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Biotic communities in shallow northern lakes are frequently used to assess environmental change; however, complex interactions among multiple factors remain understudied. Here, we present analyses of a comprehensive data set that evaluates the influence input waters, catchment characteristics, limnology, and sediment properties on diatom and chironomid assemblages in surface sediments of ~49 shallow mainly thermokarst lakes in Old Crow Flats, Yukon. Multivariate analyses and ANOSIM tests identified that composition of diatom (119 taxa) and chironomid (68 taxa) assemblages differs significantly (p &lt; 0.05) between lakes with snowmelt- versus rainfall-dominated input water. Redundancy analyses revealed strong correlation of limnological, sediment, and catchment variables with input waters. Variation partitioning analyses showed that unique effects of limnological variables account for the largest proportion of variation in diatom and chironomid assemblages (17.2% and 12.6%, respectively). Important independent roles of sediment properties (8.5% and 9.5%) and catchment characteristics (4.9% and 5.1%) were also identified. We suggest that the substantial variation shared among these classes (6.1% and 7.9%) is largely attributable to hydrological processes. Our study demonstrates the utility of multi-factor analysis in northern aquatic research and draws attention to the limitations of one-dimensional comparisons and their interpretations when modelling biotic responses to environmental change.

Biotic responses to multiple aquatic and terrestrial gradients in shallow subarctic lakes (Old Crow Flats, Yukon, Canada)