Data from: Accounting for the effects of biological variability and temporal autocorrelation in assessing the preservation of species abundance

Quantifying the effects of taphonomic processes on species abundances in time-averaged death assemblages (DAs) is pivotal for paleoecological inference. However, fidelity estimates based on conventional "live-dead" comparisons are fundamentally ambiguous: (1) data on living assemblages (LAs) are based on a very short period of sampling and thus do not account for natural variability in the LA, (2) LAs are sampled at the same time as the DA and thus do not necessarily reflect past LAs that contributed to the DAs, (3) compositions of LAs and DAs can be autocorrelated owing to shared cohorts, and (4) fidelity estimates are cross-scale estimates because DAs are time-averaged and LAs are not. Some portion of the raw (total) live-dead (LD) variation in species composition thus arises from incomplete sampling of LAs and from natural temporal variation in the local community (together = premortem component of LD variation), as contrasted with new variation created by interspecific variation in population turnover and preservation rates and by the time-averaging of skeletal input (together = postmortem component of LD variation). To tackle these problems, we introduce a modified test for homogeneity of multivariate dispersions (HMD) in order to (1) account for temporal autocorrelation in composition between LAs and DAs and (2) decompose total LD compositional variation into premortem and postmortem components, and (3) we use simulations to evaluate the contribution of within-habitat time averaging on the postmortem component. Applying this approach to 31 shallow marine molluscan datasets, each consisting of spatial replicates of LAs and DAs in a single habitat, we find that total LD variation is driven largely by premortem variation among LAs, but the increase in total LD variation owing to postmortem processes is significantly positive in 25-65% of datasets (depending on the metric) with HMD assuming autocorrelation. Had we ignored the effects of autocorrelation, the effects of postmortem processes would be negligible, inflating our overall inference about the quality of the fossil record. Simulations show that the increase in temporal scale owing to within-habitat time-averaging does not in itself increase total LD variation to a large degree – it increases postmortem variation mainly via increasing species richness, and typically rather decreases total LD variation by reducing dispersion among DAs. The compositions of DAs from habitats characterized by high variability among LAs exhibit less modification by postmortem processes than DAs from temporally stable habitats, identifying a previously unrecognized first-order factor affecting estimates of postmortem variation.Source code for partitioning live-dead variation in taphonomic analysesSource code (R language) for partitioning of total live-dead compositional variation among multiple living (individuals sampled alive) and death assemblages (individuals collected as dead) into variation caused by (1) sampling and biological variation among living assemblages and (2) new variation that arises from postmortem taphonomic processes. The balanced design is required, i.e., the same number of living and death assemblages sampled in the same (homogeneous) habitat.sourcecodeforpartitioning-TomasovychandKidwell.txtCounts of living individuals in subtidal habitats off San Juan IslandsCounts of mollusk individuals sampled alive by dredge in 2002 at several subtidal stations off San Juan Islands. The source of data and description of sampling and counting methods is in: Kowalewski M., Carroll M., Casazza L., Gupta N., Hannisdal B., Hendy A., Krause R. A. Jr., LaBarbera M., Lazo D.G., Messina C., Puchalski S., Rothfus T. A., Sälgeback J., Stempien J., Terry R.C., Tomašových A. 2003, Quantitative fidelity of brachiopod-mollusk assemblages from modern subtidal environments of San Juan Islands, USA. Journal of Taphonomy 1, 43-65SanJuanIslands-livingassemblages.txtCounts of all dead individuals in subtidal habitats off San Juan IslandsCounts of dead mollusk individuals sampled by dredge in 2002 at several subtidal stations off San Juan Islands. This is exhaustive dataset - includes all fragments and is not corrected for disarticulated elements. The source of data and description of sampling and counting methods is in: Kowalewski M., Carroll M., Casazza L., Gupta N., Hannisdal B., Hendy A., Krause R. A. Jr., LaBarbera M., Lazo D.G., Messina C., Puchalski S., Rothfus T. A., Sälgeback J., Stempien J., Terry R.C., Tomašových A. 2003, Quantitative fidelity of brachiopod-mollusk assemblages from modern subtidal environments of San Juan Islands, USA. Journal of Taphonomy 1, 43-65SanJuanIslands-deathassemblages-exhaustivedataset.txtCounts of complete dead individuals in subtidal habitats off San Juan IslandsCounts of dead mollusk individuals sampled by dredge in 2002 at several subtidal stations off San Juan Islands. This is restrictive dataset - includes complete individuals and is corrected for disarticulated elements. The source of data and description of sampling and counting methods is in: Kowalewski M., Carroll M., Casazza L., Gupta N., Hannisdal B., Hendy A., Krause R. A. Jr., LaBarbera M., Lazo D.G., Messina C., Puchalski S., Rothfus T. A., Sälgeback J., Stempien J., Terry R.C., Tomašových A. 2003, Quantitative fidelity of brachiopod-mollusk assemblages from modern subtidal environments of San Juan Islands, USA. Journal of Taphonomy 1, 43-65SanJuanIslands-deathassemblages-restrictivedataset.tx