An environmental DNA-based analysis across Beijing from ScienceAdvances finds that the water quality in urban lakes and ponds may strongly affect diversity of native fish, but not non-native species.
We measured the differences in fish community compositions among different sampling sites both qualitatively and quantitatively using the presence/absence-based Jaccard coefficient and the sequence abundance –based Bray-Curtis coefficients, respectively, calculated using the vegdist commands in vegan.
As biodiversity responses to the environment can be nonlinear and nonmonotonic, we used GAMs to analyze the relationships between selected environmental factors and fish diversity metrics. GAMs are highly flexible models in which the effects of the explanatory variables on the response are defined by data-driven smooth functions rather than a priori patterns. We implemented the GAMs by using the function gam with default settings in the R package mgcv .
In addition, we conducted Mantel tests in vegan using the mantel function with 1000 permutations to assess the correlations between fish community dissimilarities and the geographic distances among sampling sites in lentic and lotic systems. All statistical analyses were conducted in R version 4.0.3 .We thank Y. Wang, Q. Lu, W. Wang, M. Lin, D. Wang, and volunteers for assistance with sample collection; Y. Yang and L. Zhi for assistance with water quality measurements; S. Zhao, L. Yang, and L.
All data needed to evaluate the conclusions in the paper are present in the paper and/or the Supplementary Materials. Raw sequencing data related to this paper are available on NCBI’s SRA database BioProject ID: PRJNA796432 .Legends for tables S1, S3, S4, and S11Tables S1, S3, S4, and S11N. B. Grimm, S. H. Faeth, N. E. Golubiewski, C. L. Redman, J. Wu, X. Bai, J. M. Briggs, Global change and the ecology of cities.
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