Fine- and local- scale genetic structure of Dysoxylum malabaricum, a late-successional canopy tree species in disturbed forest patches in the Western Ghats, India

Conservation Genetics

Volumn 18, Issue 1, 2017, Pages 1-15

  Bodare, Sofia ^a   Ravikanth, Gudasalamani ^b,c   Ismail, Sascha A ^d   Patel, Mohana Kumara ^c   Spanu, Ilaria ^e   Vasudeva, Ramesh ^f   Shaanker, Ramanan Uma ^b,c   Vendramin, Giovanni Giuseppe ^e   Lascoux, Martin ^a   Tsuda, Yoshiaki ^a,g  

^a UPPSALA UNIVERSITY   (Sweden)

^b ASHOKA TRUST FOR RESEARCH IN ECOLOGY AND THE ENVIRONMENT   (India)

^c UNIVERSITY OF AGRICULTURAL SCIENCES   (India)

^d ETH ZURICH   (Switzerland)

^e Institute of Biosciences and BioResources   (Italy)

^f UNIVERSITY OF AGRICULTURAL SCIENCES   (India)

^g UNIVERSITY OF TSUKUBA   (Japan)

Author keywords

Disturbance; Dysoxylum malabaricum; Fragmentation; Land use; Spatial genetic structure; Western Ghats

Indexed keywords

ADULT; AGE CLASS; BIODIVERSITY; CONSERVATION GENETICS; ENDEMIC SPECIES; ENVIRONMENTAL DISTURBANCE; EVERGREEN TREE; GENE FLOW; GENETIC STRUCTURE; GENETIC VARIATION; HABITAT FRAGMENTATION; LAND USE; PATCH DYNAMICS; RELATEDNESS; SPECIES CONSERVATION;

INDIA; WESTERN GHATS;

CHAMAECYPARIS; DYSOXYLUM MALABARICUM;

EID: 84982276408     PISSN: 15660621     EISSN: 15729737     Source Type: Journal    
DOI: 10.1007/s10592-016-0877-7     Document Type: Article

References (80)

1. Abdullah SA, Nakagoshi N (2007) Forest fragmentation and its correlation to human land use change in the state of Selangor, peninsular Malaysia. For Ecol Manag 241:39–48
2. Arnaud-Haond S, Teixeira S, Massa SI, Billot C, Saenger P, Coupland G, Duarte CM, Serrão EA (2006) Genetic structure at range edge: low diversity and high inbreeding in Southeast Asian mangrove (Avicennia marina) populations. Mol Ecol 15:3515–3525
3. Banks SC, Peakall R (2012) Genetic spatial autocorrelation can readily detect sex-biased dispersal. Mol Ecol 21:2092–2105
4. Banks SC, Cary GJ, Smith AL, Davies ID, Driscoll DA, Gill AM, Lindenmayer DB, Peakall R (2013) How does ecological disturbance influence genetic diversity? Trends Ecol Evol 28(11):670–679
5. Bhagwat SA, Kushalappa CG, Williams PH, Brown ND (2005) A landscape approach to biodiversity conservation in the Western Ghats of India. Conserv Biol 19:1853–1862
6. Bodare S, Tsuda Y, Ravikanth G, Uma Shaanker R, Lascoux M (2013) Genetic structure and demographic history of the endangered tree species Dysoxylum malabaricum (Meliaceae. in Western Ghats, India: implications for conservation in a biodiversity hotspot. Ecol Evol 3:3233–3248)
7. Boraiah KT, Vasudeva R, Bhagwat AS, Kushalappa CG (2003) Do informally managed sacred groves have higher richness and regeneration of medicinal plants than state-managed reserve forests? Curr Sci 84:804–808
8. Cavers S, Degen B, Caron H, Lemes MR, Margis R, Salgueiro F, Lowe AJ (2005) Optimal sampling strategy for estimation of spatial genetic structure in tree populations. Heredity 95:281–289
9. Chandrakanth MG, Bhat MG, Accavva MS (2004) Socio-economic changes and sacred groves in South India: protecting a community-based resource management institution. Nat Res Forum 28:102–111
10. Chapuis MP, Estoup A (2007) Microsatellite null alleles and estimation of population differentiation. Mol Biol Evol 24:621–631
11. Chybicki IJ, Burczik J (2009) Simultaneous estimation of null alleles and inbreeding coefficients. J Hered 100:106–113
12. Cicotta RP, Wisnewski J, Engelman R (2000) Human population in the biodiversity hotspots. Nature 404:990–992
13. Connell JH (1971) On the role of natural enemies in preventing competitive exclusion in some marine animals and in rain forest trees. In: Den Boer PJ, Gradwell GR (eds) Dynamics of population. Pudo, Wageningen
14. 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
15. Earl DA, vonHoldt BM (2012) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Res 4:359–361
16. Eckert CG, Samis E, Lougheed C (2008) Genetic variation across species’ geographical ranges: the central–marginal hypothesis and beyond. Mol Ecol 17:1170–1188
17. 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 92:832–839)
18. Epperson BK (1992) Spatial structure of genetic variation within populations of forest trees. New For 6:257–278
19. Epperson BK (2005) Estimating dispersal from short distance spatial autocorrelation. Heredity 95:7–15
20. Epperson BK, Li T-Q (1996) Measurement of genetic structure within populations using Moran’s spatial autocorrelation statistics. Proc Natl Acad Sci USA 93:10528–10532
21. 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
22. Evanno G, Castella E, Antoine C, Paillat G, Goudet J (2009) Parallel changes in genetic diversity and species diversity following a natural disturbance. Mol Ecol 8:1137–1144
23. Finger A, Kettle CJ, Kaiser-Bunbury CN, Valentin T, Mougal J, Ghazoul J (2012) Forest fragmentation genetics in a formerly widespread island endemic tree: Vateriopsis seychellarum (Dipterocarpaceae). Mol Ecol 21:2369–2382
24. Fogelqvist J, Niittyvuopio A, Ågren J, Savolainen O, Lascoux M (2010) Cryptic population genetic structure: the number of inferred clusters depends on sample size. Mol Ecol Res 10:314–323
25. Gokhale Y (2004) Reviving traditional forest management in Western Ghats: study in Karnataka. Econ Polit Wkly 39:3556–3559
26. Goudet J (1995) Fstat version 1.2: a computer program to calculate F-statistics. J Hered 86:485–486
27. Goudet J (2001) FSTAT (version 2.9.3: a program to estimate and test gene diversities and fixation indices. www.unil.ch/izea/softwares/fstat.html)
28. Gunaga S, Rajeshwari N, Vasudeva R (2013) Tree diversity and disturbance of kaan forests: relics of a community protected climax vegetation in the Central Western Ghats. Trop Ecol 54:117–131
29. Hampe A, Petit RJ (2005) Conserving biodiversity under climate change: the rear edge matters. Ecol Lett 8:461–467
30. 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
31. Hardy OJ, Maggia L, Bandou E, Breyne P, Caron H, Chevallier MH, Doligez A, Dutech C, Kremer A, Latouche-Halle C, Troispoux V, Veron V, Degen B (2006) Fine-scale genetic structure and gene dispersal inferences in 10 Neotropical tree species. Mol Ecol 15:559–571
32. Hedrick PW (2005) A standardized genetic differentiation measure. Evolution 59:1633–1638
33. Hemmilä S, Mohana Kumara P, Gustafsson S, Sreejayan N, Raghavandra A, Vasudeva R, Ravikanth G, Ganeshaiah KN, Uma Shaanker R, Lascoux M (2010) Development of polymorphic microsatellite loci in the endangered tree species Dysoxylum malabaricum and cross amplification with Dysoxylum binectariferum. Mol Ecol Res 10:404–408
34. Hubisz MJ, Falush D, Stephens M, Pritchard JK (2009) Inferring weak population structure with the assistance of sample group information. Mol Ecol Res 9:1322–1332
35. Hufford KM, Hamrick JL (2003) Viability selection at three early life stages of the tropical tree, Platypodium elegans (Fabaceae, Papilionoideae). Evolution 57:518–526
36. Ismail SA, Ghazoul J, Ravikanth G, Uma Shaanker R, Kushalappa CG, Kettle CJ (2012) Does long distance pollen dispersal preclude inbreeding in tropical trees? Fragmentation genetics of Dysoxylum malabaricum in an agro-forest landscape. Mol Ecol 21:5484–5496
37. Ismail SA, Ghazoul J, Ravikanth G, Uma Shaanker R, Kushalappa CG, Kettle CJ (2014) Forest trees in human modified landscapes: ecological and genetic drivers of recruitment failure in Dysoxylum malabaricum. Plos One 9:e89437
38. Iwaizumi MG, Tsuda Y, Ohtani M, Tsumura Y, Takahashi M (2013) Recent distribution changes affect geographic clines in genetic diversity and structure of Pinus densiflora natural populations in Japan. For Ecol Manag 304:407–416
39. Janzen DH (1970) Herbivores and the number of tree species in tropical forests. Am Nat 104:501–528
40. Jump AS, Peñuelas J (2007) Extensive spatial genetic structure revealed by AFLP but not SSR molecular markers in the wind-pollinated tree, Fagus sylvatica. Mol Ecol 16:925–936
41. Jump AS, Rico L, Coll M, Peñuelas J (2012) Wide variation in spatial genetic structure between natural populations of the European beech (Fagus sylvatica) and its implications for SGS comparability. Heredity 108:633–639
42. Kumar AN (2009) Saving culture for biodiversity. Exploring the “Bio-Cultural” Heritage in conservation of 5 Rare, Endemic and Threatened (RET. Tree Species of Western Ghats of Kerala. Alcoa Foundation’s Practitioner Fellowship Programme 2008, IUCN, Gland)
43. Langella O (2007) Populations 1.2.30: Population genetic software (individuals or populations distances, phylogenetic trees), France. http://bioinformatics.org/~tryphon/ populations/
44. Loiselle BA, Sork VL, Nason J, Graham C (1995) Spatial genetic structure of a tropical understory shrub, Psychotria officinalis (Rubiaceae). Am J Bot 82:1420–1425
45. Manel S, Schwartz MK, Luikart G, Taberlet P (2003) Landscape genetics: combining landscape ecology and population genetics. Trend Ecol Evol 18:189–197
46. Manjunath L (2003) Reproductive biology and half-sib family performance of Dysoxylum malabaricum Bedd.: an important threatened timber species. Master of Science (Forest Biology. thesis, submitted to the University of Agricultural Sciences, Dharwad, pp. 1–73)
47. Maruyama T, Fuerst PA (1985) Population bottleneck and non-equilibrium models in population genetics. II. Number of alleles in a small population that was formed by a recent bottleneck. Genetics 111:675–689
48. Mathiasen P, Rovere AE, Premoli AC (2007) Genetic structure and early effects of inbreeding in fragmented temperate forests of a self-Incompatible tree, Embothrium coccineum. Conserv Biol 21:232–240
49. Menon ARR, Balasubramanyan K (2006) Evaluation of plant diversity in unlogged and logged forest stands of varying intensities. KFRI Research Report No. 281 ISSN 0970-8103, Published by Kerala Forest Research Institute, Peechi, Thrissur, Kerala
50. Myers N, Mittermeier RA, Mittermeier CG, da Fonseca GAB, Kent J (2000) Biodiversity hotspots for conservation priorities. Nature 403:853–858
51. Naito Y, Konuma A, Iwata H, Suyama Y, Seiwa K, Okuda T, Lee S, Muhammad N, Tsumura Y (2005) Selfing and inbreeding depression in seeds and seedlings of Neobalanocarpus heimii (Dipterocarpaceae). J Plant Res 118:423–430
52. Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New York
53. Nei M, Maruyama T, Chakraborty R (1975) The bottleneck effect and genetic variability in populations. Evolution 29:1–10
54. Nei M, Tajima F, Tateno Y (1983) Accuracy of estimated phylogenetic trees from molecular data. J Mol Evol 19(2):153–170
55. Peakall R, Smouse PE (2006) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6:288–295
56. Peakall R, Smouse PE (2012) GenAlEx Tutorial 3. Spatial genetic analysis. http://biology-assets.anu.edu.au/GenAlEx/Tutorials.html
57. Peakall R, Smouse PE, Huff DR (1995) Evolutionary implications of allozyme and RAPD variation in diploid populations of dioecious buffalo grass (Buchloë dactyloides Nutt. (Engelm)). Mol Ecol 4:135–147
58. Piry S, Luikart G, Cornuet J-M (1999) BOTTLENECK: a computer program for detecting recent reductions in the effective population size using allele frequency data. J Hered 90:502–503
59. Pritchard JK, Stephens M, Donelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959
60. Queller DC, Goodnight KF (1989) Estimating relatedness using genetic markers. Evolution 43:258–275
61. Ravikumar K, Ved DK (2000) 100 Red Listed Medicinal Plants of Conservation Concern in Southern India, Foundation for Revitalisation of Local Health Traditions, Bangalore, pp. 132–133
62. Raymond M, Rousset F (1995) GENEPOP (version 1.2.: population genetics software for exact tests and ecumenicism. Heredity 86:248–249)
63. Rosenberg NA (2004) Distruct: a program for the graphical display of population structure. Mol Ecol Notes 4:137–138
64. Rousset F (2008) Genepop’007: a complete reimplementation of the Genepop software for Windows and Linux. Mol Ecol Res 8:103–106
65. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual, 2nd edn. Cold Spring Harbor Laboratory Press, New York
66. Shivanna KR, Gladwin J, Shaanker RU (2003) Reproductive ecology and population enrichment of endemic and critically endangered plant species of the Western Ghats. National Bioresources Development Board, Department of Biotechnology, Government of India, pp. 38–61
67. Smouse PE, Peakall R (1999) Spatial autocorrelation analysis of individual multi allele and multi-locus genetic structure. Heredity 82:561–573
68. Smouse PE, Peakall R, Gonzales E (2008) A heterogeneity test for fine-scale genetic structure. Mol Ecol 17:3389–3400
69. Sork VL, Smouse PE (2006) Genetic analysis of landscape connectivity in tree populations. Landsc Ecol 21:821–836
70. Steinitz O, Troupin D, Vendramin GG, Nathan R (2011) Genetic evidence for a Janzen-Connell recruitment pattern in reproductive offspring of Pinus halepensis trees. Mol Ecol 20:4152–4164
71. Struebig MJ, Kingston T, Petit EJ, Le Comber SC, Zubaid A, Mohd-Adnan A, Rossiter SJ (2011) Parallel declines in species and genetic diversity in tropical forest fragments. Ecology Letters 14(6):582–590
72. Tabarelli M, Peres CA, Melo FP (2012) The ‘few winners and many losers’ paradigm revisited: emerging prospects for tropical forest biodiversity. Biol Conserv 155:136–140
73. Tambat B, Rajanikanth G, Ravikanth G, Uma Shaanker R, Ganeshaiah KN, Kushallappa CG (2005) Seedling mortality in two vulnerable tree species in the sacred groves of Western Ghats, South India. Curr Sci 88(3):350–352
74. Tsuda Y, Sawada H, Ohsawa T, Nakao K, Nishikawa H, Ide Y (2010) Landscape genetic structure of Betula maximowicziana in the Chichibu mountain range, central Japan. Tree Genet Genome 6:377–387
75. Vekemans X, Hardy OJ (2004) New insights from fine-scale spatial genetic structure analyses in plant populations. Mol Ecol 13:921–935
76. Vellend M (2004) Parallel effects of land-use history on species diversity and genetic diversity of forest herbs. Ecology 85:3043–3055
77. Vellend M, Geber MA (2005) Connections between species diversity and genetic diversity. Ecol Lett 8:767–781
78. 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. Mol Ecol 20:4421–4432
79. Weir B, Cockerham C (1984) Estimating F-statistics for the analysis of population structure. Evolution 38:1358–1370
80. Wright SJ, Muller-Landau HC (2006) The future of tropical forest species. Biotropica 38(2006):287–301