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 dataset[^1] downloaded from GBIF via rgbif package |
| band_mde.csv | Data generated from 10,000 replications of mid-domain effect (MDE) null model[^2] | | 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] | | kholhiraitan.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 | | siteclimatewld.csv | Climate dataset from WorldClim2 database[^4] 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 | | siteplantswcvp.csv | Combined species check-list with botanical names standardised according to World Checklist of Vascular Plants (WCVP)[^5] | | sitespecelev.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 | | speciessensitivitymde.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 | | speciessensitivityrichness.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 | | mdemean | Mean predicted species richness from 10,000 runs of MDE null model | | mdesd | Standard deviation for predicted species richness from 10,000 runs of MDE null model | | mdemin | Minimum predicted species richness from 10,000 runs of MDE null model | | mdemax | 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 | |-------------|-------------------------------------------------------------------| | givenname | Botanical name given in the published study | | powotaxa | Accepted botanical name by Plants of World Online (POWO) | | powoauthor | Accepted botanical name authorship by Plants of World Online (POWO) | | powodist | 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., Bhardwaj2017[^6], Champion1968[^7], eFI2022[^8], FOI2022[^9], Kumar2013[^10], Choudhary2007[^11], Choudhary2012[^12], Gupta1998[^13], Radha2019[^14], Subramani2014[^15], Thakur2021a[^16], Balkrishna2018a[^17], Balkrishna2018b[^18], Dhiman2020[^19], Dhiman2021[^20], Singh2014[^21]

Codebook for siteplantswcvp.csv

| Column | Description | |-----------|-------------------------------------------------------------------| | taxonname | Accepted botanical names standardised according to World Checklist of Vascular Plants (WCVP) | | taxonauthors | 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 | | powodist | Distribution status (Introduced vs. Native) of plant according to World Checklist of Vascular Plants (WCVP) | | lifeformdescription | 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 speciessensitivitymde.csv and speciessensitivityrichness.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

[^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.