kumar-a / richness-determinants

Determinants of Plant Species Richness along Elevational Gradients: Insights with Climate, Energy and Water-Energy Dynamics

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: [email protected]; [email protected]
^#Maintainer: [email protected]

Directory structure

. 
  |- R
    |- 01_make-site-map.R
    |- 02_standardise-plant-names.R
    |- 03_get-elevation-ranges.R
    |- 04_calculate-richness.R
    |- 05_extract-explanatory-variables.R
    |- 06_compare-top-model.R
    |- calculate_band_area.R
    |- extract_climate.R
  |- data
    |- hkh
    |- 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_aet_cgiar.tif
    |- site_bio_chelsa.tif
    |- site_districts.gpkg
    |- site_evihomo_earthenv.tif
    |- site_npp_chelsa.tif
    |- site_pet_cgiar.tif
    |- site_soc_soilgrid.tif
    |- site_states.gpkg
    |- site_tri_earthenv.tif
  |- gv
    |- bmod_sem.gv
    |- hypothetical_sem.gv
  |- output
    |- 0417447-210914110416597.zip
    |- band_area.csv
    |- band_richness.csv
    |- chail_elev.tif
    |- churdhar_elev.tif
    |- morni_elev.tif
    |- site_elev.tif
    |- site_env.csv
    |- site_plants_wcvp.csv
    |- site_spec_elev.csv
    |- top_mod_comparison.csv
  |- apa7.csl
  |- credit_author.csv
  |- index.qmd
  |- README.md
  |- refs.bib
  |- richness-determinants.Rproj

Description of R scripts

File name	Description
01_make-site-map.R	R codes to prepare the map for study sites (fig2_site-map.pdf)
02_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
03_get-elevation-ranges.R	R codes to retrieve the species elevational ranges from published database (Rana & Rawat 2017, 2019)
04_calculate-richness.R	R codes with function used to calculate species richness from compiled dataset for each study site
05_extract-explanatory-variables.R	R codes to extract mean values of each explanatory variable for each site
06_compare-top-model.R	R codes to compare top models for each study site
calculate_band_area.R	R codes for calculating the planar and slope-corrected area for each 100-m elevational band for each study site
extract_climate.R	R script to extract climate data from WorldClim2 database (Fick & Hijmans 2017) and process to prepare Walter-Leith Diagrams for study sites

Description of primary data files

File name	Description
hkh	Spatial boundary of Hindu Kush Himalayas (HKH) obtained from ICIMOD (2008)
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)
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_aet_cgiar.tif	Cropped actual evapotranspiration (AET) data obtained from Trabucco & Zomer (2019)
site_bio_chelsa.tif	Cropped bioclimatic variables data obtained from Karger et al. (2017)
site_districts.gpkg	Spatial boundaries for Indian districts sharing the bounding box for selected study sites in the Himalayas
site_evihomo_earthenv.tif	Cropped EVI homogeneity index data obtained from Tuanmu & Jetz (2015)
site_npp_chelsa.tif	Cropped net primary productivity (NPP) data obtained from Karger et al. (2017)
site_pet_cgiar.tif	Cropped potential evapotranspiration (PET) data obtained from Zomer et al. (2022)
site_soc_soilgrid.tif	Cropped soil organic carbon (SOC) data obtained from Hengl et al. (2017)
site_states.gpkg	Spatial boundaries for north-western Indian States covering the study sites in the Western Himalayas
site_tri_earthenv.gpkg	Cropped terrain ruggedness index (TRI) data obtained from Amatulli et al. (2018)

Description of Graphviz scripts

File name	Description
bmod_sem.gv	Graphviz script for final best path model for determinants of species richness
hypothetical_sem.gv	Graphviz script for the priori hypothetical conceptual model for determinants of species richness

Description of files derived using R

File name	Description
0417447-210914110416597.zip	Species distribution dataset (Rana & Rawat 2017, 2019) downloaded from GBIF via rgbif package
band_area.csv	Calculated planar and slope-corrected area for each elevational band using the calculate_band_area.R script
band_richness.csv	Estimated species richness for 100-m elevational bands for each site using the 04_calculate-richness.R script
chail_elev.tif	Cropped elevation data for Chail WLS downloaded using the 05_extract-explanatory-variables.R script
churdhar_elev.tif	Cropped elevation data for Churdhar WLS downloaded using the 05_extract-explanatory-variables.R script
morni_elev.tif	Cropped elevation data for Morni Hills downloaded using the 05_extract-explanatory-variables.R script
site_elev.tif	Cropped elevation data for study area downloaded using the 05_extract-explanatory-variables.R script
site_env.tif	Prepared dataset with species richness and explanatory variables for each site processed using the 05_extract-explanatory-variables.R script
site_plants_wcvp.csv	Combined species check-list with botanical names standardised according to World Checklist of Vascular Plants (WCVP, Govaerts et al., 2021) using the 02_standardise-plant-names.R script
site_spec_elev.csv	Finally prepared dataset for standardised unique species and their elevational ranges for selected study sites using the 03_get-elevation-ranges.R script
top_mod_comparison.csv	Comparison of identified top model with previously proposed models of species richness using the 06_compare-top-model.R script

Description of other files

File name	Description
apa7.csl	Citation Style Language (CSL) citation style for American Psychological Association (APA) 7th 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 initial draft of manuscript
refs.bib	Bibliographic entries for literature cited in the manuscript
richness-determinants.Rproj	R project file

Codebook for chail_plants.csv, chur_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., Bhardwaj2017¹, Champion1968², eFI2022³, FOI2022⁴, Kumar2013⁵, Choudhary2007⁶, Choudhary2012⁷, Gupta1998⁸, Radha2019⁹, Subramani2014¹⁰, Thakur2021a¹¹, Balkrishna2018a¹², Balkrishna2018b¹³, Dhiman2020¹⁴, Dhiman2021¹⁵, Singh2014¹⁶

Codebook for band_area.csv

Column	Description
elevation	Upper elevation of each 100-m elevational band in metres
site	Name of site for which the MDE null model was run
area2d	total planar area in km2 for each elevational band
area3d	total slope-corrected area in km2 for each elevational band

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_env.csv

Column	Description
site	Name of site for which the elevational species richness was estimated
S	Estimated species richness for each 100-m elevational band for selected sites
ELE	Upper elevation of each 100-m elevational band in metres
MAT	Mean annual temperature (bio1) of each 100-m elevational band in °C
TSE	Temperature seasonality (bio4) of each 100-m elevational band in °C/100
MAP	Mean annual precipitation (bio12) of each 100-m elevational band in kg m-2 yr-1
PSE	Precipitation seasonality (bio15) of each 100-m elevational band in kg m-2
NPP	Net primary productivity (NPP) of each 100-m elevational band in g C m−2 yr−1
SOC	Soil organic carbon (SOC) of each 100-m elevational band in dg/kg (= 10 × g/kg)
AET	Actual evapotranspiration (AET) of each 100-m elevational band in mm
PET	Potential evapotranspiration (PET) of each 100-m elevational band in mm
EHM	EVI homogeneity (EHM) of each 100-m elevational band
TRI	Terrain ruggedness index (TRI) of each 100-m elevational band in meters
WDF	Water deficit (WDF) of each 100-m elevational band in mm

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_spec_elev.csv

Column	Description
taxon_name	Accepted botanical names standardised according to World Checklist of Vascular Plants (WCVP)
LL	Lower elevational limit (in meters) of the species in Himalayas
UL	Upper elevational limit (in meters) of the species in Himalayas

Codebook for top_mod_comparison.csv

Column	Description
Site	Name of site for which the model was compared
Model	Species richness model in y ~ x form
logLik	log-likelihood of the model
AICc	corrected Akaike's Information Criteria
daicc	difference in corrected Akaike's Information Criteria from the top model
dev.adj	adjusted deviance-squared for model

References

• Amatulli, G., Domisch, S., Tuanmu, M.-N., Parmentier, B., Ranipeta, A., Malczyk, J., & Jetz, W. (2018). A suite of global, cross-scale topographic variables for environmental and biodiversity modeling. Scientific Data, 5, 180040. https://doi.org/10.1038/sdata.2018.40

• 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

• 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

• Hengl, T., Jesus, J. M. de, Heuvelink, G. B. M., Gonzalez, M. R., Kilibarda, M., Blagotić, A., Shangguan, W., Wright, M. N., Geng, X., Bauer-Marschallinger, B., Guevara, M. A., Vargas, R., MacMillan, R. A., Batjes, N. H., Leenaars, J. G. B., Ribeiro, E., Wheeler, I., Mantel, S., & Kempen, B. (2017). SoilGrids250m: Global gridded soil information based on machine learning. PLoS ONE, 12(2), e0169748. https://doi.org/10.1371/journal.pone.0169748

• ICIMOD (2008). Outline Boundary of Hindu Kush Himalayan (HKH) Region. http://rds.icimod.org/

• Karger, D. N., Conrad, O., Böhner, J., Kawohl, T., Kreft, H., Soria-Auza, R. W., Zimmermann, N. E., Linder, H. P., & Kessler, M. (2017). Climatologies at high resolution for the earth’s land surface areas. Scientific Data, 4, 170122. https://doi.org/10.1038/sdata.2017.122

• 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

• Rana, S. K., & Rawat, G. S. (2017). Database of Himalayan plants based on published floras during a century. Data, 2(4), 36. https://doi.org/10.3390/data2040036

• 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

• Trabucco, A., & Zomer, R. J. (2019). Global high-resolution soil-water balance (version 3). CGIAR Consortium for Spatial Information. https://doi.org/10.6084/m9.figshare.7707605.v3

• Tuanmu, M.-N., & Jetz, W. (2015). A global, remote sensing-based characterization of terrestrial habitat heterogeneity for biodiversity and ecosystem modelling. Global Ecology and Biogeography, 24(11), 1329–1339. https://doi.org/10.1111/geb.12365

• Zomer, R. J., Xu, J., & Trabucco, A. (2022). Version 3 of the global aridity index and potential evapotranspiration database. Scientific Data, 9, 409. https://doi.org/10.1038/s41597-022-01493-1

Footnotes

1. 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 ↩

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

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

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

5. 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 ↩

6. 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. ↩

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

8. 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 ↩

9. 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 ↩

10. 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 ↩

11. 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 ↩

12. 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 ↩

13. 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 ↩

14. 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. ↩

15. 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 ↩

16. 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. ↩