High genetic diversity in a potentially vulnerable tropical tree species despite extreme habitat loss

PLoS ONE

Volumn 8, Issue 12, 2013, Pages

  Noreen, Annika M E ^a   Webb, Edward L ^a  

^a NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

AGE; ALLELE; APIS; ARTICLE; BEE; CANOPY; COHORT ANALYSIS; ECOSYSTEM RESILIENCE; FABACEAE; GENE AMPLIFICATION; GENE FREQUENCY; GENETIC DISTANCE; GENETIC EROSION; GENETIC VARIABILITY; GENOTYPE; HABITAT LOSS; HETEROZYGOSITY; INBREEDING; KOOMPASSIA MALACCENSIS; MOBILE BEE; NONHUMAN; OUTCROSSING; PLANT STEM; POLLINATION; POLYMORPHIC LOCUS; POPULATION SIZE; SAPLING; SEEDLING; SINGAPORE; SPECIES HABITAT; SPECIES RICHNESS; STATISTICS; TROPICAL RAIN FOREST;

ECOSYSTEM; GENETIC VARIATION; GENETICS, POPULATION; TREES; TROPICAL CLIMATE;

EID: 84893166710     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0082632     Document Type: Article

References (69)

1. Gibson L, Lee TM, Koh LP, Brook BW, Gardner TA et al. (2011) Primary forests are irreplaceable for sustaining tropical biodiversity. Nature 478: 378-381.
2. Yee ATK, Corlett RT, Liew SC, Tan HTW (2011) The vegetation of Singapore - an updated map. Gardens' Bulletin Singapore 63: 205-212.
3. Corlett RT (1992) The ecological transformation of Singapore, 1819-1990. Journal of Biogeography 19: 411-420.
4. Turner IM, Tan HTW, Wee YC, Bin Ibrahim A, Chew PT, et al. (1994) A study of plant species extinction in Singapore: lessons for the conservation of tropical biodiversity. Conservation Biology 8: 705-712. (Pubitemid 2139324)
5. Corlett RT (1997) The vegetation in the nature reserves of Singapore. Gardens' Bulletin Singapore 49: 147-159.
6. Tilman D, May RM, Lehman CL, Nowak MA (1994) Habitat destruction and the extinction debt. Nature 371: 65.
7. Gibson L, Lynam AJ, Bradshaw CJA, He F, Bickford DP et al. (2013) Near-complete extinction of native small mammal fauna 25 years after forest fragmentation. Science 341: 1508-1510.
8. Brook BW, Sodhi NS, Ng PKL (2003) Catastrophic extinctions follow deforestation in Singapore. Nature 424: 420-423. (Pubitemid 36917488)
9. Chong KY, Tan HTW, Corlett RT (2009) A checklist of the total vascular plant flora of Singapore: native, naturalized and cultivated species. Raffles Museum of Biodiversity Research, Singapore. http://rmbr.nus.edu.sg/raffles- museum-pub/flora-of-singapore-tc.pdf.
10. van Treuren R, Bijlsma N, Ouborg J, van Delden W (1991) The significance of genetic erosion in the process of extinction. I. Genetic differentiation in Salvia pratensis and Scabiosa columbaria in relation to population size. Heredity 48: 996-1008.
11. Jamieson IG, Allendorf FW (2012) How does the 50/500 rule apply to MVPs? Trends in Ecology and Evolution 27: 578-584.
12. Allendorf FW (1986) Genetic drift and the loss of alleles versus heterozygosity. Zoo Biology 5: 181-190.
13. Keller LF, Waller DM (2002) Inbreeding effects in wild populations. Trends in Ecology and Evolution 17: 230-241. (Pubitemid 34270584)
14. Bijlsma R, Bundgaard J, Boerema A (2000) Does inbreeding affect the extinction risk of small populations?: predictions from Drosophila. Journal of Experimental Biology 13: 502-514. (Pubitemid 30300918)
15. McGreevy TJ, Dabek L, Husband TP (2010) Genetic evaluation of the association of zoos and aquariums Matschie's tree kangaroo (Dendrolagus matschiei) captive breeding program. Zoo Biology 30: 636-646.
16. Palomares F, Godoy JA, López-Bao JV, Rodríguez A, Roques S et al. (2012) Possible Extinction Vortex for a Population of Iberian Lynx on the Verge of Extirpation. Conservation Biology 26: 689-697.
17. Oostermeijer JGB, Van Eijck MW, Den Nijs HCM (1994) Offspring fitness in relation to population size and genetic variation in the rare perennial plant species Gentiana pneumonanthe (Gentianaceae). Oecologia 97: 289-296. (Pubitemid 2065116)
18. Durka W, Michalski SG (2007) High selfing and high inbreeding depression in peripheral populations of Juncus atratus. Molecular Ecology 16: 4715-4727. (Pubitemid 350135219)
19. Honnay O, Jacquemyn H (2007) Susceptibility of common and rare plant species to the genetic consequences of habitat fragmentation. Conservation Biology 21: 823-831. (Pubitemid 46802199)
20. Kramer AT, Ison JL, Ashley MV, Howe HF (2008) The paradox of forest fragmentation genetics. Conservation Biology 22: 878-885.
21. Lowe AJ, Boshier D, Ward M, Bacles CEF, Navarro C (2005) Genetic resource impacts of habitat loss and degradation; reconciling empirical evidence and predicted theory for neotropical trees. Heredity 95: 255-273. (Pubitemid 41372104)
22. Vranckx G, Jacquemyn H, Muys B, Honnay O (2012) Meta-Analysis of Susceptibility of Woody Plants to Loss of Genetic Diversity through Habitat Fragmentation. Conservation Biology 26: 228-237.
23. Rosas F, Quesada M, Lobo JA, Sork VL (2011) Effects of habitat fragmentation on pollen flow and genetic diversity of the endangered tropical tree Swietenia humilis (Meliaceae). Biological Conservation 144: 3082-3088.
24. Sebbenn AM, Carvalho ACM, Freitas MLM, Moraes SMB, Gaino APSC, et al. (2011) Low levels of realized seed and pollen gene flow and strong spatial genetic structure in a small, isolated and fragmented population of the tropical tree Copaifera langsdorffi Desf. Heredity 106: 134-145.
25. Finger A, Kettle CJ, Kaiser-Bunbury CN, Valentin T, Mougal J, et al. (2012) Forest fragmentation genetics in a formerly widespread island endemic tree: Vateriopsis seychellarum (Dipterocarpaceae). Molecular Ecology 21: 2369-2382.
26. Wang R, Compton SG, Chen X-Y (2011) Fragmentation can increase spatial genetic structure without decreasing pollen-mediated gene flow in a wind-pollinated tree. Molecular Ecology 20: 4421-4432.
27. Vieira F de A, Fajardo CG, de Souza AM, Reis CAF, de Carvalho D (2012) Fine-scale genetic dynamics of a dominant neotropical tree in the threatened Brazilian Atlantic Rainforest. Tree Genetics & Genomes 8: 1191-1201.
28. Newman D, Tallmon DA (2001) Experimental Evidence for Beneficial Fitness Effects of Gene Flow in Recently Isolated Populations. Conservation Biology 15: 1054-1063. (Pubitemid 32706844)
29. IUCN (2012) Red List of Threatened Species. Version 2012.2. Available at: www.iucnredlist.org. Accessed 10 November 2013.
30. Dutta A (2001) Biodiversity and Ecosystem Conservation, Kalpaz Publications. Pg. 173.
31. Corlett RT (1990) Flora and reproductive phenology of the rain forest at Bukit Timah, Singapore. Journal of Tropical Ecology 6: 55-63.
32. Shono K, Davies SJ, Chua YK (2007) Performance of 45 native tree species on degraded lands in Singapore. Journal of Tropical Forest Science 19: 25-34.
33. Lee KM, Wickneswari R, Choong CY (2007) Stand Structure and the Genetic Diversity of Koompassia malaccensis and Dryobalanops aromatica in Unlogged and Logged-over Stands. Sains Malaysiana 36: 233-242
34. Lee CT, Lee SL, Faridah QZ, Siraj SS, Ng KKS, et al. (2008) Genetic Diversity Assessment of Koompassia malaccensis. Pertanika Journal of Tropical Agricultural Science 31: 127-133.
35. Lee CT, Lee SL, Ng KKS, Faridah QZ, Siraj SS, et al. (2011) Estimation of outcrossing rates in Koompassia malaccensis from an open-pollinated population in peninsular Malaysia using microsatellite markers. Journal of Tropical Forest Science 23: 410-416.
36. National Parks Board (2012) Available at: www.nparks.gov.sg.Accessed 1 November 2013.
37. Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin 19: 11-15.
38. Lee CT, Lee SL, Faridah QZ, Siraj SS, Ng KKS, et al. (2006) Isolation and characterization of microsatellite markers in Koompassia malaccensis (Leguminosae), an important tropical timber species. Molecular Ecology Notes 6: 1198-1201. (Pubitemid 44807984)
39. van Oosterhout C, Hutchinson WF, Wills DPM, Shirley P (2004) MICROCHECKER: software for identifying and correcting genotyping errors in microsatellite data. Molecular Ecology Notes 4: 535-538. (Pubitemid 39147523)
40. Goudet J (2001) FSTAT (version 2.9.3), a program to estimate and test gene diversities and fixation indices.
41. Ritland K (2002) Extensions of models for the estimation of mating systems using independent loci. Heredity 88: 221-228.
42. Garza JC, Williamson EG (2001) Detection of reduction in population size using data from microsatellite loci. Molecular Ecology 10: 305-318. (Pubitemid 32232339)
43. Cornuet JM, Luikart G (1997) Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics 144: 2001-2014. (Pubitemid 26427944)
44. Peakall R, Smouse PE (2012) GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research - an update. Bioinformatics 28: 2537-2539.
45. Queller CD, Goodnight KF (1989) Estimating relatedness using genetic markers. Evolution 43: 258-275.
46. Hardy OJ, Vekemans X (2002) SPAGeDi: a versatile computer program to analyse spatial genetic structure at the individual or population levels. Molecular Ecology Notes 2: 618-620. (Pubitemid 35436766)
47. Loiselle BA, Sork VL, Nason J, Graham C (1995) Spatial genetic structure of a tropical understorey shrub, Psychotria officinalis (Rubiaceae). American Journal of Botany 82: 1420-1425. (Pubitemid 3002677)
48. Vekemans X, Hardy OJ (2004) New insights from fine-scale spatial genetic structure analysis in plant populations. Molecular Ecology 13: 921-935. (Pubitemid 38390597)
49. Fenster CB, Vekemans X, Hardy OJ (2003) Quantifying gene flow from spatial genetic structure data in a metapopulation of Chamaecrista fasciculate (Leguminosae). Evolution 57: 995-1007. (Pubitemid 36726557)
50. Hamrick JL (2012) Tropical breeding systems: one and done? Heredity 109: 330-331.
51. Fiumera AC, Parker PG, Fuerst PA (2000) Effective Population Size and Maintenance of Genetic Diversity in Captive-Bred Populations of a Lake Victoria Cichlid. Conservation Biology 14: 886-892. (Pubitemid 30390743)
52. Hauser L, Adcock GJ, Smith PJ, Bernal Ramírez JH, Carvalho GR (2002) Loss of microsatellite diversity and low effective population size in an overexploited population of New Zealand snapper (Pagrus auratus). Proceedings of the National Academy of Science U. S. A. 99: 11742-11747. (Pubitemid 34994469)
53. Pastor T, Garza JC, Allen P, Amos W, Aguilar A (2004) Low Genetic Variability in the Highly Endangered Mediterranean Monk Seal. Journal of Heredity 95: 291-300. (Pubitemid 38963181)
54. Thuillet A-C, Bru D, David J, Roumet P, Santoni S, et al. (2002) Direct Estimation of Mutation Rate for 10 Microsatellite Loci in Durum Wheat, Triticum turgidum (L.) Thell. ssp durum desf. Molecular Biology and Evolution 19: 122-125. (Pubitemid 34008055)
55. Frankham R (2005) Genetics and Extinction. Biological Conservation 126: 131-140.
56. Väli U, Einarsson A, Waits L, Ellegren H (2008) To what extent do microsatellite markers reflect genome-wide genetic diversity in natural populations? Molecular Ecology 17: 3808-3817.
57. Willi Y, Hoffmann AA (2009) Demographic factors and genetic variation influence population persistence under environmental change. Journal of Evolutionary Biology 22: 124-133.
58. Nuismer SL, MacPherson A, Rosenblum EB (2012) Crossing the threshold: gene flow, dominance and the critical level of standing genetic variation required for adaptation to novel environments. Journal of Evolutionary Biology 25: 2665-2671.
59. Lasso E, Dalling JW, Bermingham E (2011) Strong spatial genetic structure in five tropical Piper species: should the Baker-Fedorov hypothesis be revived for tropical shrubs? Ecology and Evolution 1: 502-516.
60. Harata T, Nanami S, Yamakura T, Matsuyama S, Chong L, et al. (2012) Finescale Spatial Genetic Structure of Ten Dipterocarp Tree Species in a Bornean Rain Forest. Biotropica 44: 586-594.
61. Lande R (1988) Genetics and Demography in Biological Conservation. Science 241: 1455-1460.
62. Traill LW, Bradshaw C JA, Brook BW (2007) Minimum viable population size: A meta-analysis of 30 years of published estimates. Biological Conservation 139: 159-166. (Pubitemid 47320616)
63. Flather CH, Hayward GD, Beissinger SR, Stephens PA (2011) Minimum viable populations: is there a 'magic number' for conservation practitioners? Trends in Ecology and Evolution 26: 307-316.
64. Menges ES (2000) Population viability analyses in plants: challenges and opportunities. Trends in Ecology and Evolution 15: 51-56.
65. Frankham R (1995) Effective population size/adult population size ratios in wildlife: a review. Genetical Research 66: 95-107.
66. Traill LW, Brook BW, Frankham R, Bradshaw CJA (2010) Pragmatic population viability targets in a rapidly changing world. Biological Conservation 143: 28-34.
67. Corlett RT (2011) Honeybees in natural ecosystems. Pp. 215-225 in H.R. Hepburn and S.E. Radloff (eds.) Honeybees of Asia, Springer-Verlag Berlin Heidelberg.
68. Corlett RT (2001) Pollination in a degraded tropical landscape. Journal of Tropical Ecology 17: 155-161.
69. R Core Team (2012). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. Available at: http://www.R-project.org/. Accessed 1 November 2013.