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Paleontology in the 21st Century
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Paleontology in the 21st Century

A special issue of Biology (ISSN 2079-7737). This special issue belongs to the section "Evolutionary Biology".

Deadline for manuscript submissions: closed (30 June 2022) | Viewed by 112606

Printed Edition Available!
A printed edition of this Special Issue is available here.

Special Issue Editors

Prof. Dr. Mary H. Schweitzer

E-Mail Website1 Website2
Guest Editor
1. Professor, Department of Biological Sciences, North Carolina State University, Raleigh, NC 27601, USA
2. Research Curator, North Carolina Museum of Natural Sciences, Raleigh, NC 27601, USA
3. Research Associate, Museum of the Rockies, Montana State University, Bozeman, MT 59717, USA
4. Visiting Professor, Department of Geology, Lund University, PO Box 117, SE-221 00 Lund, Sweden
Interests: fossils; molecules; evolutionary biology; vertebrate paleontology; evolution
Dr. Ferhat Kaya

E-Mail Website
Guest Editor
1. Department of Geosciences and Geography, University of Helsinki, P.O. Box 64, 00014 Helsinki, Finland
2. Archaeology Department, University of Oulu, P.O. Box 8000, FI-90014 Oulu, Finland
Interests: mammal paleontology of Eurasia and Africa from the neogene and quaternary; small mammals; great apes; paleobiology; paleoecology

Special Issue Information

Dear Colleagues,

Paleontology is the scientific discipline that investigates the origin and evolution of the biosphere. Fossils are any evidence of past life; thus in the broadest sense, fossils can refer to biomarkers indicative of life processes, microbial mats (some of the earliest evidence of life on this planet), footprints and trackways, shelly fossils, and the enigmatic Vendian and Ediacaran remains, as well as more familiar vertebrate fossils, including dinosaurs, birds, turtles, wooly mammoths, sabre tooth cats, and of course ancient humans.

Historically, paleontology emerged as a science for describing and cataloging fossils, but these early efforts were not accomplished using a rigorous and consistent evolutionary framework until the acceptance and application of Hennig’s concepts of phylogenetic systematics in the 1960s. This lag may have been facilitated by the expansion of DNA and protein phylogenies established for living organisms, while paleontology was assumed to be limited to morphological analyses. Traditionally, paleontologists mainly relied on gross anatomical information obtained from the remains of extinct organisms interred in the sedimentary record to propose hypotheses about function and evolutionary relationships, based upon shared, derived, morphological characteristics.

Moving forward to the 20th century, paleontology assumed a prominent role in evolutionary biology thanks to the paleontologist George Gaylord Simpson, who made significant contributions to the development of the Modern Synthesis in biology. This paradigm shift in paleontology was also noted by evolutionary biologist John Maynard Smith: “The paleontologists have too long been missing from the high table. Welcome back”. In the last 50 years, paleontology has undergone revolutionary transdisciplinary developments in the areas such as evolution, ecology, environmental change, climate modelling, developmental biology (evo-devo), molecular biology and analytical biochemistry, facilitated by methodological advances and sophisticated new tools.

Moving into the 21st century, the methodological advances and sophisticated new tools of molecular biology and analytical biochemistry, together with new imaging techniques and histological analyses, have provided access to novel sources of geobiologically relevant information in ancient remains. The data produced using these new approaches are challenging conventional wisdom regarding preservation, taphonomic modes and aspects of physiology, evolution and the relationships among extinct organisms. The integrative approaches in paleontology have the potential to provide crucial knowledge derived from the last 3.6 billion years of Earth’s history to inform appropriate responses to problems facing us today and into the future, including responses to hypothesized declines in biodiversity and accelerated climate change, to improve the effectiveness of present and future conservation practices and policy making in the context of climate change.

In this Special Issue, we highlight recent, groundbreaking advances in the study of ancient life on planet Earth. We welcome topics including, but not limited to:

  1. Brief reviews of the state of paleontological science, and how the study of fossil remains has changed in the last few decades.
  2. New interpretations of data resulting from applications of methods new to paleontology.
  3. New databases (such as DNA and protein sequence databases) against which to compare data derived from fossils.
  4. Advancing the understanding of tempo and mode in evolution.
  5. The integration of paleontological perspectives into various disciplines (e.g. Biology, Ecology, Microbiology, Conservation biology, Developmental Biology, Molecular Biology, Genomics, and even Computer Science.
  6. The recognition of long-term environmental change and organismal responses to it, as revealed from fossil and sedimentological data.
  7. Novel insights into evolutionary relationships between living and extinct taxa.
  8. Pathways of preservation and taphonomic modes, revealed through new biogeochemical analyses.
  9. Paleontology as a predictive science, and how trends in ancient life, recognized through in depth, multi-level analyses, may be applied to future trends affecting humans.

Prof. Dr. Mary H. Schweitzer
Dr. Ferhat Kaya
Guest Editors

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Biology is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • paleontology
  • fossils
  • dinosaurs
  • evolution
  • biomarkers

Published Papers (24 papers)

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Editorial

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5 pages, 238 KiB  
Editorial
Paleontology in the 21st Century
by Mary H. Schweitzer
Biology 2023, 12(3), 487; https://doi.org/10.3390/biology12030487 - 22 Mar 2023
Cited by 1 | Viewed by 2019
Abstract
For much of its 300+ year history, “modern” paleontology has been a descriptive science, firmly housed within geological sciences [...] Full article
(This article belongs to the Special Issue Paleontology in the 21st Century)

Research

Jump to: Editorial, Review, Other

18 pages, 15750 KiB  
Article
Independent Evidence for the Preservation of Endogenous Bone Biochemistry in a Specimen of Tyrannosaurus rex
by Jennifer Anné, Aurore Canoville, Nicholas P. Edwards, Mary H. Schweitzer and Lindsay E. Zanno
Biology 2023, 12(2), 264; https://doi.org/10.3390/biology12020264 - 7 Feb 2023
Cited by 1 | Viewed by 4248
Abstract
Biomolecules preserved in deep time have potential to shed light on major evolutionary questions, driving the search for new and more rigorous methods to detect them. Despite the increasing body of evidence from a wide variety of new, high resolution/high sensitivity analytical techniques, [...] Read more.
Biomolecules preserved in deep time have potential to shed light on major evolutionary questions, driving the search for new and more rigorous methods to detect them. Despite the increasing body of evidence from a wide variety of new, high resolution/high sensitivity analytical techniques, this research is commonly met with skepticism, as the long standing dogma persists that such preservation in very deep time (>1 Ma) is unlikely. The Late Cretaceous dinosaur Tyrannosaurus rex (MOR 1125) has been shown, through multiple biochemical studies, to preserve original bone chemistry. Here, we provide additional, independent support that deep time bimolecular preservation is possible. We use synchrotron X-ray fluorescence imaging (XRF) and X-ray absorption spectroscopy (XAS) to investigate a section from the femur of this dinosaur, and demonstrate preservation of elements (S, Ca, and Zn) associated with bone remodeling and redeposition. We then compare these data to the bone of an extant dinosaur (bird), as well as a second non-avian dinosaur, Tenontosaurus tilletti (OMNH 34784) that did not preserve any sign of original biochemistry. Our data indicate that MOR 1125 bone cortices have similar bone elemental distributions to that of an extant bird, which supports preservation of original endogenous chemistry in this specimen. Full article
(This article belongs to the Special Issue Paleontology in the 21st Century)
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16 pages, 3213 KiB  
Article
Morphological and Tissue Characterization with 3D Reconstruction of a 350-Year-Old Austrian Ardea purpurea Glacier Mummy
by Seraphin H. Unterberger, Cordula Berger, Michael Schirmer, Anton Kasper Pallua, Bettina Zelger, Georg Schäfer, Christian Kremser, Gerald Degenhart, Harald Spiegl, Simon Erler, David Putzer, Rohit Arora, Walther Parson and Johannes Dominikus Pallua
Biology 2023, 12(1), 114; https://doi.org/10.3390/biology12010114 - 11 Jan 2023
Cited by 2 | Viewed by 1995
Abstract
Glaciers are dwindling archives, releasing animal mummies preserved in the ice for centuries due to climate changes. As preservation varies, residual soft tissues may differently expand the biological information content of such mummies. DNA studies have proven the possibility of extracting and analyzing [...] Read more.
Glaciers are dwindling archives, releasing animal mummies preserved in the ice for centuries due to climate changes. As preservation varies, residual soft tissues may differently expand the biological information content of such mummies. DNA studies have proven the possibility of extracting and analyzing DNA preserved in skeletal residuals and sediments for hundreds or thousands of years. Paleoradiology is the method of choice as a non-destructive tool for analyzing mummies, including micro-computed tomography (micro-CT) and magnetic resonance imaging (MRI). Together with radiocarbon dating, histo-anatomical analyses, and DNA sequencing, these techniques were employed to identify a 350-year-old Austrian Ardea purpurea glacier mummy from the Ötztal Alps. Combining these techniques proved to be a robust methodological concept for collecting inaccessible information regarding the structural organization of the mummy. The variety of methodological approaches resulted in a distinct picture of the morphological patterns of the glacier animal mummy. The BLAST search in GenBank resulted in a 100% and 98.7% match in the cytb gene sequence with two entries of the species Purple heron (Ardea purpurea; Accession number KJ941160.1 and KJ190948.1) and a 98% match with the same species for the 16 s sequence (KJ190948.1), which was confirmed by the anatomic characteristics deduced from micro-CT and MRI. Full article
(This article belongs to the Special Issue Paleontology in the 21st Century)
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22 pages, 158562 KiB  
Article
Structure and Chemical Composition of ca. 10-Million-Year-Old (Late Miocene of Western Amazon) and Present-Day Teeth of Related Species
by Caroline Pessoa-Lima, Jonas Tostes-Figueiredo, Natalia Macedo-Ribeiro, Annie Schmaltz Hsiou, Fellipe Pereira Muniz, José Augusto Maulin, Vinícius H. Franceschini-Santos, Frederico Barbosa de Sousa, Fernando Barbosa, Jr., Sergio Roberto Peres Line, Raquel Fernanda Gerlach and Max Cardoso Langer
Biology 2022, 11(11), 1636; https://doi.org/10.3390/biology11111636 - 8 Nov 2022
Cited by 3 | Viewed by 2558
Abstract
Molecular information has been gathered from fossilized dental enamel, the best-preserved tissue of vertebrates. However, the association of morphological features with the possible mineral and organic information of this tissue is still poorly understood in the context of the emerging area of paleoproteomics. [...] Read more.
Molecular information has been gathered from fossilized dental enamel, the best-preserved tissue of vertebrates. However, the association of morphological features with the possible mineral and organic information of this tissue is still poorly understood in the context of the emerging area of paleoproteomics. This study aims to compare the morphological features and chemical composition of dental enamel of extinct and extant terrestrial vertebrates of Crocodylia: Purussaurus sp. (extinct) and Melanosuchus niger (extant), and Rodentia: Neoepiblema sp. (extinct) and Hydrochoerus hydrochaeris (extant). To obtain structural and chemical data, superficial and internal enamel were analyzed by Scanning Electron Microscopy (SEM) and Energy Dispersive Spectroscopy (SEM-EDS). Organic, mineral, and water content were obtained using polarizing microscopy and microradiography on ground sections of four teeth, resulting in a higher organic volume than previously expected (up to 49%). It is observed that both modern and fossil tooth enamel exhibit the same major constituents: 36.7% Ca, 17.2% P, and 41% O, characteristic of hydroxyapatite. Additionally, 27 other elements were measured from superficial enamel by inductively coupled mass spectrometry (ICP-MS). Zinc was the most abundant microelement detected, followed by Pb, Fe, Mg, and Al. Morphological features observed include enamel rods in the rodent teeth, while incremental lines and semiprismatic enamel were observed in the alligator species. The fossil enamel was in an excellent state for microscopic analyses. Results show that all major dental enamel’s physical, chemical, and morphological features are present both in extant and extinct fossil tooth enamel (>8.5 Ma) in both taxa. Full article
(This article belongs to the Special Issue Paleontology in the 21st Century)
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11 pages, 2576 KiB  
Article
Dental Paleobiology in a Juvenile Neanderthal (Combe-Grenal, Southwestern France)
by María Dolores Garralda, Steve Weiner, Baruch Arensburg, Bruno Maureille and Bernard Vandermeersch
Biology 2022, 11(9), 1352; https://doi.org/10.3390/biology11091352 - 14 Sep 2022
Cited by 2 | Viewed by 2132
Abstract
Combe-Grenal site (Southwest France) was excavated by F. Bordes between 1953 and 1965. He found several human remains in Mousterian levels 60, 39, 35 and especially 25, corresponding to MIS 4 (~75–70/60 ky BP) and with Quina Mousterian lithics. One of the fossils [...] Read more.
Combe-Grenal site (Southwest France) was excavated by F. Bordes between 1953 and 1965. He found several human remains in Mousterian levels 60, 39, 35 and especially 25, corresponding to MIS 4 (~75–70/60 ky BP) and with Quina Mousterian lithics. One of the fossils found in level 25 is Combe-Grenal IV, consisting of a fragment of the left corpus of a juvenile mandible. This fragment displays initial juvenile periodontitis, and the two preserved teeth (LLP4 and LLM1) show moderate attrition and dental calculus. The SEM tartar analysis demonstrates the presence of cocci and filamentous types of bacteria, the former being more prevalent. This result is quite different from those obtained for the two adult Neanderthals Kebara 2 and Subalyuk 1, where more filamentous bacteria appear, especially in the Subalyuk 1 sample from Central Europe. These findings agree with the available biomedical data on periodontitis and tartar development in extant individuals, despite the different environmental conditions and diets documented by numerous archeological, taphonomical and geological data available on Neanderthals and present-day populations. New metagenomic analyses are extending this information, and despite the inherent difficulties, they will open important perspectives in studying this ancient human pathology. Full article
(This article belongs to the Special Issue Paleontology in the 21st Century)
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14 pages, 2421 KiB  
Article
Using Macro- and Microscale Preservation in Vertebrate Fossils as Predictors for Molecular Preservation in Fluvial Environments
by Caitlin Colleary, Shane O’Reilly, Andrei Dolocan, Jason G. Toyoda, Rosalie K. Chu, Malak M. Tfaily, Michael F. Hochella, Jr. and Sterling J. Nesbitt
Biology 2022, 11(9), 1304; https://doi.org/10.3390/biology11091304 - 2 Sep 2022
Cited by 1 | Viewed by 2113
Abstract
Exceptionally preserved fossils retain soft tissues and often the biomolecules that were present in an animal during its life. The majority of terrestrial vertebrate fossils are not traditionally considered exceptionally preserved, with fossils falling on a spectrum ranging from very well-preserved to poorly [...] Read more.
Exceptionally preserved fossils retain soft tissues and often the biomolecules that were present in an animal during its life. The majority of terrestrial vertebrate fossils are not traditionally considered exceptionally preserved, with fossils falling on a spectrum ranging from very well-preserved to poorly preserved when considering completeness, morphology and the presence of microstructures. Within this variability of anatomical preservation, high-quality macro-scale preservation (e.g., articulated skeletons) may not be reflected in molecular-scale preservation (i.e., biomolecules). Excavation of the Hayden Quarry (HQ; Chinle Formation, Ghost Ranch, NM, USA) has resulted in the recovery of thousands of fossilized vertebrate specimens. This has contributed greatly to our knowledge of early dinosaur evolution and paleoenvironmental conditions during the Late Triassic Period (~212 Ma). The number of specimens, completeness of skeletons and fidelity of osteohistological microstructures preserved in the bone all demonstrate the remarkable quality of the fossils preserved at this locality. Because the Hayden Quarry is an excellent example of good preservation in a fluvial environment, we have tested different fossil types (i.e., bone, tooth, coprolite) to examine the molecular preservation and overall taphonomy of the HQ to determine how different scales of preservation vary within a single locality. We used multiple high-resolution mass spectrometry techniques (TOF-SIMS, GC-MS, FT-ICR MS) to compare the fossils to unaltered bone from extant vertebrates, experimentally matured bone, and younger dinosaurian skeletal material from other fluvial environments. FT-ICR MS provides detailed molecular information about complex mixtures, and TOF-SIMS has high elemental spatial sensitivity. Using these techniques, we did not find convincing evidence of a molecular signal that can be confidently interpreted as endogenous, indicating that very good macro- and microscale preservation are not necessarily good predictors of molecular preservation. Full article
(This article belongs to the Special Issue Paleontology in the 21st Century)
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19 pages, 5510 KiB  
Article
Crystallographic Texture of the Mineral Matter in the Bivalve Shells of Gryphaea dilatata Sowerby, 1816
by Alexey Pakhnevich, Dmitry Nikolayev and Tatiana Lychagina
Biology 2022, 11(9), 1300; https://doi.org/10.3390/biology11091300 - 31 Aug 2022
Cited by 3 | Viewed by 1696
Abstract
It is assumed that the crystallographic texture of minerals in the shells of recent and fossil mollusks is very stable. To check this, it is necessary to examine the shells of animals that had lain in sediments for millions of years and lived [...] Read more.
It is assumed that the crystallographic texture of minerals in the shells of recent and fossil mollusks is very stable. To check this, it is necessary to examine the shells of animals that had lain in sediments for millions of years and lived in different conditions. It is revealed that the crystallographic texture of calcite in the shells of Gryphaea dilatata from deposits from the Middle Callovian–Lower Oxfordian (Jurassic), which lived in different water areas, is not affected by habitat conditions and the fossilization process. The crystallographic texture was studied using pole figures measured by neutron diffraction. The neutron diffraction method makes it possible to study the crystallographic texture in large samples—up to 100 cm3 in volume without destroying them. The recrystallization features of the G. dilatata valve, which affect the crystallographic texture, were discovered for the first time. This is determined from the isolines appearance of pole figures. The crystallographic texture of the G. dilatata mollusks’ different valves vary depending on their shape. The pole figures of calcite in the thick-walled valves of G. dilatata, Pycnodonte mirabilis, and Ostrea edulis are close to axial and display weak crystallographic texture. Full article
(This article belongs to the Special Issue Paleontology in the 21st Century)
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22 pages, 5169 KiB  
Article
Fossil Biomarkers and Biosignatures Preserved in Coprolites Reveal Carnivorous Diets in the Carboniferous Mazon Creek Ecosystem
by Madison Tripp, Jasmina Wiemann, Jochen Brocks, Paul Mayer, Lorenz Schwark and Kliti Grice
Biology 2022, 11(9), 1289; https://doi.org/10.3390/biology11091289 - 30 Aug 2022
Cited by 7 | Viewed by 5729
Abstract
The reconstruction of ancient trophic networks is pivotal to our understanding of ecosystem function and change through time. However, inferring dietary relationships in enigmatic ecosystems dominated by organisms without modern analogues, such as the Carboniferous Mazon Creek fauna, has previously been considered challenging: [...] Read more.
The reconstruction of ancient trophic networks is pivotal to our understanding of ecosystem function and change through time. However, inferring dietary relationships in enigmatic ecosystems dominated by organisms without modern analogues, such as the Carboniferous Mazon Creek fauna, has previously been considered challenging: preserved coprolites often do not retain sufficient morphology to identify the dietary composition. Here, we analysed n = 3 Mazon Creek coprolites in concretions for dietary signals in preserved biomarkers, stable carbon isotope data, and macromolecular composition. Cholesteroids, metazoan markers of cholesterol, show an increased abundance in the sampled coprolites (86 to 99% of the total steranes) compared to the surrounding sediment, indicating an endogenous nature of preserved organics. Presence of unaltered 5α-cholestan-3β-ol and coprostanol underline the exceptional molecular preservation of the coprolites, and reveal a carnivorous diet for the coprolite producer. Statistical analyses of in situ Raman spectra targeting coprolite carbonaceous remains support a metazoan affinity of the digested fossil remains, and suggest a high trophic level for the coprolite producer. These currently oldest, intact dietary stanols, combined with exquisitely preserved macromolecular biosignatures in Carboniferous fossils offer a novel source of trophic information. Molecular and biosignature preservation is facilitated by rapid sedimentary encapsulation of the coprolites within days to months after egestion. Full article
(This article belongs to the Special Issue Paleontology in the 21st Century)
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61 pages, 3396 KiB  
Article
Evolution of the Family Equidae, Subfamily Equinae, in North, Central and South America, Eurasia and Africa during the Plio-Pleistocene
by Omar Cirilli, Helena Machado, Joaquin Arroyo-Cabrales, Christina I. Barrón-Ortiz, Edward Davis, Christopher N. Jass, Advait M. Jukar, Zoe Landry, Alejandro H. Marín-Leyva, Luca Pandolfi, Diana Pushkina, Lorenzo Rook, Juha Saarinen, Eric Scott, Gina Semprebon, Flavia Strani, Natalia A. Villavicencio, Ferhat Kaya and Raymond L. Bernor
Biology 2022, 11(9), 1258; https://doi.org/10.3390/biology11091258 - 24 Aug 2022
Cited by 12 | Viewed by 8161
Abstract
Studies of horse evolution arose during the middle of the 19th century, and several hypotheses have been proposed for their taxonomy, paleobiogeography, paleoecology and evolution. The present contribution represents a collaboration of 19 multinational experts with the goal of providing an updated summary [...] Read more.
Studies of horse evolution arose during the middle of the 19th century, and several hypotheses have been proposed for their taxonomy, paleobiogeography, paleoecology and evolution. The present contribution represents a collaboration of 19 multinational experts with the goal of providing an updated summary of Pliocene and Pleistocene North, Central and South American, Eurasian and African horses. At the present time, we recognize 114 valid species across these continents, plus 4 North African species in need of further investigation. Our biochronology and biogeography sections integrate Equinae taxonomic records with their chronologic and geographic ranges recognizing regional biochronologic frameworks. The paleoecology section provides insights into paleobotany and diet utilizing both the mesowear and light microscopic methods, along with calculation of body masses. We provide a temporal sequence of maps that render paleoclimatic conditions across these continents integrated with Equinae occurrences. These records reveal a succession of extinctions of primitive lineages and the rise and diversification of more modern taxa. Two recent morphological-based cladistic analyses are presented here as competing hypotheses, with reference to molecular-based phylogenies. Our contribution represents a state-of-the art understanding of Plio-Pleistocene Equus evolution, their biochronologic and biogeographic background and paleoecological and paleoclimatic contexts. Full article
(This article belongs to the Special Issue Paleontology in the 21st Century)
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24 pages, 1665 KiB  
Article
Keeping 21st Century Paleontology Grounded: Quantitative Genetic Analyses and Ancestral State Reconstruction Re-Emphasize the Essentiality of Fossils
by Tesla A. Monson, Marianne F. Brasil, Michael C. Mahaney, Christopher A. Schmitt, Catherine E. Taylor and Leslea J. Hlusko
Biology 2022, 11(8), 1218; https://doi.org/10.3390/biology11081218 - 13 Aug 2022
Cited by 6 | Viewed by 3159
Abstract
Advances in genetics and developmental biology are revealing the relationship between genotype and dental phenotype (G:P), providing new approaches for how paleontologists assess dental variation in the fossil record. Our aim was to understand how the method of trait definition influences the ability [...] Read more.
Advances in genetics and developmental biology are revealing the relationship between genotype and dental phenotype (G:P), providing new approaches for how paleontologists assess dental variation in the fossil record. Our aim was to understand how the method of trait definition influences the ability to reconstruct phylogenetic relationships and evolutionary history in the Cercopithecidae, the Linnaean Family of monkeys currently living in Africa and Asia. We compared the two-dimensional assessment of molar size (calculated as the mesiodistal length of the crown multiplied by the buccolingual breadth) to a trait that reflects developmental influences on molar development (the inhibitory cascade, IC) and two traits that reflect the genetic architecture of postcanine tooth size variation (defined through quantitative genetic analyses: MMC and PMM). All traits were significantly influenced by the additive effects of genes and had similarly high heritability estimates. The proportion of covariate effects was greater for two-dimensional size compared to the G:P-defined traits. IC and MMC both showed evidence of selection, suggesting that they result from the same genetic architecture. When compared to the fossil record, Ancestral State Reconstruction using extant taxa consistently underestimated MMC and PMM values, highlighting the necessity of fossil data for understanding evolutionary patterns in these traits. Given that G:P-defined dental traits may provide insight to biological mechanisms that reach far beyond the dentition, this new approach to fossil morphology has the potential to open an entirely new window onto extinct paleobiologies. Without the fossil record, we would not be able to grasp the full range of variation in those biological mechanisms that have existed throughout evolution. Full article
(This article belongs to the Special Issue Paleontology in the 21st Century)
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24 pages, 2924 KiB  
Article
Taphonomic and Diagenetic Pathways to Protein Preservation, Part II: The Case of Brachylophosaurus canadensis Specimen MOR 2598
by Paul V. Ullmann, Richard D. Ash and John B. Scannella
Biology 2022, 11(8), 1177; https://doi.org/10.3390/biology11081177 - 5 Aug 2022
Cited by 4 | Viewed by 2665
Abstract
Recent recoveries of peptide sequences from two Cretaceous dinosaur bones require paleontologists to rethink traditional notions about how fossilization occurs. As part of this shifting paradigm, several research groups have recently begun attempting to characterize biomolecular decay and stabilization pathways in diverse paleoenvironmental [...] Read more.
Recent recoveries of peptide sequences from two Cretaceous dinosaur bones require paleontologists to rethink traditional notions about how fossilization occurs. As part of this shifting paradigm, several research groups have recently begun attempting to characterize biomolecular decay and stabilization pathways in diverse paleoenvironmental and diagenetic settings. To advance these efforts, we assessed the taphonomic and geochemical history of Brachylophosaurus canadensis specimen MOR 2598, the left femur of which was previously found to retain endogenous cells, tissues, and structural proteins. Combined stratigraphic and trace element data show that after brief fluvial transport, this articulated hind limb was buried in a sandy, likely-brackish, estuarine channel. During early diagenesis, percolating groundwaters stagnated within the bones, forming reducing internal microenvironments. Recent exposure and weathering also caused the surficial leaching of trace elements from the specimen. Despite these shifting redox regimes, proteins within the bones were able to survive through diagenesis, attesting to their remarkable resiliency over geologic time. Synthesizing our findings with other recent studies reveals that oxidizing conditions in the initial ~48 h postmortem likely promote molecular stabilization reactions and that the retention of early-diagenetic trace element signatures may be a useful proxy for molecular recovery potential. Full article
(This article belongs to the Special Issue Paleontology in the 21st Century)
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16 pages, 1521 KiB  
Article
Midfacial Morphology and Neandertal–Modern Human Interbreeding
by Steven E. Churchill, Kamryn Keys and Ann H. Ross
Biology 2022, 11(8), 1163; https://doi.org/10.3390/biology11081163 - 3 Aug 2022
Cited by 3 | Viewed by 23510
Abstract
Ancient DNA from, Neandertal and modern human fossils, and comparative morphological analyses of them, reveal a complex history of interbreeding between these lineages and the introgression of Neandertal genes into modern human genomes. Despite substantial increases in our knowledge of these events, the [...] Read more.
Ancient DNA from, Neandertal and modern human fossils, and comparative morphological analyses of them, reveal a complex history of interbreeding between these lineages and the introgression of Neandertal genes into modern human genomes. Despite substantial increases in our knowledge of these events, the timing and geographic location of hybridization events remain unclear. Six measures of facial size and shape, from regional samples of Neandertals and early modern humans, were used in a multivariate exploratory analysis to try to identify regions in which early modern human facial morphology was more similar to that of Neandertals, which might thus represent regions of greater introgression of Neandertal genes. The results of canonical variates analysis and hierarchical cluster analysis suggest important affinities in facial morphology between both Middle and Upper Paleolithic early modern humans of the Near East with Neandertals, highlighting the importance of this region for interbreeding between the two lineages. Full article
(This article belongs to the Special Issue Paleontology in the 21st Century)
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21 pages, 14406 KiB  
Article
Soft Tissue and Biomolecular Preservation in Vertebrate Fossils from Glauconitic, Shallow Marine Sediments of the Hornerstown Formation, Edelman Fossil Park, New Jersey
by Kristyn K. Voegele, Zachary M. Boles, Paul V. Ullmann, Elena R. Schroeter, Wenxia Zheng and Kenneth J. Lacovara
Biology 2022, 11(8), 1161; https://doi.org/10.3390/biology11081161 - 2 Aug 2022
Cited by 4 | Viewed by 2919
Abstract
Endogenous biomolecules and soft tissues are known to persist in the fossil record. To date, these discoveries derive from a limited number of preservational environments, (e.g., fluvial channels and floodplains), and fossils from less common depositional environments have been largely unexplored. We conducted [...] Read more.
Endogenous biomolecules and soft tissues are known to persist in the fossil record. To date, these discoveries derive from a limited number of preservational environments, (e.g., fluvial channels and floodplains), and fossils from less common depositional environments have been largely unexplored. We conducted paleomolecular analyses of shallow marine vertebrate fossils from the Cretaceous–Paleogene Hornerstown Formation, an 80–90% glauconitic greensand from Jean and Ric Edelman Fossil Park in Mantua Township, NJ. Twelve samples were demineralized and found to yield products morphologically consistent with vertebrate osteocytes, blood vessels, and bone matrix. Specimens from these deposits that are dark in color exhibit excellent histological preservation and yielded a greater recovery of cells and soft tissues, whereas lighter-colored specimens exhibit poor histology and few to no cells/soft tissues. Additionally, a well-preserved femur of the marine crocodilian Thoracosaurus was found to have retained endogenous collagen I by immunofluorescence and enzyme-linked immunosorbent assays. Our results thus not only corroborate previous findings that soft tissue and biomolecular recovery from fossils preserved in marine environments are possible but also expand the range of depositional environments documented to preserve endogenous biomolecules, thus broadening the suite of geologic strata that may be fruitful to examine in future paleomolecular studies. Full article
(This article belongs to the Special Issue Paleontology in the 21st Century)
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31 pages, 5770 KiB  
Article
Soft-Tissue, Rare Earth Element, and Molecular Analyses of Dreadnoughtus schrani, an Exceptionally Complete Titanosaur from Argentina
by Elena R. Schroeter, Paul V. Ullmann, Kyle Macauley, Richard D. Ash, Wenxia Zheng, Mary H. Schweitzer and Kenneth J. Lacovara
Biology 2022, 11(8), 1158; https://doi.org/10.3390/biology11081158 - 2 Aug 2022
Cited by 8 | Viewed by 5507
Abstract
Evidence that organic material preserves in deep time (>1 Ma) has been reported using a wide variety of analytical techniques. However, the comprehensive geochemical data that could aid in building robust hypotheses for how soft-tissues persist over millions of years are lacking from [...] Read more.
Evidence that organic material preserves in deep time (>1 Ma) has been reported using a wide variety of analytical techniques. However, the comprehensive geochemical data that could aid in building robust hypotheses for how soft-tissues persist over millions of years are lacking from most paleomolecular reports. Here, we analyze the molecular preservation and taphonomic history of the Dreadnougtus schrani holotype (MPM-PV 1156) at both macroscopic and microscopic levels. We review the stratigraphy, depositional setting, and physical taphonomy of the D. schrani skeletal assemblage, and extensively characterize the preservation and taphonomic history of the humerus at a micro-scale via: (1) histological analysis (structural integrity) and X-ray diffraction (exogenous mineral content); (2) laser ablation-inductively coupled plasma mass spectrometry (analyses of rare earth element content throughout cortex); (3) demineralization and optical microscopy (soft-tissue microstructures); (4) in situ and in-solution immunological assays (presence of endogenous protein). Our data show the D. schrani holotype preserves soft-tissue microstructures and remnants of endogenous bone protein. Further, it was exposed to LREE-enriched groundwaters and weakly-oxidizing conditions after burial, but experienced negligible further chemical alteration after early-diagenetic fossilization. These findings support previous hypotheses that fossils that display low trace element uptake are favorable targets for paleomolecular analyses. Full article
(This article belongs to the Special Issue Paleontology in the 21st Century)
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20 pages, 4902 KiB  
Article
Environmental Factors Affecting Feather Taphonomy
by Mary Higby Schweitzer, Wenxia Zheng and Nancy Equall
Biology 2022, 11(5), 703; https://doi.org/10.3390/biology11050703 - 3 May 2022
Cited by 2 | Viewed by 4248
Abstract
The exceptional preservation of feathers in the fossil record has led to a better understanding of both phylogeny and evolution. Here we address factors that may have contributed to the preservation of feathers in ancient organisms using experimental taphonomy. We show that the [...] Read more.
The exceptional preservation of feathers in the fossil record has led to a better understanding of both phylogeny and evolution. Here we address factors that may have contributed to the preservation of feathers in ancient organisms using experimental taphonomy. We show that the atmospheres of the Mesozoic, known to be elevated in both CO2 and with temperatures above present levels, may have contributed to the preservation of these soft tissues by facilitating rapid precipitation of hydroxy- or carbonate hydroxyapatite, thus outpacing natural degradative processes. Data also support that that microbial degradation was enhanced in elevated CO2, but mineral deposition was also enhanced, contributing to preservation by stabilizing the organic components of feathers. Full article
(This article belongs to the Special Issue Paleontology in the 21st Century)
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16 pages, 7904 KiB  
Article
Preservation and Taphonomy of Fossil Insects from the Earliest Eocene of Denmark
by Miriam Heingård, Peter Sjövall, Bo P. Schultz, René L. Sylvestersen and Johan Lindgren
Biology 2022, 11(3), 395; https://doi.org/10.3390/biology11030395 - 3 Mar 2022
Cited by 8 | Viewed by 2942
Abstract
Marine sediments of the lowermost Eocene Stolleklint Clay and Fur Formation of north-western Denmark have yielded abundant well-preserved insects. However, despite a long history of research, in-depth information pertaining to preservational modes and taphonomic pathways of these exceptional animal fossils remains scarce. In [...] Read more.
Marine sediments of the lowermost Eocene Stolleklint Clay and Fur Formation of north-western Denmark have yielded abundant well-preserved insects. However, despite a long history of research, in-depth information pertaining to preservational modes and taphonomic pathways of these exceptional animal fossils remains scarce. In this paper, we use a combination of scanning electron microscopy coupled with energy-dispersive X-ray spectroscopy (SEM-EDX), transmission electron microscopy (TEM) and time-of-flight secondary ion mass spectrometry (ToF-SIMS) to assess the ultrastructural and molecular composition of three insect fossils: a wasp (Hymenoptera), a damselfly (Odonata) and a pair of beetle elytra (Coleoptera). Our analyses show that all specimens are preserved as organic remnants that originate from the exoskeleton, with the elytra displaying a greater level of morphological fidelity than the other fossils. TEM analysis of the elytra revealed minute features, including a multilayered epicuticle comparable to those nanostructures that generate metallic colors in modern insects. Additionally, ToF-SIMS analyses provided spectral evidence for chemical residues of the pigment eumelanin as part of the cuticular remains. To the best of our knowledge, this is the first occasion where both structural colors and chemical traces of an endogenous pigment have been documented in a single fossil specimen. Overall, our results provide novel insights into the nature of insect body fossils and additionally shed light on exceptionally preserved terrestrial insect faunas found in marine paleoenvironments. Full article
(This article belongs to the Special Issue Paleontology in the 21st Century)
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25 pages, 4155 KiB  
Article
Taphonomic and Diagenetic Pathways to Protein Preservation, Part I: The Case of Tyrannosaurus rex Specimen MOR 1125
by Paul V. Ullmann, Kyle Macauley, Richard D. Ash, Ben Shoup and John B. Scannella
Biology 2021, 10(11), 1193; https://doi.org/10.3390/biology10111193 - 17 Nov 2021
Cited by 11 | Viewed by 5568
Abstract
Many recent reports have demonstrated remarkable preservation of proteins in fossil bones dating back to the Permian. However, preservation mechanisms that foster the long-term stability of biomolecules and the taphonomic circumstances facilitating them remain largely unexplored. To address this, we examined the taphonomic [...] Read more.
Many recent reports have demonstrated remarkable preservation of proteins in fossil bones dating back to the Permian. However, preservation mechanisms that foster the long-term stability of biomolecules and the taphonomic circumstances facilitating them remain largely unexplored. To address this, we examined the taphonomic and geochemical history of Tyrannosaurus rex specimen Museum of the Rockies (MOR) 1125, whose right femur and tibiae were previously shown to retain still-soft tissues and endogenous proteins. By combining taphonomic insights with trace element compositional data, we reconstruct the postmortem history of this famous specimen. Our data show that following prolonged, subaqueous decay in an estuarine channel, MOR 1125 was buried in a coarse sandstone wherein its bones fossilized while interacting with oxic and potentially brackish early-diagenetic groundwaters. Once its bones became stable fossils, they experienced minimal further chemical alteration. Comparisons with other recent studies reveal that oxidizing early-diagenetic microenvironments and diagenetic circumstances which restrict exposure to percolating pore fluids elevate biomolecular preservation potential by promoting molecular condensation reactions and hindering chemical alteration, respectively. Avoiding protracted interactions with late-diagenetic pore fluids is also likely crucial. Similar studies must be conducted on fossil bones preserved under diverse paleoenvironmental and diagenetic contexts to fully elucidate molecular preservation pathways. Full article
(This article belongs to the Special Issue Paleontology in the 21st Century)
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Review

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18 pages, 2816 KiB  
Review
Was There a Cambrian Explosion on Land? The Case of Arthropod Terrestrialization
by Erik Tihelka, Richard J. Howard, Chenyang Cai and Jesus Lozano-Fernandez
Biology 2022, 11(10), 1516; https://doi.org/10.3390/biology11101516 - 17 Oct 2022
Cited by 5 | Viewed by 5906
Abstract
Arthropods, the most diverse form of macroscopic life in the history of the Earth, originated in the sea. Since the early Cambrian, at least ~518 million years ago, these animals have dominated the oceans of the world. By the Silurian–Devonian, the fossil record [...] Read more.
Arthropods, the most diverse form of macroscopic life in the history of the Earth, originated in the sea. Since the early Cambrian, at least ~518 million years ago, these animals have dominated the oceans of the world. By the Silurian–Devonian, the fossil record attests to arthropods becoming the first animals to colonize land, However, a growing body of molecular dating and palaeontological evidence suggests that the three major terrestrial arthropod groups (myriapods, hexapods, and arachnids), as well as vascular plants, may have invaded land as early as the Cambrian–Ordovician. These dates precede the oldest fossil evidence of those groups and suggest an unrecorded continental “Cambrian explosion” a hundred million years prior to the formation of early complex terrestrial ecosystems in the Silurian–Devonian. We review the palaeontological, phylogenomic, and molecular clock evidence pertaining to the proposed Cambrian terrestrialization of the arthropods. We argue that despite the challenges posed by incomplete preservation and the scarcity of early Palaeozoic terrestrial deposits, the discrepancy between molecular clock estimates and the fossil record is narrower than is often claimed. We discuss strategies for closing the gap between molecular clock estimates and fossil data in the evolution of early ecosystems on land Full article
(This article belongs to the Special Issue Paleontology in the 21st Century)
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13 pages, 1241 KiB  
Review
Integrative Phylogenetics: Tools for Palaeontologists to Explore the Tree of Life
by Raquel López-Antoñanzas, Jonathan Mitchell, Tiago R. Simões, Fabien L. Condamine, Robin Aguilée, Pablo Peláez-Campomanes, Sabrina Renaud, Jonathan Rolland and Philip C. J. Donoghue
Biology 2022, 11(8), 1185; https://doi.org/10.3390/biology11081185 - 7 Aug 2022
Cited by 2 | Viewed by 5285
Abstract
The modern era of analytical and quantitative palaeobiology has only just begun, integrating methods such as morphological and molecular phylogenetics and divergence time estimation, as well as phenotypic and molecular rates of evolution. Calibrating the tree of life to geological time is at [...] Read more.
The modern era of analytical and quantitative palaeobiology has only just begun, integrating methods such as morphological and molecular phylogenetics and divergence time estimation, as well as phenotypic and molecular rates of evolution. Calibrating the tree of life to geological time is at the nexus of many disparate disciplines, from palaeontology to molecular systematics and from geochronology to comparative genomics. Creating an evolutionary time scale of the major events that shaped biodiversity is key to all of these fields and draws from each of them. Different methodological approaches and data employed in various disciplines have traditionally made collaborative research efforts difficult among these disciplines. However, the development of new methods is bridging the historical gap between fields, providing a holistic perspective on organismal evolutionary history, integrating all of the available evidence from living and fossil species. Because phylogenies with only extant taxa do not contain enough information to either calibrate the tree of life or fully infer macroevolutionary dynamics, phylogenies should preferably include both extant and extinct taxa, which can only be achieved through the inclusion of phenotypic data. This integrative phylogenetic approach provides ample and novel opportunities for evolutionary biologists to benefit from palaeontological data to help establish an evolutionary time scale and to test core macroevolutionary hypotheses about the drivers of biological diversification across various dimensions of organisms. Full article
(This article belongs to the Special Issue Paleontology in the 21st Century)
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14 pages, 1384 KiB  
Review
Twentieth-Century Paleoproteomics: Lessons from Venta Micena Fossils
by Jesús M. Torres, Concepción Borja, Luis Gibert, Francesc Ribot and Enrique G. Olivares
Biology 2022, 11(8), 1184; https://doi.org/10.3390/biology11081184 - 6 Aug 2022
Cited by 3 | Viewed by 2750 | Correction
Abstract
Proteomics methods can identify amino acid sequences in fossil proteins, thus making it possible to determine the ascription or proximity of a fossil to other species. Before mass spectrometry was used to study fossil proteins, earlier studies used antibodies to recognize their sequences. [...] Read more.
Proteomics methods can identify amino acid sequences in fossil proteins, thus making it possible to determine the ascription or proximity of a fossil to other species. Before mass spectrometry was used to study fossil proteins, earlier studies used antibodies to recognize their sequences. Lowenstein and colleagues, at the University of San Francisco, pioneered the identification of fossil proteins with immunological methods. His group, together with Olivares’s group at the University of Granada, studied the immunological reactions of proteins from the controversial Orce skull fragment (VM-0), a 1.3-million-year-old fossil found at the Venta Micena site in Orce (Granada province, southern Spain) and initially assigned to a hominin. However, discrepancies regarding the morphological features of the internal face of the fossil raised doubts about this ascription. In this article, we review the immunological analysis of the proteins extracted from VM-0 and other Venta Micena fossils assigned to hominins and to other mammals, and explain how these methods helped to determine the species specificity of these fossils and resolve paleontological controversies. Full article
(This article belongs to the Special Issue Paleontology in the 21st Century)
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17 pages, 3493 KiB  
Review
The Rising of Paleontology in China: A Century-Long Road
by Zhonghe Zhou
Biology 2022, 11(8), 1104; https://doi.org/10.3390/biology11081104 - 25 Jul 2022
Cited by 1 | Viewed by 3363
Abstract
In this paper, the history of paleontology in China from 1920 to 2020 is divided into three major stages, i.e., 1920–1949, 1949–1978, and 1979–2020. As one of the first scientific disciplines to have earned international fame in China, the development of Chinese paleontology [...] Read more.
In this paper, the history of paleontology in China from 1920 to 2020 is divided into three major stages, i.e., 1920–1949, 1949–1978, and 1979–2020. As one of the first scientific disciplines to have earned international fame in China, the development of Chinese paleontology benefitted from international collaborations and China’s rich resources. Since 1978, China’s socio-economic development and its open-door policy to the outside world have also played a key role in the growth of Chinese paleontology. In the 21st century, thanks to constant funding from the government and the rise of the younger generation of paleontologists, Chinese paleontology is expected to make even more contributions to the integration of paleontology with both biological and geological research projects by taking advantage of new technologies and China’s rich paleontological resources. Full article
(This article belongs to the Special Issue Paleontology in the 21st Century)
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25 pages, 2833 KiB  
Review
Chemistry and Analysis of Organic Compounds in Dinosaurs
by Mariam Tahoun, Marianne Engeser, Vigneshwaran Namasivayam, Paul Martin Sander and Christa E. Müller
Biology 2022, 11(5), 670; https://doi.org/10.3390/biology11050670 - 27 Apr 2022
Cited by 10 | Viewed by 5882
Abstract
This review provides an overview of organic compounds detected in non-avian dinosaur fossils to date. This was enabled by the development of sensitive analytical techniques. Non-destructive methods and procedures restricted to the sample surface, e.g., light and electron microscopy, infrared (IR) and Raman [...] Read more.
This review provides an overview of organic compounds detected in non-avian dinosaur fossils to date. This was enabled by the development of sensitive analytical techniques. Non-destructive methods and procedures restricted to the sample surface, e.g., light and electron microscopy, infrared (IR) and Raman spectroscopy, as well as more invasive approaches including liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS), time-of-flight secondary ion mass spectrometry, and immunological methods were employed. Organic compounds detected in samples of dinosaur fossils include pigments (heme, biliverdin, protoporphyrin IX, melanin), and proteins, such as collagens and keratins. The origin and nature of the observed protein signals is, however, in some cases, controversially discussed. Molecular taphonomy approaches can support the development of suitable analytical methods to confirm reported findings and to identify further organic compounds in dinosaur and other fossils in the future. The chemical properties of the various organic compounds detected in dinosaurs, and the techniques utilized for the identification and analysis of each of the compounds will be discussed. Full article
(This article belongs to the Special Issue Paleontology in the 21st Century)
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Other

1 pages, 205 KiB  
Correction
Correction: Torres et al. Twentieth-Century Paleoproteomics: Lessons from Venta Micena Fossils. Biology 2022, 11, 1184
by Jesús M. Torres, Concepción Borja, Luis Gibert, Francesc Ribot and Enrique G. Olivares
Biology 2022, 11(10), 1515; https://doi.org/10.3390/biology11101515 - 17 Oct 2022
Cited by 1 | Viewed by 850
Abstract
There was an error in the original publication [...] Full article
(This article belongs to the Special Issue Paleontology in the 21st Century)
12 pages, 293 KiB  
Commentary
A Plea for a New Synthesis: From Twentieth-Century Paleobiology to Twenty-First-Century Paleontology and Back Again
by Marco Tamborini
Biology 2022, 11(8), 1120; https://doi.org/10.3390/biology11081120 - 26 Jul 2022
Cited by 3 | Viewed by 2721
Abstract
In this paper, I will briefly discuss the elements of novelty and continuity between twentieth-century paleobiology and twenty-first-century paleontology. First, I will outline the heated debate over the disciplinary status of paleontology in the mid-twentieth century. Second, I will analyze the main theoretical [...] Read more.
In this paper, I will briefly discuss the elements of novelty and continuity between twentieth-century paleobiology and twenty-first-century paleontology. First, I will outline the heated debate over the disciplinary status of paleontology in the mid-twentieth century. Second, I will analyze the main theoretical issue behind this debate by considering two prominent case studies within the broader paleobiology agenda. Third, I will turn to twenty-first century paleontology and address five representative research topics. In doing so, I will characterize twenty-first century paleontology as a science that strives for more data, more technology, and more integration. Finally, I will outline what twenty-first-century paleontology might inherit from twentieth-century paleobiology: the pursuit of and plea for a new synthesis that could lead to a second paleobiological revolution. Following in the footsteps of the paleobiological revolution of the 1960s and 1970s, the paleobiological revolution of the twenty-first century would enable paleontologists to gain strong political representation and argue with a decisive voice at the “high table” on issues such as the expanded evolutionary synthesis, the conservation of Earth’s environment, and global climate change. Full article
(This article belongs to the Special Issue Paleontology in the 21st Century)
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