scholar
  57. Wünsch A, Hormazaa JI (2002) Molecular characterisation of sweet cherry (Prunus avium L.) genotypes using peach [Prunus persica (L.) Batsch] SSR sequences. Heredity 89(1):56–63. doi:10.1038/sj.hdy.6800101 PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • D. Verhaegen
    • 1
  • A. Assoumane
    • 1
    • 2
  • J. Serret
    • 1
  • S. Noe
    • 1
    • 3
  • B. Favreau
    • 1
  • A. Vaillant
    • 1
  • G. Gâteblé
    • 4
  • A. Pain
    • 4
  • C. Papineau
    • 5
  • L. Maggia
    • 1
    • 4
  • J. Tassin
    • 4
    • 6
  • J.-M. Bouvet
    • 1
  1. 1.Cirad UMR AGAP «Genetic diversity and breeding of forest trees»Montpellier Cedex 5France
  2. 2.Faculté des SciencesUniversité Abdou MoumouniNiameyNiger
  3. 3.Sandrine NoeClaretFrance
  4. 4.IAC Institut Agronomique néo-Calédonien BP73PaïtaNew Caledonia
  5. 5.Programme de Conservation des Forêts Sèches (PCFS)Centre de Recherche Nord BP6PouemboutNew Caledonia
  6. 6.Cirad Tropical Forest Goods and Ecosystem Services: Facing Global Changes (BSEF) Campus international de BaillarguetMontpellier Cedex 5France

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