R code for "Effects of drying and orientation to perennial refuges on aquatic biodiversity across two basins differing in aridity"
softwareposted on 2022-03-03, 23:06 authored by Brian A. GillBrian A. Gill, Anthony Sanabria, Miranda Gonzales, Stephanie M. Carlson, Michael T. Bogan
Intermittent streams are globally distributed, comprise over half the length of the global river network, and are expected to become more prevalent. However, most studies of intermittent streams are conducted at extremes of scale, are limited in taxonomic and temporal scope, and focus exclusively on drying patterns. Here, we assessed how both flow intermittency and orientation to perennial refuges affect aquatic invertebrates and aquatic and semi-aquatic vertebrates across two years within two intermittent river basins differing in their aridity. We used loggers to characterize flow intermittency and wet-dry mapping to determine orientation to perennial refuge of reaches. In winter and summer 2015 and 2016, we collected and identified invertebrates and visually surveyed vertebrates. Using permutational multivariate analyses of variance with distance matrices, we found distinct invertebrate communities by basin, flow class (perennial or intermittent), and season, and distinct vertebrate communities by basin, and between flow classes and seasons in the more arid basin. Invertebrate communities had higher beta diversity in the more arid than mesic basin, whereas the opposite was true for vertebrates. We identified indicator species for all combinations of basin and flow class, perennial reaches combined from both basins, each basin, and some combinations of flow class and season within basins. Flow intermittency and orientation to perennial refuge predictors correlated well with both invertebrate and vertebrate communities. However, we did not find nestedness of communities that differed significantly from that expected by chance in response to increasing flow intermittency or distance to refuge. Lastly, basin, flow intermittency, and orientation to perennial refuge predictors were generally important for modeling taxon richness and densities, and richness and densities decreased with increasing flow intermittency and distance to perennial refuge. Collectively, our data suggest that intermittent streams harbor unique biodiversity, but also that some taxa have context-dependent responses to intermittency and orientation to perennial refuges. These findings also suggest that future increases in stream drying are likely to lead to changes to stream communities with high potential for the loss of aquatic biodiversity.
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This item is part of Data, R Code, and Supplemental Results for "Effects of drying and orientation to perennial refuges on aquatic biodiversity across two basins in California, USA". See References, below, for the other parts.