Structure and genetic diversity of Ixora margaretae an endangered species: A baseline study for conservation and restoration of natural dry forest of New Caledonia

Tree Genetics and Genomes

Volumn 9, Issue 2, 2013, Pages 511-524

  Verhaegen, D ^a   Assoumane, A ^a,b   Serret, J ^a   Noe, S ^a,c   Favreau, B ^a   Vaillant, A ^a   Gateble G ^d   Pain, A ^d   Papineau, C ^e   Maggia, L ^a,d   Tassin, J ^a,d   Bouvet, J M ^a  

^a CIRAD   (France)

^b UNIVERSITÉ ABDOU MOUMOUNI   (Niger)

^c Sandrine Noe   (France)

^d IAC Institut Agronomique néo Calédonien BP73   (New Caledonia)

^e Centre de Recherche Nord BP6   (New Caledonia)

Author keywords

Biodiversity hotspot; Ecology; Endemism; Gene flow; Genetic drift; Sclerophyll forests; SSR

Indexed keywords

AVES; HEXAPODA; IXORA; MOLLUSCA; RATTUS; REPTILIA;

EID: 84875225392     PISSN: 16142942     EISSN: 16142950     Source Type: Journal    
DOI: 10.1007/s11295-012-0575-7     Document Type: Article

References (57)

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): 933-944.
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.
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, 1-40.
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): 1380-1383.
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.
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, 1-30.
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: 277-288.
9. Bouchet P, Jaffré T, Veillon J-M (1995) Plant extinction in New Caledonia: protection of sclerophyll forests urgently needed. Biodivers Conserv 4(4): 415-428.
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): 922-927.
11. Collectif (2002) Le programme Foret 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): 2833-2843.
14. Crandall KA, Bininda-Emonds ORP, Mace GM, Wayne RK (2000) Considering evolutionary processes in conservation biology. Trends Ecol Evol 15(7): 290-295.
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.
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): 832-839.
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): 967-977.
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): 774-776.
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.
21. Gillespie TW, Jaffré T (2003) Tropical dry forests in New Caledonia. Biodivers Conserv 12(8): 1687-1697.
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): 712-715.
24. Hallé N (1973) Captaincookia, a new monotypic New Caledonian genus of Rubiaceae, Ixoreae. Adansonia Sér 2(13): 195-202.
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): 618-620.
26. Hequet V (2010) Ixora margaretae. In: IUCN 2011 IUCN Red List of Threatened Species.
27. Hurlbert SH (1971) The nonconcept of species diversity: a critique and alternative parameters. Ecology 52(4): 577-586.
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 Nouméa.
30. Jaffré T, Morat P, Veillon J-M (1994) La Flore Caractéristiques et composition floristique des principales formations végétales. Bois For Trop 242: 7-30.
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: 1-138.
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): 1099-1106.
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.
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): 1632-1644.
35. Lacy RC (1997) Importance of genetic variation to the viability of mammalian populations. J Mammal 78(2): 320-335.
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): 1420-1425.
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): 377-385.
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): 146-160.
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.
40. Myers N (2003) Biodiversity hotspots revisited. Biosci 53(10): 916-917.
41. Myers N, Mittermeier RA, Mittermeier CG, da Fonseca GAB, Kent J (2000) Biodiversity hotspots for conservation priorities. Nature 403: 853-858.
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): 1135-1272.
43. Nei M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genet 89(3): 583-590.
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.
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, 1-19.
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.
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): 1601-1614.
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): 757-767.
50. Rice WR (1989) Analysing tables of statistical tests. Evolution 43(1): 223-225.
51. Rigault F, Dagostini G (2004) Caractérisation floristique et physionomique de la forêt sèche de Nékoro. Programme de Conservation des Forêts Sèches, 1-27.
52. Ritland K (1996) Estimators for pairwise relatedness and individual inbreeding coefficients. Genet Res 67(2): 175-185.
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): 633-643.
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: 8014-8018.
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, 1-28.
56. Thioulouse J, Chessel D, Dolédec S, Olivier JM (1997) ADE-4: a multivariate analysis and graphical display software. Stat Comput 7: 75-83.
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.