Welcome to my personal webpage!

Overview

1. Molecular Paleobiology: an emerging field of science

As a Molecular Paleobiologist I work towards advancing our understanding of the chemical mechanisms and environmental requirements involved in biomolecule fossilization, and I apply this knowledge to develop new proxies which allow reconstructing the physiology, relationships, and behaviors of long extinct organisms. I combine data for fossil and living taxa, and interpret this information in a macroevolutionary framework to learn more about how life on our planet came to be, reacted to past environmental change, and evolved into its modern-day diversity. Ultimately, my research aims at exploring to which extent we can truly integrate molecular data for extinct and modern life forms.

I am particularly interested in applying molecular proxies to the topics of prebiotic and extraterrestrial organic chemistry, the origin(s) and early evolution of Life, the evolution and nature of animal biomineralized tissues, the amniote metabolism, and archosaur reproduction. To do so, I rely on the power of large and diverse fossil and modern sample sets that are analyzed via an array of non-destructive in situ methods for patterns in their molecular composition. My research is located at the interface of chemistry, biology, and geology, and stretches across the entire tree of life.

OVERVIEW

Geology

Chemistry

Biology

2. The building blocks of life in deep time: biomolecule fossilization

Biomolecules generate all organismic form and function, and are therefore particularly informative for reconstructing the history of life. It was long assumed that biomolecules decay rapidly postmortem. However, my research revealed that proteins, lipids, sugars, and certain pigments leave characteristic traces in the fossil record. Different classes of biomolecules undergo characteristic chemical alterations during diagenesis, and tend to transform into more stable compounds which can survive in the geological record for more than 500 million years.

RESEARCH

2a. The mechanism of biomolecule fossilization

During early diagenesis (days to years postmortem), oxidative conditions trigger the formation of Reactive Carbonyl Species (RCS) from lipids and sugars. Oxidative conditions are prevalent in, i.e., fluvial, alluvial, and shallow marine sediments. Lipid- and sugar-RCS show distinct affinities for exposed amino acid residues of omnipresent proteins. Primary targets are nucleophilic amino acid residues, such as arginine, lysine, histidine, and cystein, as well as the protein N-terminus. Observed fossilization reactions include primarily C-C-bond forming reactions, such as transition metal-catalyzed additions. The resulting crosslinking products fall either in the category of Advanced Lipoxidation End Products (ALEs), or Advanced Glycoxidation End Products (AGEs). ALEs and AGEs are composed of N-, O-, S-heterocyclic polymers – compounds that are water-insoluble, indigestible to microbes, and energetically stable. There does not seem to be an age limit for the preservation of N-, O-, S-heterocyclic polymers in the geological record!

Protein fossilization products tend to coordinate available transition metals, such as iron, stabilizing the resulting coordination complex against temperature, pressure, and dissolution stress. While advanced crosslinking consumes peptide bonds, my research provided the first evidence for intact peptide bonds in fossil organic matter. Intact peptide bonds do not imply the presence of unaltered protein or peptide fragments, since attached amino acid residues may well be chemically transformed and can, therefore, not be sequenced.

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This figure is part of Wiemann et al. 2020.

Research

2b. Assessing the degree of diagenetic alteration

I developed a new proxy based on the ratio of peptide bonds (chemically trans - amides) to crosslinking products of amine-bearing amino acid residues (cis - amides). This proxy allows to assess the degree of protein alteration in a fossil sample. My data suggest that biomineralized tissues shield contained biomolecules better against diagenetic alteration than non-biomineralized tissues.

2c. The ChemoSpace: how to rule out contamination

To rule out exogenous sources of organic matter associated with fossils, I analyzed more than 100 fossils and associated sediments in a ChemoSpace. The composition of animal organic matter is significantly different from the composition of (primarily protist-derived) sedimentary fossil organic matter. Thioethers, S-heterocycles, and peptide bonds are significantly more abundant in animal fossil organic matter than in sedimentary organic matter. An endogenous source of fossil organic matter allows for the exploration of molecular biological signals preserved in deepest time.

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Fossil organic matter, Raman spectroscopy

2d. Organic matter permineralization

Early diagenetic mineralization is often considered a key process in preserving fossil soft tissue morphologies and storing organic carbon in deep time. I analyzed more than 300 fossils and sediments to understand the mechanisms involved in phosphatization, pyritization, silicification, and clay mineral precipitation to identify endogenous or exogenous sources of mineral building blocks, potentially present bioinorganic interactions evidencing templating of organic matter, and biological and environmental parameters determining the mode of diagenetic tissue mineralization.

More information is coming soon!

Pyritized fossil

3. The biological significance of fossil organic matter

Proteins, lipids, and sugars in fresh tissue samples contain information on biomineralization, tissue composition and identity, metabolism, and organismal relationships – and so do their fossilization products. Listed below are the latest insights into the nature of these biosignatures, details on how they fossilize, and assessments of the biosignal quality through geological time.

Jump to the applications:

Archosaur eggshell biomineralization and homology

nature

3a. The biomineralization signal

The most prominent biological signal preserved in fossil organic matter identifies whether a fossil tissue was originally biomineralized or not.

In a biomineralized tissue, abundant coordinating or chelating amino acid residues on the surface of a structural protein interact with ions of the biomineral phase. Non-biomineralized tissues lack comparable quantities of coordinating and/or chelating amino acid residues. My research showed that originally biomineralized fossil tissues cluster separately from originally non-biomineralized fossil tissues, and revealed more abundant coordinating and/or chelating ligands as key feature of originally biomineralized tissues. This signal preserves even in temperature- and pressure-matured Cambrian fossils from the Burgess Shale.

I currently investigate the evolution and homology of biominerals in all stem- and crown-animals ([Stem-] Metazoa].

[More information is coming soon!]

This proxy has the potential to fundamentally advance our understanding of the nature and evolution of biomineralized tissues, as exemplified in our recent study on eggshell evolution in Nature.

RESEARCH

3b. The tissue type signal

The tissue type signal groups tissues of the same type in a ChemoSpace. By using a training data set of fossil tissues with a known identity, fossil tissues of unknown type can efficiently and non-destructively be identified.

Different tissues contain characteristic relative amounts of proteins, lipids, and sugars. These compositional fingerprints preserve in the relative amounts of lipoxidation and glycoxidation end products: during early diagenesis, lipids generate characteristic Reactive Carbonyl Species (RCS) which differ from those formed by sugars. Depending on their relative abundance in a tissue, lipid- and sugar-derived RCS crosslink with omnipresent proteins, preserving the original abundance of proteins, lipids, and sugars in the resulting composition of N-, O-, S-heterocyclic polymers in a fossil. This is the second most prominent signal in an animal tissue ChemoSpace.

Being able to unambiguously identify tissues in fossils can provide informative characters that help resolving phylogenetic affinities, as shown in our recent study on the phylogenetic affinity of the enigmatic tully monster, published in Geobiology.

Jump to the applications:

Tully monster tissue composition is consistent with chordates

3c. The metabolic signal

Metabolic stress leaves molecular traces. Such metabolic markers preserve in deep time and can be quantified to reconstruct the metabolic rates of long extinct animals. Vascularized and cellular tissues, such as bone, preserve metabolic modifications in their originally proteinaceous phase.

The metabolic proxy requires the use of homologous structures (due to intraskeletal/tissue-dependent variation) and is currently developed for amniote bone (femora). Current research is focused on expanding the phylogenetic applicability of the proxy and discriminating between minute differences in metabolic signals (i.e., true endotherms versus seasonal endotherms). Upcoming innovations include:

Clade-specific metabolic calibrations (to account for divergent strategies in ROS-scavenging across the vertebrate phylogeny)
Development of the metabolic signal for dentine (to collect complementary molecular metabolic and isotope-based paleothermometry data from the same sample)
Development of the metabolic signal for vertebrae (to include limbless [femoral proxy] and edentulous [dentine proxy] taxa)

Since aerobic mitochondrial respiration is older than the animal clade, ongoing projects explore the manifestation of molecular metabolic signals in invertebrates and extinct Neoproterozoic organisms.

Learn more about the approach:

Once calibrated based on skeletal metabolic markers of living animals, the abundance of metabolic stress markers can be translated into a metabolic rate (= the amount of oxygen respired relative to the body mass, in one hour of time). This is the most prominent biological signal in a fossil bone ChemoSpace.

Skeletal metabolic markers allow for the direct integration of modern and fossil data:

Understanding the metabolism of extinct animals allows to directly trace how organisms physiologically reacted to past environmental and ecological change, including mass extinction events. To make informed decisions on biodiversity conservation in times of global climate change, we need to trace the evolution of animal metabolism in response to comparable events evidenced in the geological record of life.

Check out our ScienceInsider Documentary:

rhea membrana testacea (18) - Copy_edite

3d. The phylogenetic signal

The phylogenetic signal relies on the compositional differences of amino acid-specific crosslinks in N-, O-, S-heterocyclic polymers. Even though no sequence information can be obtained, the similarity in the relative amino acid composition of homologous tissues provides insights into animal relationships.

Proteins represent translation products of the genetic code. A codon composed of a nucleotide triplet encodes for one out of 21 (for eukaryotes, 22 for all organisms) proteinogenic amino acids. While the sequencing of fresh tissues yields information on organismal relationships, diagenetic alteration of (most) peptide bonds in fossil N-, O-, S-heterocyclic polymers prevents the sequential cleavage of units through any conventional method. However, some amino acid residues do not engage in crosslinking chemistry during fossilization and can preserve without alteration, while others crosslink in characteristic ways: amine- and thiol-bearing amino acid residues yield diagnostic fossilization products. When comparing N-, O-, S-heterocyclic polymers of the same tissue type and from similar depositional settings, a cluster analysis of the fossil composition reflects organismal relationships. This is the least prominent biological signal in fossil organic matter, and preserves best in biomineralized tissues.

The ability to complement morphological assessments of organismal relationships with molecular data has the potential to resolve controversial nodes in the tree of life.

[More contents are coming soon!]

Click to enlarge!

Jump to the applications:

Phylogenetic signals in fossil organic matter

Phylogenetic signal in fossil organic matter

4. Applications: from molecules to macroevolution

Below, I provide links to relevant publications for some of my current key research questions (this list is not exhaustive). For a more complete overview, please reach out for my Research Statement.

How did life on Earth come to be, and is there life on other planets?

I investigate the chemical interactions between minerals and omnipresent simple organic molecules to understand how the replicator unit and its building blocks ancestral to all life on our planet evolved, and what this implies for the potentially independent emergence of life in Space.

I also explore the preservation of biological and environmental signatures in extraterrestrial carbonaceous materials.

The combined study of biomolecule fossilization on Earth and in Space provides a new perspective for the systematic search for extraterrestrial life.

The theoretical context for this work is available here:

Wiemann et al. 2020. Panbiota. In Phylonyms: a companion to the PhyloCode. Berkeley, University of California Press.

Here is the to the book chapter!

Wiemann et al. 2020. Biota. In Phylonyms: a companion to the PhyloCode. Berkeley, University of California Press.

Here is the to the book chapter!

More coming soon!

What is the material nature of modern & fossil biomineralized tissues, and how did they evolve?

Characterizing the biocomposite nature of modern and fossil animal skeletons and assessing their homology has the potential to provide spectacular insights into how life reacted to past environmental and ecological challenges. However, the geological record of biomineralized tissues can be difficult to read due to alterations and loss of the biomineral phase in fossils. Biomineralization signatures in carbonaceous fossil remains provide a powerful solution to this challenge.

The first insights into the preservation of biomineralization signatures, the fossilization of mineral-organic systems, and eggshell homology assessments are available here:

Wiemann et al. 2018. Fossilization transforms vertebrate hard tissue proteins into N-heterocyclic polymers. Nature Communications.

Here is the to the paper!

Wiemann et al. 2020. Phylogenetic and physiological signals in metazoan fossil biomolecules. Science Advances.

Here is the to the paper!

Norell*, Wiemann*, et al. 2020. The first dinosaur egg was soft. Nature.

Here is the to the paper!

More coming soon!

How did the amniote metabolism respond to past environmental perturbations?

I apply my recently developed metabolic rate proxy to trace how key extrinsic events in the evolutionary history of amniotes impacted their physiology, and how physiological responses relate to extinction.

Current projects target:

The relationship of fully aquatic adaptations and metabolism in modern and fossil marine reptiles
The role of the P/T mass extinction in the evolution of mammalian endothermy
Metabolism and megafauna extinction
Cross-methodological assessments of the extreme variation in metabolic and thermoregulatory capacities in ornithischian dinosaurs
Metabolism and gigantism: sauropod evolution
The role of mass extinctions in the exploration of physiological capacities leading to the evolution of endothermy (warm-bloodedness)

An introduction to the proxy and its application to the evolution of the avian metabolism is available here:

Wiemann*et al. 2022. Fossil biomolecules reveal an avian metabolism in the ancestral dinosaur. Nature, 10.1038/s41586-022-04770-6.

Here is the link to the paper!

More coming soon!

The dinosaur-bird transition: can reproductive features explain why birds are the only dinosaurs to survive into the modern?

The survival of mass extinction events and subsequent diversification is, at least in vertebrates, directly tied to the reproductive strategy. Analyzing organic matter preserved in fossil eggshells, I investigate how avian reproductive features evolved from their dinosaur ancestors. So far, I discovered that birds inherited colored eggs, open nests, and brooding behaviors from their maniraptoran dinosaur ancestors, and that the theropod lineage of calcified eggs evolved independently, just like calcified eggs in ornithischian and sauropod dinosaurs, from an ancestrally soft-shelled dinosaur egg. I am broadly interested in understanding how reproductive traits may have contributed to the survival of birds into the modern, as the only extant lineage of dinosaurs.

My work on this topic is available here:

Wiemann et al. 2017. Dinosaur origin of egg color: oviraptors laid blue-green eggs. PeerJ.

Here is the to the paper!

Wiemann et al. 2018. Dinosaur egg color had a single evolutionary origin. Nature.

Here is the to the paper!

Yang, Chen, Wiemann et al. 2018. Fossil eggshell cuticle elucidates dinosaur nesting ecology. PeerJ.

Here is the to the paper!

Wiemann et al. 2019. Reply to: egg pigmentation probably has an archosaurian origin. Nature.

Here is the to the paper!

Yang, Wiemann, et al. 2019. Reconstruction of oviraptorid clutches illuminates their unique nesting biology. Acta Paleontologia Electronica.

Here is the to the paper!

Norell*, Wiemann* et al. 2020. The first dinosaur egg was soft. Nature.

Here is the to the paper!

More coming soon!

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RESEARCH

5. Methodological advancement:

efficient & customizable proxies

A key challenge of geochemical approaches to the history of life is the destructive nature of most analytical routines, as well as the lack of exploratory analyses which do not require prior assumptions or knowledge of the sample composition. Fossils represent unique evidence of past life, and the trade-off between novel data and fossil specimen conservation often restricts geochemical studies to small sample sets.

I am dedicated to the exploration and optimization of non-destructive, exploratory chemical methods that allow the rapid and inexpensive molecular characterization of biological, paleontological, geological, and extraterrestrial samples.

Beyond a diverse array of established ex situ chemical analyses (mass spectrometry, X-ray spectroscopy, spectrophotometry), my current work focuses on novel in situ Raman microspectroscopy and Fourier-Transform Infrared (FT-IR) spectroscopy, two complementary non-destructive approaches that yield complete information on functional groups in organic matter, crystallinity and lattice properties in minerals, bioinorganic interactions in metal-organic systems, and hierarchical superstructures in more complex organic frameworks. Thereby, the total composition of heterogenous samples (such as fossils and sediments) can be comprehensively characterized. Spectral fingerprinting allows to perform compound presence/absence tests (compare: mass spectrometry), and individual bands or sets of bands can be mapped out over sample surfaces. The resulting spectral data can be analyzed by means of multivariate statistics (i.e., the ChemoSpace approach), following clinical standard procedures.

Here is a link to the standard strategies and procedures for analyzing spectroscopic data collected for biological materials.

Previous experience with different spectroscopic set-ups

I have - so far - collected spectral fingerprints of modern and fossil biological and geological materials with various different instruments. My personal favorite for organic work is the Horiba LabRam series, but all of these instruments are great and produced (Raman or FT-IR) data that can be integrated in a ChemoSpace, as long as the same excitation source is used:

Horiba LabRam 800 (notch filter) in Yale EPS: Great instrument for organic detection due to the excellent detector sensitivity at relatively low signal-to-noise ratios as expected for organic materials. 532 nm.
Horiba LabRam Evolution (edge filter) in Yale MCC: The upgraded model of the LabRam 800, compact and equipped with the same strengths for organic detection as the precursor model. 532 nm, 633 nm.
Agilent ATR FT-IR in Yale Chemistry: Intuitive and easy to handle.
Renishaw Invia (ULF & edge filters) in Caltech GPS Mineralogy: Equipped with an ecxeptionally high line grating option (2400 l/mm) which is great for resolving broad organic bands. 514 nm.
StellarNet homebuilt Raman (edge filter) in Caltech GPS Planetary: Versatile construction that can be easily adjusted for different experimental set-ups. 532 nm.
Nicolet ATR FT-IR in Caltech GPS Mineralogy: Connected to a microscope set-up for transmission FT-IR mapping.
WITec alpha 300 (edge filter) at the Chicago Field Museum: Excellent mapping capabilities, great for large compound maps. 532 nm.

The power of the ChemoSpace

Ordination methods, such as Principal Component Analysis (PCA) or Canonical Correspondence Analysis (CCA), are clinical standard tools celebrated for their power in (1) spectral denoising and (2) informative feature extraction. I have modelled and quantified the impact of different signal-to-noise ratios, baselines, and normalization procedures on ChemoSpace (PCA & CCA) biosignatures. ChemoSpace clustering is not significantly affected by any of these factors.

[More information is coming soon!]

Raman and FT-IR ChemoSpace biosignatures applied by other labs

It is very exciting to see how colleagues around the globe are exploring and applying the phylogenetic and physiological signals evidenced in spectroscopic data! I use this part of my homepage to showcase recent ChemoSpace applications (updated on a regular basis).