henhaobio
Sign in

bioRxivPaleontologyPreprint

Stratigraphic Paleobiology of Carbonate Systems

Niklas HohmanniD, Sidney BickertoniD, Anna JanseniD, Xianyi LiuiD, Emilia JarochowskaiD

PDFDOICodeData
In-depth full-text digest available · Jump to digest ↓

Abstract

Stratigraphic paleobiology is a newly established interdisciplinary approach, which has demonstrated that the fossil record is a joint expression of biotic and stratigraphic change, and all inferences from it must be grounded in a solid understanding of the stratigraphic context. Fossiliferous strata can be found in all depositional systems (e.g., marine, terrestrial, or lacustrine; siliciclastics or carbonates), each having a unique characteristic timescale and set of external controls, which govern the accumulation of sedimentary particles, including fossils. Consequently, the same biotic changes are preserved differently across depositional systems. While carbonate systems form a large portion of the fossil record, most studies in stratigraphic paleobiology have focused on siliciclastic systems and are not easily generalizable. As they are predominantly formed by living organisms, carbonates are both fossils and record, opening the opportunity to study the co-dependency of life and its environment. Here, we explore the stratigraphic paleobiology of carbonate systems by combining simulations of carbonate platform and ramp geometries with synthetic fossil records. We explore the preservation of extinction patterns and rates spatially and across geometries. By examining stratigraphic biases in isolation (unconformity and condensation, ecology, and abundance biases), we find characteristic differences between ramp and platform geometries due to their differential response to sea level change, spatial variability, and differences in ecological clines. Differences in the structure of the fossil record between platform geometries are traceable to the contribution and properties of the carbonate producing organisms (carbonate factories), showing that preservation of earth system data in carbonate systems will vary both latitudinally and temporally or as a result of major perturbations of the biogeosphere. Our results show that while general rules on the structure of the fossil record can be derived for entire depositional systems, accounting for the geological and ecological dynamics of a particular sedimentary basin can hugely refine interpretations of the fossil record. That is particularly true for biogenic and biologically-mediated sediments.

In-depth summary

Claude Opus 5.5 · xhigh effort · 7 Nov 2026 · from the full text of version 2 (10 Aug 2026) · CC BY 4.0

Simulated tropical carbonate platforms and temperate ramps under identical sea-level forcing yield different fossil records: platform tops push apparent extinctions into transgressive tracts, while ramp unconformity bias fades gradually offshore.

Stratigraphic paleobiology has mostly studied siliciclastic settings, yet carbonates hold a large share of the fossil record, are produced largely by organisms and differ in sequence stratigraphy. Coupling a carbonate forward model with synthetic fossil records, the study separates unconformity/condensation, ecological and abundance biases and compares platform with ramp geometries.

Key results

  1. SuggestedUnder the same subsidence and sea-level forcing, the platform splits sharply into a gap-dominated platform top and a near-continuous slope. The distally steepened ramp changes gradually from onshore to offshore.

    Platform top: completeness below 25 % at 1 kyr; the highstand (HST) and regressive (RST) systems tracts are lost to gaps. Prograding edge near 100 %; distal slope approx. 80 % with sedimentation around 10 m/Myr. Ramp: 40 % on the inner ramp, rising to almost 100 % on the distal outer ramp. The platform edge progrades 2 km, while the ramp shows no net progradation over 4 Myr. · Stratigraphic architectures; Platform; Ramp

  2. SuggestedAge misassignment bias (unconformity plus condensation) was scored with a condensation ratio against a naive constant-sedimentation age model. It is high on the platform top and prograding edge, absent on the platform slope, and declines gradually down the ramp.

    The condensation ratio stays close to 1 on the platform distal slope, ramp slope and outer ramp, but spans below 0.3 to 10 on the prograding platform edge. On the platform top, rates are overestimated 10-fold across the unconformity between the transgressive (TST) and lowstand (LST) systems tracts, and underestimated more than 3-fold within the TST. · Unconformity and condensation bias; Unconformity and condensation bias; Unconformity and condensation biases and the…

  3. SuggestedOn the platform top, extinction pulses from the HST, RST and LST are recovered in the TST, while pulses that occur during the TST are diluted. Pulses are better preserved distally and easier to correlate laterally on the ramp.

    Pulses are recovered from the TST with a temporal misassignment of more than 1.5 Myr; TST pulses are diluted threefold by rapid platform growth. On the ramp, HST pulses stay in the correct tract. Setup: extinction elevated 25-fold within one systems tract, conditioned on 1000 taxa, 10 fossils per Myr in the main figures. · Preservation of extinction pulses; Extinctions by systems tracts; Spatial correlation of extinction pulses; Preservation of extinction pulses and abundance…

  4. SuggestedBiostratigraphic precision is coarse. Temporal range offset peaks where the platform progrades, because shallowing-upward adds ecological bias to unconformity bias, and it falls offshore. Elsewhere, water-depth (ecological) bias is weak because in situ production keeps pace with sea level.

    Median temporal range offset: about 700 kyr on the platform top; 1.04 Myr (Q3 1.97 Myr) at the proximal prograding edge; 280 and 220 kyr on the slope; 600 kyr on the inner ramp down to 160 kyr on the distal outer ramp. Median stratigraphic range offset is 25 m at the proximal prograding edge and around 4 m on the ramp. No rapid water-depth changes occur across unconformities. · Ecological bias; Range offset; Ecological bias and water depth as principal…; Range offset

  5. SuggestedLow fossil abundance (the Signor-Lipps effect) is a secondary bias that can either strengthen or erase stratigraphic artefacts. It is most misleading at intermediate sampling rates.

    At the proximal prograding platform edge, backward smearing peaks at 10 and 22 fossils per Myr. With abundant fossils, last occurrences cluster at the RST1/LST1 and TST2/LST2 unconformities; with rare fossils, none of the long gaps show. On the distal slope there is no smearing at any sampling rate (tested range 2 to 100 fossils per Myr). · Abundance bias and preservation of extinction…; Abundance effects; Preservation of extinction pulses and abundance…

Methods, data and reproducibility

Two carbonate platforms were simulated for 4 Myr in CarboKitten.jl under identical subsidence and sea-level forcing: a tropical euphotic-factory platform with rapid cementation and little transport, and a temperate oligophotic-factory ramp with slow lithification and more transport. Age-depth models and water depths along dip transects drove synthetic fossil-record simulations in R (admtools, StratPal).

  • Simulated tropical carbonate platform (euphotic factory dominant): 7.5 x 22.5 km box, 150 m cells, 4 Myr main run at 100-year steps after a 1 Myr pre-run · 10.5281/zenodo.20670764
  • Simulated temperate carbonate ramp (oligophotic factory dominant), same box, subsidence 20 m/Myr, sea-level periods 2 and 0.2 Myr with amplitudes 15 and 2.5 m · 10.5281/zenodo.20670764
  • Synthetic extinction scenarios: constant baseline plus 25-fold rate elevation within one systems tract (HST, TST, LST or RST), sampling 2 to 100 fossils per Myr · n = conditioned on 1000 taxa going extinct
  • Synthetic taxa for range offset: log-uniform sampling 2 to 100 fossils per Myr, preferred depth uniform 0 to 120 m, depth tolerance gamma (shape 1, scale 10) · n = 1000 taxa per geometry and examined location
Methods & tools
CarboKitten.jl v0.6.0, Julia, R 4.5.3, admtools, StratPal (p3_var_rate, p3, range_offset, snd_niche), Burgess (2013) cellular automaton as re-implemented in CarboKitten, CarboKitten empirical denudation model, Holland and Patzkowsky (1999) probability of collection niche model, Bosscher and Schlager (1992) production-depth parametrization
Software & environment
CarboKitten.jl v0.6.0 (Julia) for the stratigraphic runs; R version 4.5.3 with admtools and StratPal for post-processing and fossil simulation.
Reproducibility gaps
No versions are given for Julia, admtools or StratPal, and no hardware or run time is reported.
Limitations (6)
  • Fossils are never moved or reworked. The fossil simulation runs after the stratigraphic model with no feedback to it, so lateral transport, erosional entrainment and bioturbation are ignored. · stated by the authors
  • Records are treated as continuous at the 1 kyr model resolution on the assumption of time-averaging, whereas time-averaging in many depositional systems spans several kyr. · stated by the authors
  • Water depth is the only ecological gradient. In shallow (< 40 m) carbonate settings over short distances (< 10 km) it no longer predicts facies reliably, and salinity or hydrodynamic energy may matter more. · stated by the authors
  • The two runs are conceptual endmembers, not reproductions of real platforms. Systems tracts were assigned from the known sea-level curve and may differ from a field interpretation based on stacking patterns. · stated by the authors
  • Results rest on one parameter set per geometry and a single sea-level curve. Neither a sensitivity analysis nor a comparison with measured carbonate sections is reported. · noted in this summary
  • The text contradicts itself in places. S18 puts the median range-offset peak at the proximal prograding edge, but S24 puts it at the distal edge, and S10 and S17 disagree on which HST/RST intervals the proximal prograding edge preserves. · noted in this summary

Read this if you infer extinction, origination or evolutionary rates from fossils in carbonate successions, or want a forward-modelling setup for testing how platform versus ramp stratigraphy distorts those signals.

Citations
1

Reproducibility ledger

Nobody has reported trying to reproduce this paper yet. Did you replicate an experiment or run the code? Your report saves the next lab a week.

Sign in to file a reproducibility report.

Related papers

Similarity Map
SelectedSame fieldCross-field
THISHohmann '25Hohmann '23Rojas '26Pei '20Rojas '20Roopnarine '17
62% semantic matchPaleontology
Niklas Hohmann, Emilia Jarochowska·Methods in Ecology and Evolution·Feb 11, 2025· 3 citations