DOI: 10.5061/dryad.0vt4b8h54
title: Bioturbation increases time averaging despite promoting shell disintegration: a test using anthropogenic gradients in sediment accumulation and burrowing on the southern California shelf

description: Bioturbation can increase time averaging by downward and upward movements
 of young and old shells within the entire mixed layer and by accelerating
 the burial of shells into a sequestration zone (SZ), allowing them to
 bypass the uppermost taphonomically active zone (TAZ). However,
 bioturbation can increase shell disintegration concurrently, neutralizing
 the positive effects of mixing on time averaging. Bioirrigation by
 oxygenated pore water promotes carbonate dissolution in the TAZ, and
 biomixing itself can mill shells weakened by dissolution or microbial
 maceration, and/or expose them to damage at the sediment-water interface.
 Here, we fit transition rate matrices to bivalve age-frequency
 distributions from four sediment cores from the southern California middle
 shelf (50-75 m) to assess the competing effects of bioturbation on
 disintegration and time averaging, exploiting a strong gradient in rates
 of sediment accumulation and bioturbation created by historic wastewater
 pollution. We find that disintegration covaries positively with mixing at
 all four sites, in accord with the scenario where bioturbation ultimately
 fuels carbonate disintegration. Both mixing and disintegration rates
 decline abruptly at the base of the 20-40 cm-thick, age-homogenized
 surface mixed layer at the three well-bioturbated sites, despite different
 rates of sediment accumulation. In contrast, mixing and disintegration
 rates are very low in the upper 25 cm at an effluent site with legacy
 sediment toxicity, despite recolonization by bioirrigating lucinid
 bivalves. Assemblages that formed during maximum wastewater emissions vary
 strongly in time averaging, with millennial scales at the low-sediment
 accumulation non-effluent sites, a centennial scale at the effluent site
 where sediment accumulation was high but bioturbation recovered quickly,
 and a decadal scale at the second high-sedimentation effluent site where
 bioturbation remained low for decades. Thus, even though disintegration
 rates covary positively with mixing rates, reducing postmortem shell
 survival, bioturbation has the net effect of increasing the time averaging
 of skeletal remains on this warm-temperate siliciclastic shelf.
description: # Bioturbation increases time averaging despite promoting shell
 disintegration: a test using anthropogenic gradients in sediment
 accumulation and burrowing on the southern California shelf
 [https://doi.org/10.5061/dryad.0vt4b8h54](https://doi.org/10.5061/dryad.0vt4b8h54) ## Description of the data and file structure ### Southern California age data in cores.txt source age data from four sediment cores, with original amino acid racemization data /and also surface age data from Van Veen grabs. * Sediment core ID - Station column * Postmortem shell age - Age (years) column, years before the time of sampling /AD 2012/, based on radiocarbon-amino acid calibration, using the Bayesian calibration approach used in Tomašových, A., Kidwell, S.M., Alexander, C.R. and Kaufman, D.S., 2019. Millennial‐scale age offsets within fossil assemblages: Result of bioturbation below the taphonomic active zone and out‐of‐phase production. *Paleoceanography and Paleoclimatology*, *34*, 954-977. * Species name - taxon column * Shell collected alive or dead - State column * Increment number in high-resolution models - Fine-scale unit column /topmost increment is 1, progressing downcore/ ### Layer number in low-resolution models Coarse-scale unit column 1 - upper layer that is age-homogeneous and can be equivalent to the taphonomically active zone, 2  - subsurface layer that is below the age-homogeneous well-mixed layer and can be equivalent to the sequestration zone Information about the sediment core ID, boxcore, or vibracore BC or VC - Site-core-section-depth column. Original sediment depth - Upper and Lower depth columns in cm below the sediment-water interface Composite depths - Increment upper and lower depth columns. ## Code/Software ### upload age data.txt R script that uploads the postmortem age data from "Southern California age data in cores.txt", depending on the core that is analyzed and the model (low-resolution or high-resolution) that is fitted. Increments are numbered from the top of cores (1) to their bottom (11-13). When fitting ages to transition matrices, ages (in years) are divided by a factor of 1,000, and maximum-likelihood estimates of rates are then divided by 1000 to bring them back to years-1. ### source high-resolution transition matrix models.txt R script with functions that find maximum-likelihood estimates of disintegration, symmetric mixing, and sediment accumulation rates (myest) and functions (Amat) that create transition-rate matrices with 11-13 increments (INCREMENTS argument), used in high-resolution models. In models with diagenetic stabilization, the number of increments in the TAZ, i.e., increments that receive shells from the SZ, must be apriori specified (TAZ argument), even when estimates of disintegration are estimated independently of this argument. There are four versions of transition-rate matrices defined in Amat functions - /1/without diagenetic stabilization (stabilization=FALSE) and without temporal shift in sediment accumulation (argument SED.SHIFT=0), /2/ without diagenetic stabilization and with temporal shift in sediment accumulation (argument SED.SHIFT equal to increment at which sedimentation changes), /1/with diagenetic stabilization and without temporal shift in sediment accumulation, /1/with diagenetic stabilization and with temporal shift in sediment accumulation. ### source transition matrix models-2 layers.txt R script with functions that find maximum-likelihood estimates of disintegration, burial, and exhumation rates (myest function) and functions that create transition-rate matrices (Amat functions) for simple models with two layers (surface TAZ layer-taphonomically active zone, and subsurface SZ layer - sequestration zone), used in low-resolution models, with stabilization (stabilization=TRUE) or without diagenetic stabilization (stabilization=FALSE). ### R script for high-resolution models.R age distributions in each core are fitted to two matrices, with and without diagenetic stabilization. This script is used in high-resolution models and the production of Figures 7 and 8. ### R script for low-resolution models with two layers.R age distributions in each core are fitted to two matrices, with and without diagenetic stabilization. This script is used in low-resolution models and production of Figure 9. ### R script for SoCal bioturbation ms - data analyses.R documentation of all analyses of age-frequency distributions, with figures 5 and 10, using "Southern California age data in cores.txt" as input. Age-frequency distributions fitted to transition matrices correspond to "high-resolution" binning.