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Phylogenetic signal of sub-arctic beetle communities

Citation

Majoros, Sam (2022), Phylogenetic signal of sub-arctic beetle communities, Dryad, Dataset, https://doi.org/10.5061/dryad.cjsxksn70

Abstract

Post-glacial dispersal and colonization processes have shaped community patterns in sub-Arctic regions such as Churchill, Manitoba, Canada. This study investigates evolutionary community structure within the beetle (Coleoptera) families of Churchill and tests whether biological traits have played a role in governing colonization patterns from refugial and southerly geographic regions. This study quantifies sub-Arctic beetle phylogenetic community structure for each family using the net relatedness index (NRI) and nearest taxon index (NTI), calculated using publicly available data from the Barcode of Life Data Systems (BOLD); compares patterns across families with different traits (habitat, diet) using standard statistical analysis (ANOVA) as well as phylogenetic generalized least squares (PGLS) using a family-level beetle phylogeny obtained from the literature; and compares community structure in Churchill with a region in southern Canada (Guelph, Ontario). These analyses were also repeated at a genus level. The dominant pattern detected in our study was that aquatic families were much better represented in Churchill compared to terrestrial families, when compared against richness sampled from across Canada and Alaska. Individually, most families showed significant phylogenetic clustering in Churchill, likely due to the strong environmental filtering present in Arctic environments. There was no significant difference in phylogenetic structure between Churchill and Guelph but with a trend towards stronger clustering in the North. Fungivores were significantly more overdispersed than other feeding modes, predators were significantly more clustered, and aquatic families showed significantly stronger clustering compared to terrestrial. This study contributes to our understanding of the traits and processes structuring insect biodiversity and macroecological trends in the sub-Arctic.

Methods

The data here includes character matrices and phylogenetic trees used in the analysis outlined at github.com/S-Majoros/Phylogenetic_Community_Structure_Code.r. A family-level phylogenetic tree, i.e. treating each family as one tip, was created using the phylogenetic hypothesis provided in Zhang et al. (2018) based upon 95 protein-coding genes. A genus-level tree was created using Zhang et al. (2018) and some additional trees (Michat et al. (2017) was used for Dytiscidae, Nie et al. (2017) for Chrysomelidae, and Gusarov (2018) for Staphylinidae). All trees were constructed manually using Mesquite (Maddison & Maddison 2019).

Character matrices were built for each analysis. Characters/traits were found for each family based on the literature (references are available in Appendix 3 of the paper). The traits that describe the majority of members of a given family were used; this included habitat (terrestrial or aquatic) and feeding mode (predaceous, phytophagous, or fungivorous).We defined terrestrial as taxa that live primarily in land habitats and aquatic as taxa that live primarily in water bodies and habitats. Predaceous taxa were defined as those who prey on other insects or animals, phytophagous taxa as those who feed primarily on plant material, and fungivores as those who feed primarily on fungi. Each character matrix contains the family or genus name, NRI/NTI value, habitat, adult diet and larval diet. 

 

Gusarov, V.I. (2018). Phylogeny of the family Staphylinidae based molecular data: a review. In Betz, O., Irmler, U. & Klimaszewski, J. (Eds.), Biology of rove beetles (Staphylinidae): Life history, evolution, ecology and distribution (pp. 7-25). Springer International Publishing, Switzerland

Maddison, W.P. & Maddison, D.R. (2019). Mesquite: a modular system for evolutionary analysis. Version 3.61. http://www.mesquiteproject.org

Michat, M.C., Alarie, Y & Miller, K.B. (2017). Higher-level phylogeny of diving beetles (Coleoptera: Dytiscidae) based on larval characters. Systematic Entomology, 42(4), 734-767. doi: 10.1111/syen.12243

Nie, R-E, Breeschoten, T., Timmermans, M.J.T.N., Nadein, K., Xue, H-J., Bai, M., Huang, Y., Yang, X-K & Vogler, A.P. (2018). The phylogeny of Galerucinae (Coleoptera: Chrysomelidae) and the performance of mitochondrial genomes in phylogenetic inference compared to nuclear rRNA genes. Cladistics, 34(2), 113-130. doi: 10.1111/cla.12196

Zhang, S.-Q., Che, L.-H., Li, Y., Liang, D., Pang, H., Ślipiński, S.A. & Zhang, P. (2018). Evolutionary history of Coleoptera revealed by extensive sampling of genes and species. Nature Communications, 9(1), 1-11. doi: 10.1038/s41467-017-02644-4

Usage Notes

All information needed for reuse of this dataset, as well as additonal files, is avaliable at github.com/S-Majoros/Phylogenetic_Community_Structure_Code.r. For character matrices: the Churchill family matrices are Coleoptera_Matrix_NRI.csv and Coleoptera_Matrix_NTI.csv, the Churchill genus matrices are Genus_NRI_Matrix_Churchill.csv and Genus_NTI_Matrix_Churchill.csv, the Guelph family matrices are Guelph_Matrix_NRI.csv and Guelph_Matrix_NTI.csv, and the Guelph genus matrices are Guelph_Genus_Matrix_NRI.csv and Guelph_Genus_Matrix_NTI.csv. For the phylogenetic trees, the Churchill family tree is Coleoptera_Tree_2020, the Churchill genus tree is Churchill_Genus_Tree, the Guelph family tree is Guelph_Tree_2, and the Guelph genus tree is GGTree. 

Funding

Natural Sciences and Engineering Research Council of Canada, Award: USRA

Natural Sciences and Engineering Research Council of Canada, Award: Discovery Grant

Government of Canada through Genome Canada and Ontario Genomics , Award: Grant in Bioinformatics and Computational Biology

Ontario Ministry of Economic Development, Job Creation and Trade, Award: Grant in Bioinformatics and Computational Biology