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
  |- 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_spec_elev.csv
    |- species_sensitivity_mde.csv
    |- species_sensitivity_richness.csv
  |- README.md
  |- apa6.csl
  |- credit_author.csv
  |- index.qmd
  |- refs.bib
  |- richness-patterns.Rproj

Description of files

The R folder contains the scripts used for analysis of the primary data in data folder and the processed data is stored in output folder.

File name	Description
0417447-210914110416597.zip	Species distribution dataset1 downloaded from GBIF via rgbif package
band_mde.csv	Data generated from 10,000 replications of mid-domain effect (MDE) null model2
band_richness.csv	Estimated species richness for 100-m elevational bands for each site
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)3
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_climate_wld.csv	Climate dataset from WorldClim2 database4 processed for preparing the Walter-Leith Diagrams for study sites
site_districts.gpkg	Spatial boundaries for Indian districts sharing the bounding box for selected study sites in the Himalayas
site_elev.tif	Elevation raster data cropped for bounding box of the selected study sites
site_plants_wcvp.csv	Combined species check-list with botanical names standardised according to World Checklist of Vascular Plants (WCVP)5
site_spec_elev.csv	Finally prepared dataset for standardised unique species and their elevational ranges for selected study sites
siwalik_states.gpkg	Spatial boundaries for north-western Indian States covering the Siwalik foothills of Himalayas
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
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
apa6.csl	Citation Style Language citation styles for American Psychological Association 6th edition
credit_author.csv	Documentation of each authors' contribution in CRediT (Contributor Roles Taxonomy) author statement
index.qmd	Quarto markdown file with embedded R codes to reproduce the draft of manuscript
refs.bib	Bibliographic entries for literature cited in the manuscript

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 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 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 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

References

Footnotes

1. 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 ↩

2. 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 ↩

3. 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 ↩

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. ↩