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Evolutionary inferences from fossil data often require accurately reconstructing differences in richness and morphological disparity between fossil sites across space and time. Biases such as sampling and rock availability are commonly accounted for in large-scale studies; however, preservation bias is usually dealt with only in smaller, more focused studies. Birds represent a diverse, but taphonomically fragile, group commonly used to infer environmental conditions in recent (Pleistocene and later) fossil assemblages, and their relative scarcity in the fossil record has led to controversy over the timing of their radiation. Here, I use simulations to show how even weak taphonomic biases can distort estimates of richness, and render variance sensitive to sample size. I then apply an ecology-based filtering model to recent bird assemblages to quantify the distortion induced by taphonomy. Certain deposit types, such as caves, show less evidence of taphonomic distortion than others, such as fluvial and lacustrine deposits. Archaeological middens unsurprisingly show some of the strongest evidence for taphonomic bias, and they should be avoided when reconstructing Pleistocene and early Holocene environments. Further, these results support previously suggested methods for detecting fossil assemblages that are relatively faithfully preserved (e.g., presence of difficult-to-preserve taxa), and I use these results to recommend that future large-scale studies include facies diversity along with metrics such as rock volume, or compare only sites with similar taphonomic histories.