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Exploring Elevational Patterns of Plant Species Richness: Insights from Western Himalayas

Authors: Abhishek Kumar#, Meenu Patil, Pardeep Kumar, Anand Narain Singh*
Affiliation: Soil Ecosystem and Restoration Ecology Lab, Department of Botany, Panjab University, Chandigarh 160014, India
*Corresponding author: dranand1212@gmail.com; ansingh@pu.ac.in
#Maintainer: abhikumar.pu@gmail.com

Directory structure

.
  |- R
    |- 01_make_site_map.R
    |- 02_make_climate_diagram.R
    |- 03_standardise_plant_names.R
    |- 04_get_elevation_ranges.R
    |- 05_calculate_species_richness.R
    |- 06_get_mde_predictions.R
    |- 07_test_species_sensitivity.R
    |- 08_calculate_rarefaction_curves.R
    |- 09_make_site_map_ggplot.R
  |- data
    |- chail_plants.csv
    |- chail.gpkg
    |- churdhar_plants.csv
    |- churdhar.gpkg
    |- ecs22945-sup-0004-datas1.csv
    |- khol_hi_raitan.gpkg
    |- morni_plants.csv
    |- morni.gpkg
    |- site_districts.gpkg
    |- siwalik_states.gpkg
  |- output
    |- 0417447-210914110416597.zip
    |- band_mde.csv
    |- band_richness.csv
    |- site_climate_wld.csv
    |- site_elev.tif
    |- site_plants_wcvp.csv
    |- site_rarefaction_coverage.csv
    |- site_rarefaction_size.csv
    |- site_spec_elev.csv
    |- species_sensitivity_mde.csv
    |- species_sensitivity_richness.csv
  |- README.md
  |- credit_author.csv
  |- forests.csl
  |- index.qmd
  |- index.pdf
  |- journal-abbreviations.json
  |- math-rendered-by-lua-filter.html
  |- refs.bib
  |- richness-patterns.Rproj
  |- title.tex

Description of R scripts

File name Description
01_make_site_map.R R codes to prepare the map for study sites (fig1.pdf)
02_make_climate_diagram.R R codes to prepare the climate diagrams for study sites (fig2.pdf)
03_standardise_plant_names.R R codes to standardise botanical names according to WCVP (Govaerts et al., 2021). The standardised botanical names are saved as site_plants_wcvp.csv
04_get_elevation_ranges.R R codes to retrieve the species elevational ranges from published database (Rana & Rawat 2017, 2019)
05_calculate_species_richness.R R codes with function used to calculate species richness from compiled dataset for each study site
06_get_mde_predictions.R R codes to simulate mid-domain effect predictions
07_test_species_sensitivity.R R codes to test the effects of number of observed species
08_calculate_rarefaction_curves.R R codes for calculating the coverage and size-based rarefaction curves for estimating species richness for each study site
09_make_site_map_ggplot.R Alternative R script to prepare the map for study sites (fig1.pdf) using ggplot2 package. Note: tmap package is under major redevelopment

Description of primary data files

File name Description
chail_plants.csv Recorded plant species from literature survey for Chail Wildlife Sanctuary
chail.gpkg Digitised spatial boundary for Chail Wildlife Sanctuary
churdhar_plants.csv Recorded plant species from literature survey for Churdhar Wildlife Sanctuary
churdhar.gpkg Digitised spatial boundary for Churdhar Wildlife Sanctuary
ecs22945-sup-0004-datas1.csv Additional species distribution data from Rana, Price, & Qian (2019)1
khol_hi_raitan.gpkg Digitised spatial boundary for Khol Hi Raitan Wildlife Sanctuary
morni_plants.csv Recorded plant species from literature survey for Morni Hills
morni.gpkg Digitised spatial boundary for Morni Hills
site_districts.gpkg Spatial boundaries for Indian districts sharing the bounding box for selected study sites in the Himalayas
siwalik_states.gpkg Spatial boundaries for north-western Indian States covering the Siwalik foothills of Himalayas

Description of files derived using R

File name Description
0417447-210914110416597.zip Species distribution dataset2 downloaded from GBIF via rgbif package using 04_get_elevation_ranges.R script
band_mde.csv Data generated from 10,000 replications of mid-domain effect (MDE) null model3 using 06_get_mde_predictions.R script
band_richness.csv Estimated species richness for 100-m elevational bands for each site using the 05_calculate_species_richness.R script
site_climate_wld.csv Climate dataset from WorldClim2 database4 processed for preparing the Walter-Leith Diagrams for study sites using the 02_make_climate_diagram.R script
site_elev.tif Elevation raster data cropped for bounding box of the selected study sites. The R code used to download this file is available in 01_make_site_map.R script
site_plants_wcvp.csv Combined species check-list with botanical names standardised according to World Checklist of Vascular Plants (WCVP)5 using the 03_standardise_plant_names.R script
site_rarefaction_coverage.csv Sample coverage-based rarefaction curves for species richness estimation using the script 08_calculate_rarefaction_curves.R
site_rarefaction_size.csv Sample size-based rarefaction curves for species richness estimation using the 08_calculate_rarefaction_curves.R script
site_spec_elev.csv Finally prepared dataset for standardised unique species and their elevational ranges for selected study sites using the 04_get_elevation_ranges.R script
species_sensitivity_mde.csv Results of sensitivity analysis to test the influence of total number of observed species on the relationship between observed richness and the predictions of mid-domain effect null model using the 07_test_species_sensitivity.R script
species_sensitivity_richness.csv Results of sensitivity analysis to test the influence of total number of observed species on the elevational patterns of plant species richness using the 07_test_species_sensitivity.R script

Other files

File name Description
README.md README file for current repository
credit_author.csv Documentation of each authors' contribution in CRediT (Contributor Roles Taxonomy) author statement
forests.csl Citation Style Language citation styles for Forests journal published by MDPI
index.pdf Rendered draft of manuscript in pdf format
index.qmd Quarto markdown file with embedded R codes to reproduce the draft of manuscript
journal-abbreviations.json A json file to define journal abbreviations to be used for citation style for forests.csl
math-rendered-by-lua-filter.html Pandoc Lua filter to process and display mathematical expressions in html format
refs.bib Bibliographic entries for literature cited in the manuscript
richness-patterns.Rproj A project file of RStudio for organisation of project directory
title.tex A tex file to enable inclusion of author affiliations in rendered pdf output (index.pdf)

Codebook for chail_plants.csv, churdhar_plants.csv and morni_plants.csv

Column Description
given_name Botanical name given in the published study
powo_taxa Accepted botanical name by Plants of World Online (POWO)
powo_author Accepted botanical name authorship by Plants of World Online (POWO)
powo_dist Distribution status (Introduced vs. Native) of plant according to Plants of World Online (POWO)

All other columns refer to citation keys for studies identified through literature survey, i.e., Bhardwaj20176, Champion19687, eFI20228, FOI20229, Kumar201310, Choudhary200711, Choudhary201212, Gupta199813, Radha201914, Subramani201415, Thakur2021a16, Balkrishna2018a17, Balkrishna2018b18, Dhiman202019, Dhiman202120, Singh201421

Codebook for band_mde.csv

Column Description
elevation Upper elevation of each 100-m elevational band in metres
mde_mean Mean predicted species richness from 10,000 runs of MDE null model
mde_sd Standard deviation for predicted species richness from 10,000 runs of MDE null model
mde_min Minimum predicted species richness from 10,000 runs of MDE null model
mde_max Maximum predicted species richness from 10,000 runs of MDE null model
site Name of site for which the MDE null model was run

Codebook for band_richness.csv

Column Description
elevation Upper elevation of each 100-m elevational band in metres
richness Estimated species richness for each 100-m elevational band for selected sites
site Name of site for which the elevational species richness was estimated

Codebook for site_climate_wld.csv

Column Description
ID Names of study sites
Clim Climatic variables; Mean total precipitation (prec), Mean maximum daily temperature (tmax), Mean minimum daily temperature (tmin), and Absolute minimum daily temperature (abstmin)

Codebook for site_plants_wcvp.csv

Column Description
taxon_name Accepted botanical names standardised according to World Checklist of Vascular Plants (WCVP)
taxon_authors Accepted botanical authorship standardised according to World Checklist of Vascular Plants (WCVP)
genus Accepted botanical genus epithet standardised according to World Checklist of Vascular Plants (WCVP)
family Accepted family of plant species standardised according to World Checklist of Vascular Plants (WCVP), which follows Angiosperm Phylogeny Group (APG) classification
powo_dist Distribution status (Introduced vs. Native) of plant according to World Checklist of Vascular Plants (WCVP)
lifeform_description Lifeform description of selected plant species according to World Checklist of Vascular Plants (WCVP)
climate_description Climate description of selected plant species according to World Checklist of Vascular Plants (WCVP)
Morni Short for Morni Hills
Chail Short for Chail Wildlife Sanctuary
Churdhar Short for Churdhar Wildlife Sanctuary

Codebook for site_rarefaction_coverage.csv and site_rarefaction_size.csv

Column Description
Assemblage Names of the study sites
SC Sample coverage estimate for the reference sample
t Sample size for corresponding sampling coverage
Method Method (Rarefaction, Observed, or Extrapolation) depending on whether the sample size t is less than, equal to, or greater than the reference sample size
Order.q The diversity order of Hill diversity numbers, species richness (q = 0), Shannon diversity (q = 1), and Simpson diversity (q = 2)
qD The diversity estimate of order q (qD)
qD.LCL Lower limit of the 95% confidence interval for qD estimate
qD.UCL Upper limit of the 95% confidence interval for qD estimate
SC.LCL Lower limit of the 95% confidence interval for SC estimate
SC.UCL Upper limit of the 95% confidence interval for SC estimate

Codebook for site_spec_elev.csv

Column Description
taxon_name Botanical name of the plant taxon
taxon_authors Botanical authority of the taxon name
LL Lower elevational limit of the distribution
UL Upper elevational limit of the distribution

Codebook for species_sensitivity_mde.csv and species_sensitivity_richness.csv

Column Description
elevation Upper elevation of each 100-m elevational band in metres
mde Predictions of MDE null model
richness Estimated species richness
species Total number of included species for estimation of species richness and MDE
site Name of study site

Citation

  • Kumar, A., Patil, M., Kumar, P., & Singh, A. N. (2025). Elevational Patterns of Plant Species Richness: Insights from Western Himalayas. Forests, 16(10), 1591. https://doi.org/10.3390/f16101591

  • Kumar, A., Patil, M., Kumar, P., & Singh, A. N. (2025). Dataset and R Codes for Elevational Patterns of Plant Species Richness: Insights from Western Himalayas. Figshare. Journal contribution. https://doi.org/10.6084/m9.figshare.23828784.v3

References

Footnotes

  1. Rana, S. K., Price, T. D., & Qian, H. (2019). Plant species richness across the Himalaya driven by evolutionary history and current climate. Ecosphere, 10(11), e02945. https://doi.org/10.1002/ecs2.2945 ↩

  2. Rana, S. K., & Rawat, G. S. (2019). Database of vascular plants of Himalaya. Version 1.6. Dehradun: Wildlife Institute of India. https://doi.org/10.15468/zdeuix ↩

  3. Colwell, R. K., & Lees, D. C. (2000). The mid-domain effect: Geometric constraints on the geography of species richness. Trends in Ecology & Evolution, 15(2), 70–76. https://doi.org/10.1016/s0169-5347(99)01767-x ↩

  4. Fick, S. E., & Hijmans, R. J. (2017). WorldClim 2: New 1-km spatial resolution climate surfaces for global land areas. International Journal of Climatology, 37(12), 4302–4315. https://doi.org/10.1002/joc.5086 ↩

  5. Govaerts, R., Lughadha, E. N., Black, N., Turner, R., & Paton, A. (2021). The World Checklist of Vascular Plants, a continuously updated resource for exploring global plant diversity. Scientific Data, 8(1), 215. https://doi.org/10.1038/s41597-021-00997-6 ↩

  6. Bhardwaj, A. (2017). Study on dynamics of plant bioresources in Chail wildlife sanctuary of Himachal Pradesh (PhD thesis, Forest Research Institute (Deemed) University; p. 342). Forest Research Institute (Deemed) University, Dehradun. Retrieved from http://hdl.handle.net/10603/175719 ↩

  7. Champion, H. G., & Seth, S. K. (1968). A revised survey of the forest types of India (p. 404). Delhi: Government of India. ↩

  8. eFI. (2022). eFlora of India: Database of plants of Indian subcontinent. Retrieved from https://efloraofindia.com/ ↩

  9. FOI. (2022). Flowers of India. Retrieved from http://www.flowersofindia.net/ ↩

  10. Kumar, R. (2013). Studies on plant biodiversity of Chail wildlife sanctuary in Himachal Pradesh (Master’s thesis, Dr Yashwant Singh Parmar University of Horticulture and Forestry; p. 119). Dr Yashwant Singh Parmar University of Horticulture and Forestry, Solan. Retrieved from http://krishikosh.egranth.ac.in/handle/1/91126 ↩

  11. Choudhary, A. K., Punam, Sharma, P. K., & Chandel, S. (2007). Study on the physiography and biodiversity of Churdhar wildlife sanctuary of Himachal Himalayas, India. Tigerpaper, 34, 27–32. ↩

  12. Choudhary, R. K., & Lee, J. (2012). A floristic reconnaissance of Churdhar wildlife sanctuary of Himachal Pradesh, India. Manthan, 13, 2–12. ↩

  13. Gupta, H. (1998). Comparative studies on the medicinal and aromatic flora of Churdhar and Rohtang areas of Himachal Pradesh (Master’s thesis, Dr Yashwant Singh Parmar University of Horticulture and Forestry; p. 228). Dr Yashwant Singh Parmar University of Horticulture and Forestry, Solan. Retrieved from http://krishikosh.egranth.ac.in/handle/1/5810135063 ↩

  14. Radha, Puri, S., Chandel, K., Pundir, A., Thakur, M. S., Chauhan, B., … Kumar, S. (2019). Diversity of ethnomedicinal plants in Churdhar wildlife sanctuary of district Sirmour of Himachal Pradesh, India. Journal of Applied Pharmaceutical Science, 9(11), 48–53. https://doi.org/10.7324/japs.2019.91106 ↩

  15. Subramani, S. P., Kapoor, K. S., & Goraya, G. S. (2014). Additions to the floral wealth of Sirmaur district, Himachal Pradesh from Churdhar wildlife sanctuary. Journal of Threatened Taxa, 6(11), 6427–6452. https://doi.org/10.11609/jott.o2845.6427-52 ↩

  16. Thakur, U., Bisht, N. S., Kumar, M., & Kumar, A. (2021). Influence of altitude on diversity and distribution pattern of trees in Himalayan temperate forests of Churdhar wildlife sanctuary, India. Water, Air, & Soil Pollution, 232, 205. https://doi.org/10.1007/s11270-021-05162-8 ↩

  17. Balkrishna, A., Srivastava, A., Shukla, B., Mishra, R., & Joshi, B. (2018). Medicinal plants of Morni Hills, Shivalik Range, Panchkula, Haryana. Journal of Non-Timber Forest Products, 25(1), 1–14. https://doi.org/10.54207/bsmps2000-2018-ir3j0n ↩

  18. Balkrishna, A., Joshi, B., Srivastava, A., & Shukla, B. (2018). Phyto-resources of Morni Hills, Panchkula, Haryana. Journal of Non-Timber Forest Products, 25(2), 91–98. https://doi.org/10.54207/bsmps2000-2018-p430i5 ↩

  19. Dhiman, H., Saharan, H., & Jakhar, S. (2020). Floristic diversity assessment and vegetation analysis of the upper altitudinal ranges of Morni Hills, Panchkula, Haryana, India. Asian Journal of Conservation Biology, 9(1), 134–142. ↩

  20. Dhiman, H., Saharan, H., & Jakhar, S. (2021). Study of invasive plants in tropical dry deciduous forests – biological spectrum, phenology, and diversity. Forestry Studies, 74(1), 58–71. https://doi.org/10.2478/fsmu-2021-0004 ↩

  21. Singh, N., & Vashistha, B. D. (2014). Flowering plant diversity and ethnobotany of Morni Hills, Siwalik Range, Haryana, India. International Journal of Pharma and Bio Sciences, 5(2), B214–B222. ↩

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Dataset and R Codes for Elevational Patterns of Plant Species Richness: Insights from Western Himalayas

doi.org/10.6084/m9.figshare.23828784

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species-richness himalayas mid-domain-effect

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