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Semi‐quantitative metabarcoding reveals how climate shapes arthropod community assembly along elevation gradients on Hawaii Island

Citation

Lim, Jun Ying et al. (2022), Semi‐quantitative metabarcoding reveals how climate shapes arthropod community assembly along elevation gradients on Hawaii Island, Dryad, Dataset, https://doi.org/10.5061/dryad.wdbrv15p5

Abstract

Spatial variation in climatic conditions along elevation gradients provides an important backdrop by which communities assemble and diversify. Lowland habitats tend to be connected through time, whereas highlands can be continuously or periodically isolated, conditions that have been hypothesized to promote high levels of species endemism. This tendency is expected to be accentuated among taxa that show niche conservatism within a given climatic envelope. While species distribution modeling approaches have allowed extensive exploration of niche conservatism among target taxa, a broad understanding of the phenomenon requires sampling of entire communities. Species-rich groups such as arthropods are ideal case studies for understanding ecological and biodiversity dynamics along elevational gradients given their important functional role in many ecosystems, but community-level studies have been limited due to their tremendous diversity. Here, we develop a novel semi-quantitative metabarcoding approach that combines specimen counts and size-sorting to characterize arthropod community-level diversity patterns along two elevational gradients across two volcanoes on the island of Hawai`i. We find that arthropod communities between the two transects become increasingly distinct compositionally at higher elevations. Resistance surface approaches suggest that climatic differences between sampling localities are an important driver in shaping beta-diversity patterns, though the relative importance of climate varies across taxonomic groups. Nevertheless, the climatic niche position of OTUs between transects was highly correlated, suggesting that climatic filters shape the colonization between adjacent volcanoes. Taken together, our results highlight climatic niche conservatism as an important factor shaping ecological assembly along elevational gradients and suggest topographic complexity as an important driver of diversification.

Methods

See Materials & Methods section of Reference

Usage Notes

Contact: Jun Ying Lim (junyinglim@gmail.com), Henrik Krehenwinkel (krehenwinkel@uni-trier.de)

Reference: Lim, J.Y., Patiño, J, Noriyuki, S., Simmari, L.C., Gillespie, R.G. & Krehenwinkel, H. (submitted) Climatic niche conservatism shapes the ecological assembly of Hawaiian arthropod communities.

Contents

This online repository consists of the following files:

  1. Read me Word document (current file) containing more details on each file ("ReadMe.docx")
  2. Data on site localities and climate ("siteData.csv")
  3. Data on specimen counts for each size class category ("specimennumber.txt")
  4. Zip file containing raw fasta files ("Hawaii_Elevation_Fastas.zip")
  5. zOTU table for COI locus MCO ("otuMCO_clean.txt")
  6. zOTU table for COI locus ARF ("otuARF_clean.txt")
  7. Raster file containing total annual precipitation values for Stainback area ("annPrecip_steinb.rds")
  8. Raster file containing total annual precipitation values for the Laupahoehoe area ("annPrecip_laup.rds")
  9. Raster file containing mean annual temperature values for Stainback area ("annTemp_steinb.rds")
  10. Raster file containing mean annual temperature values for Laupahoehoe area ("annTemp_laup.rds")
  11. Data on taxonomic identity of each zOTU ("taxonData.csv")
  12. R script to generate rarefied OTU tables ("generateRarefiedMatrices.R")
  13. R script to clean up rarefied OTU tables ("prepOTUs.R")
  14. R script to perform resistance analyses ("resistance_analyses.R")
  15. R script to perform all other analyses ("analysis.R")

To run each R script on your local machine, you will need to first specify your working directory using the setwd() function to set the directory to the folder containing all files.

Scripts

To reproduce our analysis, the following R scripts need to run in this sequence:

  1. generateRarefiedMatrices.R
  2. prepOTUs.R
  3. resistance_analysis.R
  4. analysis.R

R script to generate rarefied OTU tables ("generateRarefiedMatrices.R")

This script implements the rarefaction procedure. This is performed by subsampling raw OTU tables for each size-category and primer pair separately. Read counts for each OTU are then summed across all size categories and both primer pairs to obtain rarefied read abundances for each OTU for each sampling site. This procedure is repeated 100 times so inherent differences in OTU recovery can be accounted for. This script outputs each "summed" rarefied OTU table as a separate file for ease of processing. Output files will be saved in the "data" folder and have the following naming convention – "combinedOTUdata_rXX.rds" – where XX is the replicate number.

R script to clean up rarefied OTU tables ("prepOTUs.R")

This script performs several housekeeping procedures: 1) excludes taxonomic orders where vast majority of specimens are non-native, 2) generate zOTU tables, 3) randomly subsamples rarefied OTU tables for downstream "resistance" analyses (see below).

R script to perform "resistance" analyses ("resistance_analysis.R")

This script performs the climatic resistance analysis by iterate over the Laupahoehoe and Stainback transects and each taxonomic order. This code was designed to be performed on a high-performance computing cluster.

R script to perform all other analyses ("analysis.R")

This script performs all other analyses as described in manuscript: testing patterns of community dissimilarity with elevation, niche conservatism etc.

System requirements

To run the code you will need an installation of R and some R packages. Output directories will be automatically created. Code was tested on R version 4.0.3 with the following packages attached (version number in parentheses; dependencies not listed): `vegan` (v.2.5-7), `stringr` (v.1.4.0), `reshape2` (v.1.4.4), `plyr` (v.1.8.6), `ResistanceGA` (v.4.2), `raster` (v.3.4-5), `doParallel (v.1.0.16)`. 

Data and metadata

Site localities and climate ("siteData.csv")

This file contains metadata on the sampling localities. Column definitions are as follows:

  • site.id: Unique identifier for each sampling locality
  • elevation: Elevation (meters above sea level) of sampling localities
  • island: Island where sampling locality is located (all on the " Big Island" of Hawai`i)
  • site: Name of transect (Laupahoehoe or Stainback)
  • rf_ann: Total annual rainfall experienced by sampling locality. Obtained by extracting raster information from Giambelluca, T.W., Chen, Q., Frazier, A.G., Price, J.P., Chen, Y.L., Chu, P.S., Eischeid, J.K. & Delparte, D.M. (2013) Online rainfall atlas of Hawai`i. Bulletin of the American Meteorological Society, 94, 313–316. 
  • t_ann: Mean annual temperature experienced by sampling locality. Obtained by extracting raster information from Giambelluca, T., Shuai, X., Barnes, M., Alliss, R., Longman, R., Miura, T. et al. (2014) Evapotranspiration of Hawai‘i. Final report submitted to the US Army Corps of Engineers. 
  • latitude: Latitude (decimal degrees) of sampling locality
  • longitude: Longitude (decimal degrees) of sampling locality

Specimen count information ("specimennumber.txt"):

This file contains information of the number of individuals that were sorted into each sorting category for each sampling locality

  • site.id: Sampling locality identifier
  • site: Name of transect
  • island: Island where sampling locality is located (all on the " Big Island" of Hawai`i)
  • year: Sampling year
  • size_class: Sorting category for specimens of various size intervals: < 2mm ("0to2"), 2 – 4 mm ("2-4"), 4 – 7 mm ("4-7"), > 7 mm ("lg7"); as well as specimens in the collembola category ("Col")
  • count: Number of individuals sorted into respective category for each sampling locality 

Raw fasta files ("Hawaii_Elevation_Fastas.zip")

The files are named using the following convention: [siteID]_[size_class]_[locus].fasta

  • [siteID]: Sampling locality identifier (see "siteData.csv" for metadata of sites)
  • [size_class]: Sorting category for specimens of various size intervals: < 2mm ("0to2"), 2 – 4 mm ("2-4"), 4 – 7 mm ("4-7"), > 7 mm ("lg7"); as well as specimens in the collembola category ("Col")
  • [locus]: COI locus amplified (MCO or ARF)

zOTU table for COI locus "MCO" ("otuMCO_clean.txt"):

This file contains information of the number of raw reads for each zOTU (rows) recovered for each sampling locality and sorting category (columns) obtained using the MCO primer pair.

zOTU table for COI locus "ARF" ("otuARF_clean.txt"):

This file contains information of the number of raw reads for each zOTU (rows) recovered for each sampling locality and sorting category (columns) obtained using the ARF primer pair.

Taxonomic identity for each zOTU ("taxonData.csv")

This file contains information on the OTU assignments for each zOTU (3% threshold), as well as the taxonomic order for each zOTU (mostly identified using BLAST but also using a phylogeny of zOTU sequences).

  • zOTU_ID: Unique identifier for each zOTU 
  • OTU_ID: Assigned OTU identity for each zOTU
  • TaxonomicOrder: Taxonomic order of each zOTU

Climatic raster data ("annPrecip_steinb.rds", "annPrecip_laup.rds", "annTemp_steinb.rds", "annTemp_laup.rds")

These R object files (".rds") contain Raster objects of total annual precipitation and man annual temperature for the area surrounding the Stainback and Laupahoehoe transects. These rasters are derived from raster maps generated by Giambelluca et al. 2013 and Giambelluca et al. 2014, respectively. These files are used to calculate the climatic dissimilarity between sites on each transect. The afore-mentioned analysis is implemented in the "resistance_analysis.R" R script.

References

  • Giambelluca, T., Shuai, X., Barnes, M.L., Alliss, R.J., Longman, R.J., Miura, T., Chen, Q., Frazier, A.G., Mudd, R.G., Cuo, L. & Businger, A.D. (2014) Evapotranspiration of Hawai‘i. Final report submitted to the US Army Corps of Engineers. Honolulu District, and the Commission on Water Resource Management, State of Hawai ‘i. 
  • Giambelluca, T., Shuai, X., Barnes, M.L., Alliss, R.J., Longman, R.J., Miura, T., Chen, Q., Frazier, A.G., Mudd, R.G., Cuo, L. & Businger, A.D. (2014) Evapotranspiration of Hawai‘i. Final report submitted to the US Army Corps of Engineers. Honolulu District, and the Commission on Water Resource Management, State of Hawai ‘i. 

Funding

National Science Foundation, Award: DEB 1241253