Fossil Record Research Articles

Origins of mammalian vertebral function revealed through digital bending experiments.

Unravelling the functional steps that underlie major transitions in the fossil record is a significant challenge for biologists owing to the difficulties of interpreting functional capabilities of extinct organisms. New computational modelling approaches provide exciting avenues for testing function in the fossil record. Here, we conduct digital bending experiments to reconstruct vertebral function in non-mammalian synapsids, the extinct forerunners of mammals, to provide insights into the functional underpinnings of the synapsid-mammal transition. We estimate range of motion and stiffness of intervertebral joints in eight non-mammalian synapsid species alongside a comparative sample of extant tetrapods, including salamanders, reptiles and mammals. We show that several key aspects of mammalian vertebral function evolved outside crown Mammalia. Compared to early diverging non-mammalian synapsids, cynodonts stabilized the posterior trunk against lateroflexion, while evolving axial rotation in the anterior trunk. This was later accompanied by posterior sagittal bending in crown mammals, and perhaps even therians specifically. Our data also support the prior hypothesis that functional diversification of the mammalian trunk occurred via co-option of existing morphological regions in response to changing selective demands. Thus, multiple functional and evolutionary steps underlie the origin of remarkable complexity in the mammalian backbone.

Late Ordovician eurypterid preserves oldest euchelicerate musculature in pyrite.

Pyritization of soft tissues of invertebrates is rare in the fossil record. InNewYork State, it occurs in black shales of the Lorraine Group (Late Ordovician), the best-known example of which is Beecher's Trilobite Bed. Exceptional preservation at the quarry where this bed is exposed allowed detailed examination of trilobite and ostracod soft-tissue anatomy. Here, we present the first example of a eurypterid (sea scorpion) currently ascribed to Carcinosomatidae from this deposit that also preserves the first evidence for mesosomal musculature in eurypterids. This specimen demonstrates thateurypterid musculature can be preserved in pyrite and evidences the oldest example of euchelicerate muscles within the fossil record. Sulfur isotope data illustrate that pyrite rapidly replicated muscle tissue in the early burial environment, prior to the pyritization of biomineralized exoskeleton and cuticular trilobite limbs. This discovery therefore expands thelimited fossil record of euchelicerate musculature, while extending the taphonomic scope for preservation of detailed internal structures, more broadly, within arthropods.

The temperate marine Peruvian Province: How history accounts for its unusual biota.

The Peruvian Province, from 6° S in Peru to 42° S in Chile, is a highly productive coastal marine region whose biology and fossil record have long been studied separately but never integrated. To understand how past events and conditions affected today's species composition and interactions, we examined the role of extinction, colonization, geologic changes to explain previously unrecognized peculiar features of the biota and to compare the Peruvian Province's history to that of other climatically similar temperate coasts. We synthesized all available data on the benthic (or benthically feeding) biota, with emphasis on fossilizable taxa, for the interval from the Miocene (23-5.4 Ma) and Pliocene (5.4-2.5 Ma) to the present. We outline the history of ecological guilds including primary producers, herbivores, predators, and suspension-feeders and document patterns of extinction, colonization, and geographic restriction. We identify twelve unusual attributes of the biota, most of which are the result of repeated episodes of extinction. Several guilds present during the Miocene and Pliocene are not represented in the province today, while groups such as kelps and perhaps intertidal predatory sea stars are relative newcomers. Guilds on soft bottoms and in sheltered habitats were severely affected by extinction, whereas those on hard bottoms were most affected by colonists and held their own in diversity. The Peruvian Province has not served as a biogeographic refuge, in contrast to the coasts of Australasia and Argentina, where lineages no longer present in the Peruvian Province survive. The loss of sheltered habitats since the Pliocene explains many of the present-day peculiarities of the biota. The history of the province's biota explains its unique attributes. High productivity, a rich Southern Hemisphere heritage, and colonization from the north account for the present-day composition and unusual characteristics of the biota.

Sustained increases in atmospheric oxygen and marine productivity in the Neoproterozoic and Palaeozoic eras

A geologically rapid Neoproterozoic oxygenation event is commonly linked to the appearance of marine animal groups in the fossil record. However, there is still debate about what evidence from the sedimentary geochemical record—if any—provides strong support for a persistent shift in surface oxygen immediately preceding the rise of animals. We present statistical learning analyses of a large dataset of geochemical data and associated geological context from the Neoproterozoic and Palaeozoic sedimentary record and then use Earth system modelling to link trends in redox-sensitive trace metal and organic carbon concentrations to the oxygenation of Earth’s oceans and atmosphere. We do not find evidence for the wholesale oxygenation of Earth’s oceans in the late Neoproterozoic era. We do, however, reconstruct a moderate long-term increase in atmospheric oxygen and marine productivity. These changes to the Earth system would have increased dissolved oxygen and food supply in shallow-water habitats during the broad interval of geologic time in which the major animal groups first radiated. This approach provides some of the most direct evidence for potential physiological drivers of the Cambrian radiation, while highlighting the importance of later Palaeozoic oxygenation in the evolution of the modern Earth system.

Estimation of maximum body size in fossil species: A case study using Tyrannosaurus rex.

Among extant species, the ability to sample the extremes of body size-one of the most useful predictors of an individual's ecology-is highly unlikely. This improbability is further exaggerated when sampling the already incomplete fossil record. We quantify the likelihood of sampling the uppermost limits of body size in the fossil record using Tyrannosaurus rex Osborn, 1905 as a model, selected for its comparatively well-understood life history parameters. We computationally generate a population of 140 million T. rex (based on prior estimates), modelling variation about the growth curve both with and without sexual dimorphism (the former modelled after Alligator mississippiensis), and building in sampling limitations related to species survivorship and taphonomic bias, derived from fossil data. The 99th percentile of body mass in T. rex has likely already been sampled, but it will probably be millennia before much larger giants (99.99th percentile) are sampled at present collecting rates. Biomechanical and ecological limitations notwithstanding, we estimate that the absolute largest T. rex may have been 70% more massive than the currently largest known specimen (~15,000 vs. ~8800 kg). Body size comparisons of fossil species should be based on ontogenetically controlled statistical parameters, rather than simply comparing the largest known individuals whose recovery is highly subject to sampling intensity.

Abundance-diversity relationship as a unique signature of temporal scaling in the fossil record.

Species diversity increases with the temporal grain of samples according to the species-time relationship (STR), impacting palaeoecological analyses because the temporal grain (time averaging) of fossil assemblages varies by several orders of magnitude. We predict a positive relation between total abundance and sample size-independent diversity (ADR) in fossil assemblages because an increase in time averaging, determined by a decreasing sediment accumulation, should increase abundance and depress species dominance. We demonstrate that, in contrast to negative ADR of non-averaged living assemblages, the ADR of Holocene fossil assemblages is positive, unconditionally or when conditioned on the energy availability gradient. However, the positive fossil ADR disappears when conditioned on sediment accumulation, demonstrating that ADR is a signature of diversity scaling induced by variable time averaging. Conditioning ADR on sediment accumulation can identify and remove the scaling effect caused by time averaging, providing an avenue for unbiased biodiversity comparisons across space and time.

Diversification over deep and shallow temporal scales in the Holarctic genus Perpolita (Gastropoda: Gastrodontidae)

Abstract The Holarctic land snail genus Perpolita was used to explore the influence of past and current biogeography on diversification. The number of empirically-supported species was determined using a consensus between mtDNA sequence, nDNA sequence, conchology, and geographic and ecological range with five valid temperate-boreal species (Perpolita binneyana, Perpolita electrina, Perpolita hammonis, Perpolita petronella, and Perpolita radiatella) being recognized. Only P. petronella was unchanged in both nomenclature and diagnostic characteristics with the remainder requiring alterations. Perhaps the most important of these was elevation of P. radiatella to a valid species, with its populations having been previously lumped either under European P. hammonis or North American P. electrina. Divergence times of 18.7–10.0 Mya were suggested through genome-wide SNPs in combination with the fossil record, indicating a pre-Pleistocene origin for all Perpolita species. Using genetically-confirmed diagnostic shell characters, we accumulated > 2000 valid occurrences and used these to estimate appropriate modern and Last Glacial Maximum climate extents for all species. These models suggest that modern intra-specific gene pool diversity may generally reflect Pleistocene palaeoclimatology.

New data and redescription of Kellnerius jamacaruensis Santana et al., 2013, a Palaemonidae shrimp from the Araripe Basin in northeastern Brazil

The preservation of shrimp in the fossil record is difficult due to their rapid decomposition. In this study, we provide new taxonomic insights into Kellnerius jamacaruensis from the Lower Cretaceous Romualdo Formation in the Araripe Basin, northeastern Brazil. A comprehensive taxonomic review, including a more meticulous preparation of the holotype and additional fossil material, enabled the disclosure of previously unknown anatomical features, reaffirming its classification within the family Palaemonidae.

New early Pliocene Rhinocerotidae findings from Tuscany (Italy) and the Pliocene rhinocerotine record in Italy

An almost complete mandible from the Lower Pliocene deposits of Arcille (Tuscany) is described and investigated for the first time. The specimen is assigned to Pliorhinus megarhinus, which is documented in Italy from the latest Miocene to the mid-Pliocene. The studied specimen is larger than Stephanorhinus etruscus and S. jeanvireti, and morphologically fits P. megarhinus from the Early Pliocene of Montpellier (France), Vera Basin (Spain) and Val di Pugna Fangonero (Italy). This specimen represents the first stratigraphically well-documented Pliocene record of this species in Italy, the previous discoveries dating back to the 19th century or the beginning of the 20th century, hence lacking stratigraphic control. According to the obtained results, it is possible to assess the occurrence of P. megarhinus during the earliest Pliocene in Italy as well as to confirm the long-lasting persistence of this species, whose fossil record covers a timespan between 6.7 Ma and 3.5 Ma. During that time, P. megarhinus did seemingly undergo a trend of body mass reduction.

Cenozoic seeds of Vitaceae reveal a deep history of extinction and dispersal in the Neotropics.

The remarkably diverse plant communities of the Neotropics are the result of diversification driven by multiple biotic (for example, speciation, extinction and dispersal) and abiotic (for example, climatic and tectonic) processes. However, in the absence of a well-preserved, thoroughly sampled and critically assessed fossil record, the associated processes of dispersal and extinction are poorly understood. We report an exceptional case study documenting patterns of extinction in the grape family (Vitaceae Juss.) on the basis of fossil seeds discovered in four Neotropical palaeofloras dated between 60 and 19 Ma. These include a new species that provides the earliest evidence of Vitaceae in the Western Hemisphere. Eight additional species reveal the former presence of major clades of the family that are currently absent from the Neotropics and elucidate previously unknown dispersal events. Our results indicate that regional extinction and dispersal have substantially impacted the evolutionary history of Vitaceae in the Neotropics. They also suggest that while the Neotropics have been dynamic centres of diversification through the Cenozoic, extant Neotropical botanical diversity has also been shaped by extensive extinction over the past 66 million years.

The rise and fall of the Iberian cobras (Elapidae, Naja) in the context of their European and global fossil record

AbstractVery few remains of elapid snakes are known from the Iberian Peninsula, but these include a probable endemic extinct species of cobra, Naja iberica from the Late Miocene. We here describe isolated cobra vertebrae from several Middle–Late Miocene localities in the Vallès‐Penedès Basin (Catalonia, Spain). All of these fossils are herein referred to an indeterminate species of the genus Naja. These remains are the first conclusive evidence that cobras were present in Iberia before the Messinian Salinity Crisis, and that they persisted there throughout the Miocene (and ultimately until the Pliocene). Recently, a phylogeny of extinct Naja based on cranial and vertebral morphology recognized N. iberica as a distinct lineage separate from the Central European one, represented mainly by Naja romani. However, due to taxonomic uncertainties, it is still unclear whether Iberian cobras were all part of a single lineage or whether several Naja lineages inhabited the Iberian Peninsula. They went extinct in Iberia before the end of the Pliocene. In the Vallès‐Penedès Basin, cobras were living in a mosaic environment, surviving through different phases characterized by different environmental features.

Energetic Particles and High-Energy Processes in Cosmological Filaments and Their Astronomical Implications

Large-scale cosmic filaments connect galaxies, clusters, and voids. They are permeated by magnetic fields with a variety of topologies. Cosmic rays with energies up to 1020eV can be produced in astrophysical environments associated with star-formation and AGN activities. The fate of these cosmic rays in filaments, which cannot be directly observed on Earth, are rarely studied. We investigate the high-energy processes associated with energetic particles (cosmic rays) in filaments, adopting an ecological approach that includes galaxies, clusters/superclusters, and voids as key cosmological structures in the filament ecosystem. We derive the phenomenology for modelling interfaces between filaments and these structures, and investigate how the transfer and fate of energetic cosmic ray protons are affected by the magnetism of the interfaces. We consider different magnetic field configurations in filaments and assess the implications for cosmic ray confinement and survival against hadronic pion-producing and photo-pair interactions. Our analysis shows that the fate of the particles depends on the location of their origin within a filament ecosystem, and that filaments act as ‘highways’, channelling cosmic rays between galaxies, galaxy clusters, and superclusters. Filaments can also operate as cosmic ‘fly paper’, capturing cosmic ray protons with energies up to 1018eV from cosmic voids. Our analysis predicts the presence of a population of ∼1012–1016eV cosmic ray protons in filaments and voids accumulated continually over cosmic time. These protons do not suffer significant energy losses through photo-pair or pion production, nor can they be cooled efficiently. Instead, they form a cosmic ray fossil record of the power generation history of the Universe.

A long-headed Cambrian soft-bodied vertebrate from the American Great Basin region.

The fossil record suggests that chordates might have been minor components of marine ecosystems during the first major diversification of animal life in the Cambrian. Vertebrates are represented by a handful of rare soft-bodied stem-lineage taxa known from Konservat-Lagerstätten, including Myllokunmingia and Yunnanozoon from the Stage 3 of South China, and Emmonsaspis and Metaspriggina from Stage 4-Drumian deposits of northeast USA and British Columbia. Here, we describe the first soft-bodied vertebrate from the American Great Basin, a region home to a dozen Cambrian Konservat-Lagerstätten. Found in the Drumian Marjum Formation of Utah, Nuucichthys rhynchocephalus gen. et sp. nov. is characterized by a finless torpedo-shaped body that includes a snout-like anterior head bearing anterolateral eyes, approximately 25 thick myomeres, a large branchial chamber with a keel and approximately seven putative dorsal bars and a spiniform caudal process. Using Bayesian inference, our analysis recovers Nuucichthys within the vertebrate stem, closer to the crown than Pikaia, Yunnanozoon and Myllokunmingia, where it forms a polytomy with its Laurentian relatives, Emmonsaspis and Metaspriggina, and a scion consisting of conodonts and crown-group vertebrates. Based on the eye orientation and absence of fins, we tentatively reconstruct Nuucichthys as a pelagic organism with limited swimming abilities (planktonektic).

Stranger in the nest: On the biostratigraphic relevance of a new record of a traversodontid cynodont in southern Brazil (Candelária Sequence, Upper Triassic)

The Várzea do Agudo is an Upper Triassic site of the Candelária Sequence of Southern Brazil that boasts an extensive fossil record. It is assigned to the Exaeretodon subzone of the Hyperodapedon AZ (mid-late Carnian) mainly due to the prevalent presence of the traversodontid Exaeretodon riograndensis — up to now the sole traversodontid discovered at the site. In this study, we report the first record of the traversodontid Siriusgnathus niemeyerorum in the Várzea do Agudo site. The new specimen was excavated from the upper layers of the outcrop. Its identification as S. niemeyerorum is substantiated by diagnostic features such as a poorly developed interorbital depression, an inconspicuous suborbital process of the jugal, a not deeply concave base of the lambdoidal crest, the distal accessory labial cusp of the upper postcanines more labially oriented than E. riograndensis, and two upper incisors — so far, a trait autapomorphic to the species among traversodontids. The age of the type locality of S. niemeyerorum has been a subject of debate. Whereas the Siriusgnathus-bearing sites had been associated with younger levels than those of the Hyperodapedon AZ, the absence of index fossils hampered proper biostratigraphic approaches. The finding of a S. niemeyerorum specimen in the same site as E. riograndensis poses a challenging scenario for the biostratigraphy of the fossiliferous outcrops of the municipality of Agudo. It is noteworthy, however, that the new specimen was excavated above the layers yielding E. riograndensis. This raises the question of whether the fossiliferous stratum of the Várzea do Agudo site was deposited in a single event or in a short period, or if it reflects two different time horizons. In the case of the latter, the existence of early Norian sites with distinct faunal composition near the Siriusgnathus-bearing sites could imply the existence of an intermediate fauna between this AZ and the Exaeretodon subzone of the Hyperodapedon AZ, of which S. niemeyerorum would be a constituent. Considering this context, this study discusses the possible biostratigraphic implications of the new record for the biostratigraphy of the sites of the Candelária Sequence.

Assessing the performance of short 18S rDNA markers for environmental DNA metabarcoding of marine protists

AbstractMarine protists are globally distributed and sensitive to environmental conditions, which makes them a focal group when studying the effects of climate change on biodiversity and ocean health. However, they are a highly diverse group with varying evolutionary histories and morphologies and widely variable preservation potential in the fossil record. Thus, their past diversity and composition are poorly known. Paleogenetics, which relies, among other approaches, on DNA metabarcoding of sedimentary ancient DNA (sedaDNA), provides a promising avenue to explore the past history and responses of marine protists to global change. Choosing the right marker for sedaDNA studies is critical, striking a balance between marker length and taxonomic resolution. While marker guides exist for modern environmental DNA surveys, a thorough assessment of existing short markers for sedaDNA studies targeting protists is lacking. In this study, we report on a comparison of in silico PCR for eight short 18S rDNA markers, including one from the Tara Oceans initiative and a longer marker commonly used in modern marine eDNA studies. We analyze their taxonomic coverage and resolution, taxonomic overlap and uniqueness between markers, co‐amplification of non‐protist taxa, and amplicon size differences across taxonomic groups. Additionally, we provide a detailed analysis of diatoms, dinoflagellates, haptophytes, and chlorophytes. Our study is aimed at supporting project‐specific marker choices for characterizing protist composition and diversity. While we focus on marine protists, our results are applicable to other aquatic and terrestrial environments.

Spatiotemporal distribution and morphological diversity of the Cambrian Wiwaxia: New insights from South China

Wiwaxia is a well-known Cambrian animal and a relative of annelids and molluscs, characterized by its densely arranged, imbricated dorsal sclerites. Despite its prevalence in the fossil record, the scarcity of articulated specimens leading to persistent uncertainties regarding its morphological diversities and evolutionary history has fueled ongoing investigations. This study presents an additional articulated specimen and isolated sclerites from the Cambrian Stage 4 Douposi Formation in Yunnan Province, South China, representing a new species—Wiwaxia douposiensis sp. nov. The newly described materials, originating from a new Cambrian Konservat-Lagerstätte, exhibit typical Burgess Shale-type preservation. They unveil a distinctive two-order rib pattern and aspect ratios of sclerites. The temporal and spatial distribution of Wiwaxia suggests a potential origination centered in South China during the Cambrian Age 3, with an expanding pattern from shallow to deep waters and from warm-humid to dry-cold climates during the Cambrian Age 4 to Drumian. Statistical and phylogenetic analyses highlight the dual aspects of conservative aspect ratios in sclerites, and morphological variations observed at the species levels within Wiwaxia.

Dawn of diverse shelled and carbonaceous animal microfossils at ~ 571 Ma

The Ediacaran-Cambrian transition documents a critical stage in the diversification of animals. The global fossil record documents the appearance of cloudinomorphs and other shelled tubular organisms followed by non-biomineralized small carbonaceous fossils and by the highly diversified small shelly fossils between ~ 550 and 530 Ma. Here, we report diverse microfossils in thin sections and hand samples from the Ediacaran Bocaina Formation, Brazil, separated into five descriptive categories: elongate solid structures (ES); elongate filled structures (EF); two types of equidimensional structures (EQ 1 and 2) and elongate hollow structures with coiled ends (CE). These specimens, interpreted as diversified candidate metazoans, predate the latest Ediacaran biomineralized index macrofossils of the Cloudina-Corumbella-Namacalathus biozone in the overlying Tamengo Formation. Our new carbonate U–Pb ages for the Bocaina Formation, position this novel fossil record at 571 ± 9 Ma (weighted mean age). Thus, our data point to diversification of metazoans, including biomineralized specimens reminiscent of sections of cloudinids, protoconodonts, anabaritids, and hyolithids, in addition to organo-phosphatic surficial coverings of animals, demonstrably earlier than the record of the earliest known skeletonized metazoan fossils.

Insights into digit evolution from a fate map study of the forearm using Chameleon, a new transgenic chicken line.

The cellular and genetic networks that contribute to the development of the zeugopod (radius and ulna of the forearm, tibia and fibula of the leg) are not well understood, although these bones are susceptible to loss in congenital human syndromes and to the action of teratogens such as thalidomide. Using a new fate-mapping approach with the Chameleon transgenic chicken line, we show that there is a small contribution of SHH-expressing cells to the posterior ulna, posterior carpals and digit 3. We establish that although the majority of the ulna develops in response to paracrine SHH signalling in both the chicken and mouse, there are differences in the contribution of SHH-expressing cells between mouse and chicken as well as between the chicken ulna and fibula. This is evidence that, although zeugopod bones are clearly homologous according to the fossil record, the gene regulatory networks that contribute to their development and evolution are not fixed.

Practical guidelines for Bayesian phylogenetic inference using Markov Chain Monte Carlo (MCMC)

Phylogenetic estimation is, and has always been, a complex endeavor. Estimating a phylogenetic tree involves evaluating many possible solutions and possible evolutionary histories that could explain a set of observed data, typically by using a model of evolution. Modern statistical methods involve not just the estimation of a tree, but also solutions to more complex models involving fossil record information and other data sources. Markov Chain Monte Carlo (MCMC) is a leading method for approximating the posterior distribution of parameters in a mathematical model. It is deployed in all Bayesian phylogenetic tree estimation software. While many researchers use MCMC in phylogenetic analyses, interpreting results and diagnosing problems with MCMC remain vexing issues to many biologists. In this manuscript, we will offer an overview of how MCMC is used in Bayesian phylogenetic inference, with a particular emphasis on complex hierarchical models, such as the fossilized birth-death (FBD) model. We will discuss strategies to diagnose common MCMC problems and troubleshoot difficult analyses, in particular convergence issues. We will show how the study design, the choice of models and priors, but also technical features of the inference tools themselves can all be adjusted to obtain the best results. Finally, we will also discuss the unique challenges created by the incorporation of fossil information in phylogenetic inference, and present tips to address them.

Testing the near-far connection with FIRE simulations: Inferring the stellar mass function of the proto-Local Group at z > 6 using the fossil record of present-day galaxies

Testing the near-far connection with FIRE simulations: Inferring the stellar mass function of the proto-Local Group at z > 6 using the fossil record of present-day galaxies