Species distribution modelling and population genetic analysis of Yushania anceps; an endemic temperate woody bamboo of the Uttarakhand Himalayas

Yushania anceps is a temperate woody bamboo taxon of high socio-economic importance occurring in the sub-alpine zone of the western Himalayas. This study was carried out to delineate the potential distribution of Y. anceps in the western Himalayas through species distribution modelling (SDM), and genetic characterization using sequence-tagged microsatellite (STMS) markers. The present study revealed an endemic distribution of this species in the Uttarakhand Himalayas, with an estimated area of 211.59 km2. The maximum probability of occurrence was recorded in the moderately dense forests between the altitudinal ranges of 2500 and 2700 m. The model output was well supported with high values of different statistical measures, such as the AUC (0.911) and Kappa coefficient (K = 0.513). Environmental variables related to precipitation, temperature and topography were identified as the most contributory in current SDM. In addition, diversity measures, namely allelic richness (Ar), expected heterozygosity (He), and fixation index (FST), were calculated in five sampled populations with eight STMS markers, which indicated high genetic diversity (Ar = 4.24; He = 0.689) and little differentiation (FST = 0.062). The diversity maps displayed that the populations located in the Kumaon region captured relatively more genetic diversity than the Garhwal region. Further, genetic clustering and STRUCTURE analysis revealed a substantial level of genetic admixing across the analysed populations, and as a result, no sub-structuring was detected. Due to the rare and endemic distribution of Y. anceps, it requires immediate conservation measures, and the knowledge base generated here will be of paramount importance to forest managers, researchers and policymakers.

[1]  S. Pandey,et al.  Ecological niche modelling and population genetic analysis of Indian temperate bamboo Drepanostachyum falcatum in the western Himalayas , 2023, Journal of Plant Research.

[2]  J. Franklin.  Species distribution modelling supports the study of past, present and future biogeographies , 2023, Journal of Biogeography.

[3]  G. Sileshi,et al.  Modeling and Mapping Habitat Suitability of Highland Bamboo under Climate Change in Ethiopia , 2022, Forests.

[4]  Yessica Rico,et al.  A population genetics study of three native Mexican woody bamboo species of Guadua (Poaceae: Bambusoideae: Bambuseae: Guaduinae) using nuclear microsatellite markers , 2021 .

[5]  M. Bhandari,et al.  Genome skimming-based STMS marker discovery and its validation in temperate hill bamboo Drepanostachyum falcatum , 2021, Journal of Genetics.

[6]  M. Hyder,et al.  Genetic diversity, population structure, and gene flow analysis of lowland bamboo [Oxytenanthera abyssinica (A. Rich.) Munro] in Ethiopia , 2020, Ecology and evolution.

[7]  Yun Zhou,et al.  Population genetic structure of the giant panda staple food bamboo (Fargesia spathacea complex) and its taxonomic implications , 2020, Journal of Systematics and Evolution.

[8]  H. Preisler,et al.  Precipitation is the most crucial factor determining the distribution of moso bamboo in Mainland China , 2020, Global Ecology and Conservation.

[9]  Yulong Ding,et al.  The Bamboo Flowering Cycle Sheds Light on Flowering Diversity , 2020, Frontiers in Plant Science.

[10]  N. Xie,et al.  Mixed mating system and variable mating patterns in tropical woody bamboos , 2019, BMC Plant Biology.

[11]  De‐Zhu Li,et al.  Rapid diversification of alpine bamboos associated with the uplift of the Hengduan Mountains , 2019, Journal of Biogeography.

[12]  J. Kaur,et al.  Discovery and Utilization of EST-SSR Marker Resource for Genetic Diversity and Population Structure Analyses of a Subtropical Bamboo, Dendrocalamus hamiltonii , 2019, Biochemical Genetics.

[13]  R. Meena,et al.  Genetic diversity and structure of Dendrocalamus hamiltonii natural metapopulation: a commercially important bamboo species of northeast Himalayas , 2019, 3 Biotech.

[14]  De‐Zhu Li,et al.  Genetic structure and differentiation in Dendrocalamus sinicus (Poaceae: Bambusoideae) populations provide insight into evolutionary history and speciation of woody bamboos , 2018, Scientific Reports.

[15]  Wenju Zhang,et al.  Microsatellite markers revealed moderate genetic diversity and population differentiation of moso bamboo (Phyllostachys edulis)—a primarily asexual reproduction species in China , 2017, Tree Genetics & Genomes.

[16]  De-Zhu Li,et al.  Breeding system and pollination of two closely related bamboo species , 2017, AoB PLANTS.

[17]  Timothy J. Gallaher,et al.  Genetic diversity and population structure of the threatened temperate woody bamboo Kuruna debilis (Poaceae: Bambusoideae: Arundinarieae) from Sri Lanka based on microsatellite analysis , 2017 .

[18]  Hamidur Rahaman,et al.  ISSR Marker Based Population Genetic Study of Melocanna baccifera (Roxb.) Kurz: A Commercially Important Bamboo of Manipur, North-East India , 2017, Scientifica.

[19]  D. Richardson,et al.  The global distribution of bamboos: assessing correlates of introduction and invasion , 2016, AoB PLANTS.

[20]  M. Lauteri,et al.  Mapping the Genetic Diversity of Castanea sativa: Exploiting Spatial Analysis for Biogeography and Conservation Studies , 2016 .

[21]  Vikas Sharma,et al.  Development and crosstransferability of functionally relevant microsatellite markers in Dendrocalamus latiflorus and related bamboo species , 2015, Journal of Genetics.

[22]  Y. El-Kassaby,et al.  Assessment of the Genetic Diversity in Forest Tree Populations Using Molecular Markers , 2014 .

[23]  Wan-qin Yang,et al.  Genetic Structure in Dwarf Bamboo (Bashania fangiana) Clonal Populations with Different Genet Ages , 2013, PloS one.

[24]  P. Roy,et al.  Maxent modeling for predicting the potential distribution of medicinal plant, Justicia adhatoda L. in Lesser Himalayan foothills , 2013 .

[25]  Rod Peakall,et al.  GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research—an update , 2012, Bioinform..

[26]  Sunil Kumar,et al.  Environmental conditions associated with bat white‐nose syndrome mortality in the north‐eastern United States , 2012 .

[27]  Han-Qi Yang,et al.  Genetic Diversity and Differentiation of Dendrocalamus membranaceus (Poaceae: Bambusoideae), a Declining Bamboo Species in Yunnan, China, as Based on Inter-Simple Sequence Repeat (ISSR) Analysis , 2012, International journal of molecular sciences.

[28]  Matthew E. Watts,et al.  Conservation planning under climate change : Toward accounting for uncertainty in predicted species distributions to increase confidence in conservation investments in space and time , 2011 .

[29]  J. Pannell,et al.  Characterization of microsatellite loci and reliable genotyping in a polyploid plant, Mercurialis perennis (Euphorbiaceae). , 2011, The Journal of heredity.

[30]  C. Ricotta,et al.  Accounting for uncertainty when mapping species distributions: The need for maps of ignorance , 2011 .

[31]  Trevor Hastie,et al.  A statistical explanation of MaxEnt for ecologists , 2011 .

[32]  Antoine Guisan,et al.  Overcoming the rare species modelling paradox: a novel hierarchical framework applied to an Iberian endemic plant. , 2010 .

[33]  M. Nei,et al.  POPTREE2: Software for constructing population trees from allele frequency data and computing other population statistics with Windows interface. , 2010, Molecular biology and evolution.

[34]  Michael Matschiner,et al.  TANDEM: integrating automated allele binning into genetics and genomics workflows , 2009, Bioinform..

[35]  B. Benito,et al.  Assessing extinction-risk of endangered plants using species distribution models: a case study of habitat depletion caused by the spread of greenhouses , 2009, Biodiversity and Conservation.

[36]  J. Elith,et al.  Species Distribution Models: Ecological Explanation and Prediction Across Space and Time , 2009 .

[37]  A. Estoup,et al.  Microsatellite null alleles and estimation of population differentiation. , 2007, Molecular biology and evolution.

[38]  Omri Allouche,et al.  Assessing the accuracy of species distribution models: prevalence, kappa and the true skill statistic (TSS) , 2006 .

[39]  B. Javornik,et al.  Robust CTAB-activated charcoal protocol for plant DNA extraction , 2006, Acta agriculturae Slovenica.

[40]  B. Rudolf,et al.  World Map of the Köppen-Geiger climate classification updated , 2006 .

[41]  A. Lehmann,et al.  Using Niche‐Based Models to Improve the Sampling of Rare Species , 2006, Conservation biology : the journal of the Society for Conservation Biology.

[42]  Robert P. Anderson,et al.  Maximum entropy modeling of species geographic distributions , 2006 .

[43]  D. Richardson,et al.  Niche‐based modelling as a tool for predicting the risk of alien plant invasions at a global scale , 2005, Global change biology.

[44]  Kejun Liu,et al.  PowerMarker: an integrated analysis environment for genetic marker analysis , 2005, Bioinform..

[45]  S. Kalinowski.  hp-rare 1.0: a computer program for performing rarefaction on measures of allelic richness , 2005 .

[46]  S. Schneider,et al.  Arlequin (version 3.0): An integrated software package for population genetics data analysis , 2005, Evolutionary bioinformatics online.

[47]  Miroslav Dudík,et al.  A maximum entropy approach to species distribution modeling , 2004, ICML.

[48]  P. Donnelly,et al.  Inference of population structure using multilocus genotype data. , 2000, Genetics.

[49]  J. L. Gittleman,et al.  The Future of Biodiversity , 1995, Science.

[50]  J A Swets,et al.  Measuring the accuracy of diagnostic systems. , 1988, Science.

[51]  N. Mantel.  The detection of disease clustering and a generalized regression approach. , 1967, Cancer research.

[52]  A. E. Osmaston.  Notes on the Forest Communities of the Garhwal Himalaya , 1922 .

[53]  Theunis Piersma,et al.  The interplay between habitat availability and population differentiation , 2012 .

[54]  Vikas Sharma,et al.  AFLP and RAPD based genetic diversity assessment of industrially important reed bamboo (Ochlandra travancorica Benth) , 2012, Journal of Plant Biochemistry and Biotechnology.

[55]  Published online in Wiley InterScience (www.interscience.wiley.com). DOI: 10.1002/joc.1276 VERY HIGH RESOLUTION INTERPOLATED CLIMATE SURFACES FOR GLOBAL LAND AREAS , 2005 .

[56]  Andreas Graner,et al.  Genic microsatellite markers in plants: features and applications. , 2005, Trends in biotechnology.

[57]  H. Nybom,et al.  Effects of life history traits and sampling strategies on genetic diversity estimates obtained with RAPD markers in plants , 2000 .