DOI: 10.5061/dryad.1637
title: Data from: Accounting for the effects of biological variability and temporal autocorrelation in assessing the preservation of species abundance

description: 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.
description: 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.txt