Abstract
The highly valuable timber species Dalbergia cochinchinensis is severely threatened due to habitat loss and illegal logging throughout its distribution in mainland Southeast Asia and is listed on CITES Appendix II. This study proposes a strategy for conservation and sustainable management of the species based on assessment of genetic structure within and among natural populations. We developed SNP markers from RAD sequencing and used these in combination with SSR genotypes from a previous study to assess the genetic diversity in 26 populations of D. cochinchinensis across its entire range in Laos, Thailand, Cambodia and Vietnam. The species is able of clonal reproduction and we found that trees closer than 45 meters from each other can be clones. Genetic diversity and clustering analysis showed a clear division of populations into five geographical groups with differing levels of diversity. Assignment tests correctly identified the region of origin for approximately 90% of the samples, which demonstrates that despite a low number of successfully identified SNPs, the SSR + SNP marker panel has the potential for tracking the geographic origin of D. cochinchinensis timber for use in CITES regulation and enforcement. We propose the five identified groups to be considered as Management Units and that conservation and breeding programs should be based on a network of in situ and ex situ conservation stands representing the genetic variation among and within these units. We recommend that conservation efforts are directed towards community owned and managed lands, as this has proven an effective strategy locally.
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Data availability
A FASTA file with the 43 SNPs and flanking sequences and the dataset with 500 SNPs + SSR genotypes are available from the University of Copenhagen Electronic Research Data Archive at https://sid.erda.dk/public/archives/e701584e549fe59472596f5f4e793959/published-archive.html and https://sid.erda.dk/public/archives/6c53d7edfa9195829eec09903a8fb110/published-archive.html, respectively.
References
Amaral W, Thomson L, Yanchuk A (2004a) Conservation of genetic resources in their natural environment. In: FAO, FLD, IPGRI (ed) Forest genetic resources conservation and management. Overview, concepts and some systematic approaches. International Plant Genetic Resources Institute, Rome, pp 1–4
Amaral W, Yanshuk A, Kjaer ED (2004b) Methodologies for ex situ conservation. In: FAO, FLD, IPGRI (ed) Forest genetic resources: conservation and management. Vol 3: In plantations and gene banks (ex situ). International Plant Genetic Resources Institute, Rome, pp 3–8
Baird NA, Etter PD, Atwood TS et al (2008) Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS ONE. https://doi.org/10.1371/journal.pone.0003376
Barnes R (1995) The breeding seedling orchard in the multiple population breeding strategy. Silvae Genet 44:81–88
Blanc-Jolivet C, Liesebach M (2015) Tracing the origin and species identity of Quercus robur and Quercus petraea in Europe: a review. Silvae Genetica 64:182–193. https://doi.org/10.1515/sg-2015-0017
Blanc-Jolivet C, Kersten B, Dainou K et al (2017) Development of nuclear SNP markers for genetic tracking of Iroko, Milicia excelsa and Milicia regia. Conserv Genet Resour 9:531–533. https://doi.org/10.1007/s12686-017-0716-2
Bray DB, Duran E, Ramos VH et al (2008) Tropical deforestation, community forests, and protected areas in the Maya Forest. Ecol Soc 13:56
Cannon SB, McKain MR, Harkess A et al (2015) Multiple polyploidy events in the early radiation of nodulating and nonnodulating legumes. Mol Biol Evol 32:193–210. https://doi.org/10.1093/molbev/msu296
Catchen J, Hohenlohe PA, Bassham S, Amores A, Cresko WA (2013) Stacks: an analysis tool set for population genomics. Mol Ecol 22:3124–3140. https://doi.org/10.1111/mec.12354
CITES (2017) Appendices I, II and III. https://cites.org/eng/app/appendices.php
CoP16 C (2013) CoP16 Prop. 60. Proposal for amenment of appendices I and II. Dalbergia cochinchinensis. http://www.cites.org/sites/default/files/eng/cop/16/prop/E-CoP16-Prop-60.pdf
CTSP (2004) Cambodian tree species. Monographs. Cambodia Tree Seed Project, FA, Cambodia and DANIDA, Denmark
Degen B, Blanc L, Caron H et al (2006) Impact of selective logging on genetic composition and demographic structure of four tropical tree species. Biol Conserv 131:386–401. https://doi.org/10.1016/j.biocon.2006.02.014
Degen B, Ward SE, Lemes MR et al (2013) Verifying the geographic origin of mahogany (Swietenia macrophylla King) with DNA-fingerprints. Forens Sci Int-Genet 7:55–62. https://doi.org/10.1016/j.fsigen.2012.06.003
DePristo MA, Banks E, Poplin R et al (2011) A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 43:491–498. https://doi.org/10.1038/ng.806
Dhakal LP, Lillesø JPB, Kjær ED, Jha PK, Aryal HL (2005) Seed sources of agroforestry trees in a farmland context—a guide to tree seed source establishment in Nepal. Hørsholm, Denmark
Earl DA, Vonholdt BM (2012) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resour 4:359–361. https://doi.org/10.1007/s12686-011-9548-7
EIA (2015) Adressing ASEAN´s regional rosewood crisis: an urgent call to action. Environmental Investigation Agency, London
Ellis EA, Porter-Bolland L (2008) Is community-based forest management more effective than protected areas? A comparison of land use/land cover change in two neighboring study areas of the Central Yucatan Peninsula, Mexico. For Ecol Manag 256:1971–1983. https://doi.org/10.1016/j.foreco.2008.07.036
Eriksson G, Namkoong G, Roberds JH (1993) Dynamic gene conservation for uncertain futures. For Ecol Manag 62:15–37. https://doi.org/10.1016/0378-1127(93)90039-P
Etter PD, Preston JL, Bassham S, Cresko WA, Johnson EA (2011) Local de novo assembly of RAD paired-end contigs using short sequencing reads. PLoS ONE. https://doi.org/10.1371/journal.pone.0018561
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. https://doi.org/10.1111/j.1365-294X.2005.02553.x
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
Fady B, Aravanopoulos FA, Alizoti P et al (2016) Evolution-based approach needed for the conservation and silviculture of peripheral forest tree populations. For Ecol Manag 375:66–75. https://doi.org/10.1016/j.foreco.2016.05.015
FAO (2014) State of the world´s forest genetic resources. Food and Agriculture Organization of the United Nations, Rome
FAO (2016) State of the World´s Forests 2016. Forest and agriculture: land-use challenges and opportunities. Food and Agriculture Organization of the United Nations, Rome
Fischer MC, Rellstab C, Leuzinger M et al (2017) Estimating genomic diversity and population differentiation—an empirical comparison of microsatellite and SNP variation in Arabidopsis halleri. Bmc Genomics. https://doi.org/10.1186/s12864-016-3459-7
Frankham R, Bradshaw CJA, Brook BW (2014) Genetics in conservation management: revised recommendations for the 50/500 rules, Red List criteria and population viability analyses. Biol Conserv 170:56–63. https://doi.org/10.1016/j.biocon.2013.12.036
Gibson L, Lee TM, Koh LP et al (2011) Primary forests are irreplaceable for sustaining tropical biodiversity. Nature 478:378–381. https://doi.org/10.1038/Nature10425
Gonzalez-Martinez SC, Krutovsky KV, Neale DB (2006) Forest-tree population genomics and adaptive evolution. New Phytol 170:227–238. https://doi.org/10.1111/j.1469-8137.2006.01686.x
Graudal L, Yanshuk A, Kjaer ED (2004) National Planning. In: FAO, FLD, IPGRI (ed) Forest genetic resources: conservation and management. Vol 1: Overview, concepts and some systematic approaches. International Plant Genetic Resources Institute, Rome, pp 25–36
GW (2015) The cost of luxury: Cambodia´s illegal trade in precious wood with China. Global Witness, London, UK
Hansen MC, Potapov PV, Moore R et al (2013) High-resolution global maps of 21st-century forest cover change. Science 342:850–853. https://doi.org/10.1126/science.1244693
Hansen/UMD/Google/USGS/NASA (2018) Global Forest Change 2000–2016
Hartvig I, Czako M, Kjaer ED, Nielsen LR, Theilade I (2015) The use of DNA barcoding in identification and conservation of rosewood (Dalbergia spp.). Plos ONE. https://doi.org/10.1371/journal.pone.0138231
Hartvig I, So T, Changtragoon S et al (2018) Population genetic structure of the endemic rosewoods Dalbergia cochinchinensis and D. oliveri at a regional scale reflects the Indochinese landscape and life-history traits. Ecol Evol 8:530–545. https://doi.org/10.1002/ece3.3626
Hiremath SC, Nagasampige MH (2004) Genome size variation and evolution in some species of Dalbergia Linn.f. (Fabaceae). Caryologia 57:367–372. https://doi.org/10.1080/00087114.2004.10589418
Hodel RDGJ, Segovia-Salcedo MC, Landis JB et al (2016) The report of my death was an exaggeration: a review for researchers using microsatellites in the 21st century. Appl Plant Sci. https://doi.org/10.3732/apps.1600025
Houston RD, Davey JW, Bishop SC et al (2012) Characterisation of QTL-linked and genome-wide restriction site-associated DNA (RAD) markers in farmed Atlantic salmon. Bmc Genomics. https://doi.org/10.1186/1471-2164-13-244
Jakobsson M, Rosenberg NA (2007) CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23:1801–1806. https://doi.org/10.1093/bioinformatics/btm233
Jardine DI, Blanc-Jolivet C, Dixon RRM et al (2016) Development of SNP markers for Ayous (Triplochiton scleroxylon K. Schum) an economically important tree species from tropical West and Central Africa. Conserv Genet Resour 8:129–139. https://doi.org/10.1007/s12686-016-0529-8
Jolivet C, Degen B (2012) Use of DNA fingerprints to control the origin of sapelli timber (Entandrophragma cylindricum) at the forest concession level in Cameroon. Forensic Sci Int-Genet 6:487–493. https://doi.org/10.1016/j.fsigen.2011.11.002
Jombart T, Ahmed I (2011) adegenet 1.3-1: new tools for the analysis of genome-wide SNP data. Bioinformatics 27:3070–3071. https://doi.org/10.1093/bioinformatics/btr521
Jombart T, Devillard S, Balloux F (2010) Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. BMC Genet. https://doi.org/10.1186/1471-2156-11-94
Kammesheidt L (1999) Forest recovery by root suckers and above-ground sprouts after slash-and-burn agriculture, fire and logging in Paraguay and Venezuela. J Trop Ecol 15:143–157. https://doi.org/10.1017/S0266467499000723
Kjaer ED, Graudal L, Nathan I (2001) Ex situ conservation of genetic resources of commercial tropical tree species. In: Theilges BA, Sastrapradja SD, Rimbawanto A (eds) In situ and ex situ conservation of commercial tropical trees. Gadjah Mada University, Yogyakarta, pp 127–146
Korneliussen TS, Albrechtsen A, Nielsen R (2014) ANGSD: analysis of next generation sequencing data. BMC Bioinform. https://doi.org/10.1186/s12859-014-0356-4
Li H, Handsaker B, Wysoker A et al (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25:2078–2079. https://doi.org/10.1093/bioinformatics/btp352
Lowe AJ, Cross HB (2011) The application of DNA methods to timber tracking and origin verification. Iawa J 32:251–262
Lowe AJ, Boshier D, Ward M, Bacles CFE, Navarro C (2005) Genetic resource impacts of habitat loss and degradation; reconciling empirical evidence and predicted theory for neotropical trees. Heredity 95:255–273. https://doi.org/10.1038/sj.hdy.6800725
Mantel N (1967) Detection of disease clustering and a generalized regression approach. Cancer Res 27:209–220
Moritsuka E, Chhang P, Tagane S et al (2017) Genetic variation and population structure of a threatened timber tree Dalbergia cochinchinensis in Cambodia. Tree Genet Genomes. https://doi.org/10.1007/s11295-017-1199-8
Mostacedo B, Putz FE, Fredericksen TS, Villca A, Palacios T (2009) Contributions of root and stump sprouts to natural regeneration of a logged tropical dry forest in Bolivia. For Ecol Manag 258:978–985. https://doi.org/10.1016/j.foreco.2008.09.059
Nepstad D, Schwartzman S, Bamberger B et al (2006) Inhibition of Amazon deforestation and fire by parks and indigenous lands. Conserv Biol 20:65–73. https://doi.org/10.1111/j.1523-1739.2006.00351.x
Newton AC, Oldfield S (2008) Red Listing the world´s tree species: a review of recent progress. Endanger Species Res 6:137–147
Niyomdham C, Hô PH, Dy Phon P, Vidal JE (1997) Leguminoseae-Papilionoideae Dalbergieae. In: Morat P (ed) Flore du Cambodge du Laos et du Viêtnam. Muséum National d’Histoire Naturelle, Paris
ODC (2017) Natural Protected Areas in Cambodia (1993-2017). Open Development Cambodia, Phnom Penh, Cambodia https://opendevelopmentcambodia.net/
Ogden R, Dawney N, McEwing R (2009) Wildlife DNA forensics—bridging the gap between conservation genetics and law enforcements. Endanger Species Res 9:179–195
Ouborg NJ, Pertoldi C, Loeschcke V, Bijlsma R, Hedrick PW (2010) Conservation genetics in transition to conservation genomics. Trends Genet 26:177–187. https://doi.org/10.1016/j.tig.2010.01.001
Pakull B, Mader M, Kersten B et al (2016) Development of nuclear, chloroplast and mitochondrial SNP markers for Khaya sp. Conserv Genet Resour 8:283–297. https://doi.org/10.1007/s12686-016-0557-4
Palsboll PJ, Berube M, Allendorf FW (2007) Identification of management units using population genetic data. Trends Ecol Evol 22:11–16. https://doi.org/10.1016/j.tree.2006.09.003
Paradis E (2010) pegas: an R package for population genetics with an integrated-modular approach. Bioinformatics 26:419–420. https://doi.org/10.1093/bioinformatics/btp696
Parchman TL, Jahner JP, Uckele KA, Galland LM, Eckert AJ (2018) RADseq approaches and applications for forest tree genetics. Tree Genet Genomes. https://doi.org/10.1007/s11295-018-1251-3
Peakall R, Smouse PE (2006) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6:288–295. https://doi.org/10.1111/j.1471-8286.2005.01155.x
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. https://doi.org/10.1093/bioinformatics/bts460
Piry S, Alapetite A, Cornuet JM et al (2004) GENECLASS2: a software for genetic assignment and first-generation migrant detection. J Hered 95:536–539. https://doi.org/10.1093/jhered/esh074
Porter-Bolland L, Ellis EA, Guariguata MR et al (2012) Community managed forests and forest protected areas: an assessment of their conservation effectiveness across the tropics. For Ecol Manag 268:6–17. https://doi.org/10.1016/j.foreco.2011.05.034
Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959
Rannala B, Mountain JL (1997) Detecting immigration by using multilocus genotypes. Proc Natl Acad Sci USA 94:9197–9201. https://doi.org/10.1073/pnas.94.17.9197
Ravindran PN, Bentzen P, Bradbury IR, Beiko RG (2018) PMERGE: computational filtering of paralogous sequences from RAD-seq data. Ecol Evol 8:7002–7013. https://doi.org/10.1002/ece3.4219
Rognes T, Flouri T, Nichols B, Quince C, Mahe F (2016) VSEARCH: a versatile open source tool for metagenomics. Peerj. https://doi.org/10.7717/peerj.2584
Schleicher J, Peres CA, Amano T, Llactayo W, Leader-Williams N (2017) Conservation performance of different conservation governance regimes in the Peruvian Amazon. Sci Rep. https://doi.org/10.1038/s41598-017-10736-w
Schubert M, Ermini L, Sarkissian CD et al (2014) Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX. Nat Protoc 9:1056–1082. https://doi.org/10.1038/nprot.2014.063
Schubert M, Lindgreen S, Orlando L (2016) AdapterRemoval v2: rapid adapter trimming, identification, and read merging. BMC Res Notes. https://doi.org/10.1186/s13104-016-1900-2
Siriwat P, Nijman V (2018) Using online media-sourced seizure data to assess the illegal wildlife trade in Siamese rosewood. Environ Conserv 45:352–360. https://doi.org/10.1017/S037689291800005x
So NV (2000) The potential of local tree species to accelerate natural forest succesion on marginal grasslands in Southern Vietnam. In: Elliot S, Kerby J, Blakesly K et al (eds) Proceedings of the workshop on forest restoration for wildlife conservation. International Tropical Timber Organization and The Forest Restoration Unit, Chiang Mai University, Chiang Mai
So T, Theilade I, Dell B (2010) Conservation and utilization of threatened hardwood species through reforestation—an example of Afzelia xylocarpa (Kruz.) Craib and Dalbergia cochinchinensis Pierre in Cambodia. Pac Conserv Biol 16:110–116
Theilade I, Yanshuk A, Hald S (2004) Establishment and management of ex situ conservation stands In: FAO/FLD/IPGRI (ed) Forest genetic resources conservation and management. Vol 3: In plantations and genebanks (ex situ). International Plant Genetic Resources Institute, Rome
UNEP-WCMC, IUCN (2018) Protected planet: the world database on protected areas (WDPA). UNEP-WCMC and IUCN, Cambridge
Verdu CF, Guichoux E, Quevauvillers S et al (2016) Dealing with paralogy in RADseq data: in silico detection and single nucleotide polymorphism validation in Robinia pseudoacacia L. Ecol Evol 6:7323–7333. https://doi.org/10.1002/ece3.2466
Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population-structure. Evolution 38:1358–1370. https://doi.org/10.2307/2408641
Young A, Boyle T, Brown T (1996) The population genetic consequences of habitat fragmentation for plants. Trends Ecol Evol 11:413–418. https://doi.org/10.1016/0169-5347(96)10045-8
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This work was supported by DANIDA grant no 11073-LIFE and IH was funded by a PhD scholarship from University of Copenhagen.
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Study concept and design: IH, ST, SC, HTT, SB, RO, HS, IT, LRN, EDK. RAD sequencing design: IH, RO, FT, RT. Bioinformatics: HS, FGV. SNP genotyping: IH. Analysis and interpretation of data: IH, EDK, LRN. Drafting of manuscript: IH, IT, LRN, EDK Critical revision: IH, ST, SC, HTT, SB, RO, HS, FGV, FT, RT, IT, LRN, EDK.
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Hartvig, I., So, T., Changtragoon, S. et al. Conservation genetics of the critically endangered Siamese rosewood (Dalbergia cochinchinensis): recommendations for management and sustainable use. Conserv Genet 21, 677–692 (2020). https://doi.org/10.1007/s10592-020-01279-1
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DOI: https://doi.org/10.1007/s10592-020-01279-1