Biology subjects

Jarochowska, E.

Publications and source records attributed to Jarochowska, E..

6 recordsLinked to original sources

bioRxiv2026

Phylogenetic inference from an incomplete fossil record

Fossil data is crucial to construct phylogenetic time trees, which serve as the basis to test a wide range of evolutionary hypotheses. While the fossil record is known to be incomplete, modern stratigraphy provides predictions of the structure of the fossil record as expressed by gap location and duration. Advances in phylogenetic model development allow us to propagate this information into Bayesian phylogenetic inference in the form of priors on time-variable fossil sampling. However, the impact and role of stratigraphic architectures on time tree inference has so far remained unexplored. We introduce a novel simulation framework that combines realistic stratigraphic forward models with phylogenetic simulations. Using this framework, we examine (1) how stratigraphically plausible model violations of fossil sampling due to gaps affect total-evidence inference under the fossilized birth-death model and (2) if stratigraphic knowledge on gap duration and timing improves inference when incorporated in priors on fossil sampling. We find that total-evidence analysis is robust to stratigraphically plausible distribution of gaps in disparate stratigraphic architectures, with results being instead dominated by the number of morphological characters. Surprisingly, incorporating information on prominent gaps in the stratigraphic record does not improve phylogenetic inference. Our results suggest that phylogenetic inference is robust to model violations introduced by stratigraphic gaps over short timescales, with results being dominated by a priori known data availability constraints such as morphological character matrix size. This research establishes the foundations for joint modeling of phylogenetic and stratigraphic processes and narrows the knowledge gap between paleontology, stratigraphy, and neontology.

paleontology↗

bioRxiv2026

Stratigraphic Paleobiology of Carbonate Systems

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.

paleontology↗

bioRxiv2024

StratPal: An R package for creating stratigraphic paleobiology modeling pipelines

O_LIThe fossil record is an important source of information to understand biological processes that take place over timescales not accessible to human observation or experiments. Fossil data is not a perfect reflection of past biological change, but a joint expression of stratigraphic, ecological, evolutionary, and taphonomic effects. Stratigraphic biology is a field dedicated to identifying these effects and accounting for them. C_LIO_LIWe present StratPal, a R package in which stratigraphic, ecological, evolutionary, and taphonomic modules can be combined into modeling pipelines for stratigraphic paleobiology. C_LIO_LIWe describe the types of data that can be modified and transformed using this approach, and briefly discuss potential extensions. C_LIO_LIAs working examples, we show how the pipeline can be used to model clustering of last occurrences at hiatuses and condensation surfaces, leading to artefactual "extinction events" caused by stratigraphic gaps. C_LI

paleontology↗

bioRxiv2023

Identification of the Mode of Evolution in Incomplete Carbonate Successions

AbstractO_ST_ABSBackgroundC_ST_ABSThe fossil record provides the unique opportunity to observe evolution over millions of years, but is known to be incomplete. While incompleteness varies spatially and is hard to estimate for empirical sections, computer simulations of geological processes can be used to examine the effects of the incompleteness in silico. We combine simulations of different modes of evolution (stasis, (un)biased random walks) with deposition of carbonate platforms strata to examine how well the mode of evolution can be recovered from fossil time series, and how test results vary between different positions in the carbonate platform and multiple stratigraphic architectures generated by different sea level curves. ResultsStratigraphic architecture and position along an onshore-offshore gradient has only a small influence on the mode of evolution recovered by statistical tests. For simulations of random walks, support for the correct mode decreases with time series length. Visual examination of trait evolution in lineages shows that rather than stratigraphic incompleteness, maximum hiatus duration determines how much fossil time series differ from the original evolutionary process. Gradual directional evolution is more susceptible to stratigraphic effects, turning it into punctuated evolution. In contrast, stasis remains unaffected. ConclusionsO_LIFossil time series favor the recognition of both stasis and complex, punctuated modes of evolution. C_LIO_LINot stratigraphic incompleteness, but the presence of rare, prolonged gaps has the largest effect on trait evolution. This suggests that incomplete sections with regular hiatus frequency and durations can potentially preserve evolutionary history without major biases. Understanding external controls on stratigraphic architectures such as sea level fluctuations is crucial for distinguishing between stratigraphic effects and genuine evolutionary process. C_LI

evolutionary biology↗

bioRxiv2021

Does time matter in phylogeny? A perspective from the fossil record

The role of time (i.e. taxa ages) in phylogeny has been a source of intense debate within palaeontology for decades and has not yet been resolved fully. The fossilised birth-death range process is a model that explicitly accounts for information about species through time. It presents a fresh opportunity to examine the role of stratigraphic data in phylogenetic inference of fossil taxa. Here, we apply this model in a Bayesian framework to an exemplar dataset of well-dated conodonts from the Late Devonian. We compare the results to those obtained using traditional unconstrained tree inference. We show that the combined analysis of morphology and stratigraphic data under the FBD range process reduces overall phylogenetic uncertainty, compared to unconstrained tree inference. We find that previous phylogenetic hypotheses based on parsimony and stratophenetics are closer to trees generated under the FBD range process. However, the results also highlight that irrespective of the inclusion of age data, a large amount of topological uncertainty will remain. Bayesian inference provides the most intuitive way to represent the uncertainty inherent in fossil datasets and new flexible models increase opportunities to refine hypotheses in palaeobiology.

paleontology↗

bioRxiv2021

Growth allometry and dental topography in Upper Triassic conodonts supports trophic differentiation and molar-like element function

Conodont elements have high rates of morphological evolution, but the drivers of this disparity are debated. Positive allometric relationships between dimensions of food-processing surfaces and entire P1 elements have been used in to argue that these elements performed mechanical digestion. If involved in food processing, the surface of the element should grow at a rate proportional to the increase in energy requirements of the animal. This inference of function relies on the assumption that the energy requirements of the animal grew faster ({cong} mass0.75) than the tooth area ({cong} mass0.67). We re-evaluate this assumption based on metabolic rates across animals, and calculate the allometry in platform-bearing P1 elements of Late Triassic co-occurring taxa, Metapolygnathus communisti and Epigondolella rigoi, using 3D models of ontogenetic series. Positive allometry is found in platform and element dimensions in both species, supporting a grasping-tooth hypothesis, based on the assumption that metabolic rate in conodonts scaled with body mass similarly to that in fish and ectoterms. We also calculate the curvature of P1 platform surface using the Dirichlet Normal Energy (DNE) as a proxy for diet.DNE values increase with body mass, supporting the assumption that conodont metabolic rates increased faster than mass0.67. We finally find that adults in both taxa differ in their food bases, which supports trophic diversification as an important driver of the remarkable disparity of conodont elements.

paleontology↗