Abstract
The present study was conducted to understand the key ecological and biological questions of conservation importance in Drepanostachyum falcatum which aimed to map potential distribution in the western Himalayas and decipher spatial genetic structure. Eco-distribution maps were generated through ecological niche modelling using the Maximum Entropy (MaxEnt) algorithm implemented with 228 geocoordinates of species presence and 12 bioclimatic variables. Concomitantly, 26 natural populations in the western Himalayas were genetically analysed using ten genomic sequence-tagged microsatellite (STMS) markers. Model-derived distribution was adequately supported with appropriate statistical measures, such as area under the ‘receiver operating characteristics (ROC)’ curve (AUC; 0.917 ± 0.034)”, Kappa (K; 0.418), normalized mutual information (NMI; 0.673) and true skill statistic (TSS; 0.715). Further, Jackknife test and response curves showed that the precipitation (pre- and post-monsoon) and temperature (average throughout the year and pre-monsoon) maximize the probabilistic distribution of D. falcatum. We recorded a wide and abundant (4096.86 km2) distribution of D. falcatum in the western Himalayas with maximum occurrence at 1500 to 2500 m asl. Furthermore, marker analysis exemplified high gene diversity with low genetic differentiation in D. falcatum. Relatively, the populations of Uttarakhand are more genetically diverse than Himachal Pradesh, whereas within the Uttarakhand, the Garhwal region captured a higher allelic diversity than Kumaon. Clustering and structure analysis indicated two major gene pools, where genetic admixing appeared to be controlled by long-distance gene flow, horizontal geographical distance, aspect, and precipitation. Both the species distribution map and population genetic structure derived herein may serve as valuable resources for conservation and management of Himalayan hill bamboos.
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References
Allouche O, Tsoar A, Kadmon R (2006) Assessing the accuracy of species distribution models: prevalence, kappa and the true skill statistic (TSS). J Appl Ecol 43:1223–1232. https://doi.org/10.1111/j.1365-2664.2006.01214.x
Arnfield AJ (2022) Köppen climate classification. Encyclopedia Britannica. https://www.britannica.com/science/Koppen-climate-classification
Attigala L, Gallaher T, Nason J, et al. (2017) Genetic diversity and population structure of the threatened temperate woody bamboo Kuruna debilis (Poaceae: Bambusoideae: Arundinarieae) from Sri Lanka based on microsatellite analysis. J Natl Sci Found Sri 45:53. https://doi.org/10.4038/jnsfsr.v45i1.8038
Baldeck CA, Harms KE, Yavitt JB, et al. (2013) Soil resources and topography shape local tree community structure in tropical forests. Proc R Soc B Biol Sci 280:323–326. https://doi.org/10.1098/rspb.2012.2532
Banik RL (2016) Silviculture of South Asian Priority Bamboos. Springer, Singapore
Barros MJF, Diniz-Filho JAF, Freitas LB (2018) Ecological drivers of plant genetic diversity at the southern edge of geographical distributions: Forestal vines in a temperate region. Genet Mol Biol 41: 318–326. https://doi.org/10.1590/1678-4685-GMB-2017-0031
Beck HE, Zimmermann NE, McVicar TR, et al. (2018) Present and future Köppen-Geiger climate classification maps at 1-km resolution. Sci Data 5:180–214. https://doi.org/10.6084/m9.figshare.6396959
Beerli P, Felsenstein J (2001) Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach. Proc Natl Acad Sci 98:4563–4568. https://doi.org/10.1073/pnas.081068098
Bhandawat A, Sharma V, Singh P, et al. (2019) Discovery and utilization of EST-SSR marker resource for genetic diversity and population structure analyses of a subtropical bamboo, Dendrocalamus hamiltonii. Biochem Genet 57: 652–672. https://doi.org/10.1007/s10528-019-09914-4.
Chiocchini F, Mattioni C, Pollegioni et al. (2016) Map** the genetic diversity of Castanea sativa: exploiting spatial analysis for biogeography and conservation studies. J Geogr Inf Syst 8:248. https://doi.org/10.4236/jgis.2016.82022.
De Kort H, Prunier JG, Ducatez S, et al. (2021) Life history, climate and biogeography interactively affect worldwide genetic diversity of plant and animal populations. Nat Commun 12:516. https://doi.org/10.1038/s41467-021-20958-2
Desai P, Gajera B, Mankad M, et al. (2015) Comparative assessment of genetic diversity among indian bamboo genotypes using RAPD and ISSR markers. Mol Biol Rep 42:1265–1273. https://doi.org/10.1007/s11033-015-3867-9
DeSalle R, Amato G (2004) The expansion of conservation genetics. Nat Rev Genet 5:702–712. https://doi.org/10.1038/nrg1425
Dida JJV, Araza AB, Eduarte GT, et al. (2021) Towards nationwide map** of bamboo resources in the Philippines: testing the pixel-based and fractional cover approaches. Int J Remote Sens 2:3380–3404. https://doi.org/10.1080/01431161.2020.1871099
Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf material. Environ Conserv 19:11–15.
Du H, Fangjie F, Li X, et al. (2018) Map** global bamboo forest distribution using multisource remote sensing data. IEEE J Sel Top Appl Earth Obs Remote Sens 11:1458–1471. https://doi.org/10.1109/JSTARS.2018.2800127
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
Eckert CG, Samis KE, Lougheed SC (2008) Genetic variation across species geographical ranges: the central – marginal hypothesis and beyond. Mol Ecol 17:1170–1188. https://doi.org/10.1111/j.1365-294X.2007.03659.x
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
Fielding AH, Bell JF (1997) A review of methods for the assessment of prediction errors in conservation presence/absence models. Environ Conserv 24:38–49. https://doi.org/10.1017/S0376892997000088
Garcia-Verdugo C, Calleja JA, Vargas P, et al. (2013) Polyploidy and microsatellite variation in the relict tree Prunus lusitanica L.: how effective are refugia in preserving genotypic diversity of clonal taxa? Mol Ecol 22:1546–1557. https://doi.org/10.1111/mec.12194
Guisan A, Zimmermann NE (2000) Predictive habitat distribution models in ecology. Ecol Model 135:147–186. https://doi.org/10.1016/S0304-3800(00)00354-9
Guo ZH, Ma PF, Yang GQ, et al. (2019) Genome sequences provide insights into the reticulate origin and unique traits of woody bamboos. Mol Plant 12:1353–1365. https://doi.org/10.1016/j.molp.2019.05.009
Hamrick JL, Godt MJW, Sherman-Broyles SL (1992) Factors influencing levels of genetic diversity in woody plant species. New For 6:95–124. https://doi.org/10.1007/BF00120641
Hengl T (2009) A practical guide to geostatistical map**. University of Amsterdam, Amsterdam, pp 1–26. http://spatial-analyst.net/book/
Huang L, **ng XC, Li WW, et al. (2021) Population genetic structure of the giant panda staple food bamboo (Fargesia spathacea complex) and its taxonomic implications. J Syst Evol 59:1051–1064. https://doi.org/10.1111/jse.12594
ICFRE (2017) Bamboo conservation, management and utilisation: a status report. Indian Council of Forestry Research and Education, Dehradun
ISFR (2019) India state of forest report. Forest Survey of India (Ministry of Environment Forests and Climate Change, New Delhi), Dehradun
Jiang W, Bai T, Dai H, et al. (2017) Microsatellite markers revealed moderate genetic diversity and population differentiation of moso bamboo (Phyllostachys edulis)—a primarily asexual reproduction species in China. Tree Genet Genomes 13. doi:https://doi.org/10.1007/s11295-017-1212-2
Jones AG, Ardren WR (2003) Methods of parentage analysis in natural populations. Mol Ecol 12:2511–23. https://doi.org/10.1046/j.1365-294x.2003.01928.x
Kalinowski ST (2005) HP-Rare: a computer program for performing rarefaction on measures of allelic diversity. Mol Ecol Notes 5:187–189. https://doi.org/10.1111/J.1471-8286.2004.00845.X
Kelchner SA, Bamboo Phylogeny Group (2013) Higher level phylogenetic relationships within the bamboos (Poaceae: Bambusoideae) based on five plastid markers. Mol Phylogenet Evol 67:404–413. https://doi.org/10.1016/j.ympev.2013.02.005
Kottek MJ, Grieser C, Beck B, et al. (2006) World Map of the Köppen-Geiger climate classification updated. Meteorol Z 15:259–263. https://doi.org/10.1127/0941-2948/2006/0130
Krizman M, Jakse J, Baricevic D, et al. (2006) Robust CTAB-activated charcoal protocol for plant DNA extraction. Acta Agric Slov 87:427–433
Landis JR, Koch GC (1977) The measurement of observer agreement for categorical data. Biometrics 33:159–174. https://doi.org/10.2307/2529310
Lesica P, Allendorf FW (1995) “When are peripheral populations Valuable for Conservation?” Conserv Biol 9:753–760. https://doi.org/10.1046/j.1523-1739.1995.09040753.x
Liu K, Muse SV (2005) PowerMarker: integrted analysis environment for genetic marker data. Bioinformatics 21:2128–2129. https://doi.org/10.1093/bioinformatics/bti282
Lobovikov M, Ball L, Guardia M, et al. (2007) World bamboo resources: a thematic study prepared in the framework of the Global Forest Resources Assessment 2005. FAO, Rome
Luo MX, Lu HP, Chai MW, et al. (2021) Environmental heterogeneity leads to spatial differences in genetic diversity and demographic structure of Acer caudatifolium. Plants (Basel) 10:1646. https://doi.org/10.3390/plants10081646
Manel S, Schwartz MK, Luikart G. et al. (2003) Landscape genetics: combining landscape ecology and population genetics. Trends Ecol Evol 18:189–197. https://doi.org/10.1016/s0169-5347(03)00008-9
Mantel N (1967) The detection of disease clustering and a generalized regression approach. Cancer Res 27:209–220
Matschiner M, Salzburger W (2009) TANDEM: integrating automated allele binning into genetics and genomics workflows. Bioinformatics 25: 1982–1983. https://pubmed.ncbi.nlm.nih.gov/19420055/
McDermott JM, McDonald BA (1993) Gene flow in plant pathosystems. Annu Rev Phytopathol 31:353–373.
Meena RK, Bhandhari MS, Barhwal S, et al. (2019) Genetic diversity and structure of Dendrocalamus hamiltonii natural metapopulation: a commercially important bamboo species of northeast Himalayas. 3 Biotech 9:60. https://doi.org/10.1007/s13205-019-1591-1
Meena RK, Negi N, Uniyal N, et al. (2021) Genome skimming based STMS marker discovery and its validation in temperate hill bamboo, Drepanostachyum falcatum. J Genet 100:28. https://doi.org/10.1007/s12041-021-01273-7
Naithani HB, Chandra S (1998) Gregarious flowering of bamboo (Drepanostachyum falcatum). Indian Forester 124:663–666
Pandey M, Rajora OP (2012) Genetic diversity and differentiation of core vs. peripheral populations of eastern white cedar, Thuja occidentalis (cupressaceae). Am J Bot 99:690–699. http://www.amjbot.org/
Peakall R, Smouse PE (2012) GenAlEx 6.5: genetic analysis in Excel. Population genetics software for teaching and research-an update. Bioinformatics 28:2537–2539. https://doi.org/10.1093/bioinformatics/bts460
Peel MC, Finlayson BL, McMahon TA (2007) Updated world map of the Köppen-Geiger climate classification. Hydrol Earth Syst Sci 11:1633–1644. https://doi.org/10.5194/hess-11-1633-2007
Pérez-Alquicira J, Aguilera-López S, Rico Y, Ruiz-Sanchez E (2021) A population genetics study of three native mexican woody bamboo species of Guadua (Poaceae: Bambusoideae: Bambuseae: Guaduinae) using nuclear microsatellite markers. Bot Sci 99:542–559. https://doi.org/10.17129/botsci.2795
Pfeiffer T, Roschanski AM, Pannell JR, et al. (2011) Characterization of microsatellite loci and reliable genoty** in a polyploid plant, Mercurialis perennis (Euphorbiaceae). J Hered 102:479–88. https://doi.org/10.1093/jhered/esr024
Phillips SJ, Anderson RP, Schapire RE (2006) Maximum entropy modelling of species geographic distributions. Ecol Modell 190:231–259. https://doi.org/10.1016/j.ecolmodel.2005.03.026
Porth I, El-Kassaby YA (2014) Assessment of the genetic diversity in forest tree populations using molecular markers. Diversity 6:283–295. https://doi.org/10.3390/d6020283
Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959. https://doi.org/10.1093/genetics/155.2.945
Rocchini D, Hortal J, Lengyel S, et al. (2011) Accounting for uncertainty when map** species distributions: the need for maps of ignorance. Prog Phys Geogr 35:211–226. https://doi.org/10.1177/0309133311399491
Sampson JF, Byrne M (2012) Genetic diversity and multiple origins of polyploid Atriplex nummularia Lindl. (Chenopodiaceae). Biol J Linn Soc 105:218–230. https://doi.org/10.1111/j.1095-8312.2011.01787.x
Shepard D (1968) A two-dimensional interpolation function for irregularly-spaced data. In: Proceedings of the 1968 ACM National Conference, pp 517–524
Stift M, Berenos C, Kuperus P, et al. (2008) Segregation models for disomic, tetrasomic and intermediate inheritance in tetraploids: a general procedure applied to Rorippa (yellow cress) microsatellite data. Genetics 179:2113–2123. https://doi.org/10.1534/genetics.107.085027
Swets JA (1988) Measuring the accuracy of diagnostic systems. Science 240:285–1293. https://doi.org/10.1126/science.3287615
Thakur A, Barthwal S, Ginwal HS (2015) Genetic diversity in bamboos: conservation and improvement for productivity. In: Kaushik S, Singh YP, Kumar D, et al. (eds) Bamboos in India. ENVIS Centre on Forestry, Dehradun, pp 131–146
Triplett JK, Clark LG, Fisher AE, et al. (2014) Independent allopolyploidization events preceded speciation in the temperate and tropical woody bamboos. New Phytol 204:66–73. https://doi.org/10.1111/nph.12988
Tuanmua M, Viña A, Bearer S, et al. (2010) Map** understory vegetation using phenological characteristics derived from remotely sensed data. Remote Sens Environ 114:1833–1844. https://doi.org/10.1016/j.rse.2010.03.008
Van Oosterhout C, Hutchinson WF, Wills DPM, et al. (2004) MICRO-CHECKER: software for identifying and correcting genoty** errors in microsatellite data. Mol Ecol Notes 4:535–538. https://doi.org/10.1111/j.1471-8286.2004.00684.x
Vieira JP, Schnadelbach AS, Hughes FM, et al. (2019) Ecological niche modelling and genetic diversity of Anomochloa marantoidea (Poaceae): filling the gaps for conservation in the earliest-diverging grass subfamily. Bot J Linn Soc 192:258–280. https://doi.org/10.1093/botlinnean/boz039
Woodward FI, Williams BG (1987) Climate and plant distribution at global and local scales. Vegetatio 69:189–197. https://doi.org/10.1007/BF00038700
Yang JB, Dong YR, Wong KM, et al. (2018) Genetic structure and differentiation in Dendrocalamus sinicus (Poaceae: Bambusoideae) populations provide insight into evolutionary history and speciation of woody bamboos. Sci Rep 8:16933. https://doi.org/10.1038/s41598-018-35269-8.
Yebeyen D, Nemomissa S, Hailu BT, et al. (2022) Modeling and map** habitat suitability of highland bamboo under climate change in Ethiopia. Forests 13:859. https://doi.org/10.3390/f13060859
Zhang C, Li X, Chen L, et al. (2016). Effects of topographical and edaphic factors on tree community structure and diversity of subtropical mountain forests in the Lower Lancang River Basin. Forests 7: 222; https://doi.org/10.3390/f7100222
Zhang M, Gong P, Qi S, et al. (2019) Map** bamboo with regional phenological characteristics derived from dense landsat time series using Google Earth Engine. Int J Remote Sen 40:9541–9555. https://doi.org/10.1080/01431161.2019.1633702
Zheng X, Lin S, Fu H, et al. (2020) The bamboo flowering cycle sheds light on flowering diversity. Front Plant Sci 11:381. https://doi.org/10.3389/fpls.2020.00381
Acknowledgements
We thank the Director, Forest Research Institute, Dehradun and the Director, Himalayan Forest Research Institute, Shimla for providing laboratory and field facilities. The officials of state forest departments of Uttarakhand and Himachal Pradesh are also duly acknowledged for their assistance and permissions in surveying and sample collection from their jurisdictional forest area.
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The work was financially supported by Indian Council of Forestry Research and Education (ICFRE), Dehradun as a research project [OG-49/CR-19].
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RKM, MSB and RS (Rajesh Sharma) conceptualized the problem and perform the task of field sampling, data analysis and interpretation, and preparation of draft manuscript. NN and NK performed field as well as laboratory work for population genetic analysis. RS (Rajeev Shankhwar) carried out geo-spatial analysis. RK, SP and HSG contributed in manuscript editing.
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Meena, R.K., Negi, N., Shankhwar, R. et al. Ecological niche modelling and population genetic analysis of Indian temperate bamboo Drepanostachyum falcatum in the western Himalayas. J Plant Res 136, 483–499 (2023). https://doi.org/10.1007/s10265-023-01465-5
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DOI: https://doi.org/10.1007/s10265-023-01465-5