Most downloaded biology preprints, all time
in category paleontology
186 results found. For more information, click each entry to expand.
887 downloads bioRxiv paleontology
Extended parental care (XPC) is a complex reproductive strategy in which progenitors actively look after their offspring up to - or beyond - the first juvenile stage in order to maximize their fitness. Although the euarthropod fossil record has produced several examples of brood-care, the appearance of XPC within this phylum remains poorly constrained given the scarcity of developmental data for Palaeozoic stem-group representatives that would link juvenile and adult forms in an ontogenetic sequence. Here, we describe the post-embryonic growth of Fuxianhuia protensa from the early Cambrian Chengjiang Lagerstätte, and show parental care in this stem-group euarthropod. We recognize fifteen distinct ontogenetic stages based on the number and shape of the trunk tergites, and their allocation between the morphologically distinct thorax and abdomen. Our data demonstrate anamorphic post-embryonic development in F. protensa, in which tergites were sequentially added from a posterior growth zone. A life assemblage consisting of a sexually mature F. protensa adult alongside four ontogenetically coeval juveniles, constitutes the oldest occurrence of XPC in the panarthropod fossil record. These findings provide the most phylogenetically basal evidence of anamorphosis in the evolutionary history of total-group Euarthropoda, and reveal a complex post-embryonic reproductive ecology for its early representatives.
881 downloads bioRxiv paleontology
Unbiased time series of diversity dynamics are vital for quantifying the grand history of life. Applications include identifying ancient mass extinctions and inferring both biotic and abiotic controls on diversification rates. We introduce divDyn, a new R package that facilitates the calculation of taxonomic richness, extinction and origination rates from time-binned fossil sampling data. State-of-the-art sampling completeness metrics, counting protocols, and sampling standardisation functions permit the reconstruction of biologically meaningful time series. Additional functions permit the partitioning of turnover rates by trait and environmental affinity. We display Phanerozoic-scale diversity dynamics of marine invertebrates using the divDyn package. Using the core function and standard subsampling options, we revisit earlier assessments of declining extinction and origination rates over time and of equilibrial diversity dynamics to assess their methodological dependency. The modular and fast implementation of published methods ensures traceability, reproducibility, and comparability of future studies.
881 downloads bioRxiv paleontology
Claims for the widespread preservation of fossilized biomolecules in many fossil animals have recently been reported in six studies, based on Raman microspectroscopy. Here, we show that the putative Raman signatures of organic compounds in these fossils are actually instrumental artefacts resulting from intense background luminescence. Raman spectroscopy relies upon the detection of photons scattered inelastically by matter as a result of its interaction with a laser beam. For many natural materials, this interaction also generates a luminescence signal that is often orders of magnitude more intense than the light produced by Raman scattering. Such luminescence, coupled with the transmission properties of the spectrometer, induced quasi-periodic ripples in the measured spectra that have been incorrectly interpreted as Raman signatures of organic molecules. Although several analytical strategies have been developed to overcome this common issue, Raman microspectroscopy as used in the studies questioned here cannot be used to identify fossil biomolecules. ### Competing Interest Statement The authors have declared no competing interest.
880 downloads bioRxiv paleontology
The Cretaceous-Paleogene (K-Pg) boundary interval represents one of the most significant mass extinctions and ensuing biotic recoveries in Earth history. Earliest Paleocene fossil mammal faunas corresponding to the Puercan North American Land Mammal Age (NALMA) are thought to be highly endemic and potentially diachronous, necessitating precise chronostratigraphic controls at key fossil localities to constrain recovery dynamics in continental biotas following the K-Pg mass extinction. The Laramide synorgenic sedimentary deposits within the Denver Basin preserve one of the most continuous and fossiliferous records of the K-Pg boundary interval in North America. However, poor exposure in much of the Denver Basin makes it difficult to correlate between outcrops. In order to constrain fossil localities across the basin, previous studies have relied upon chronostratigraphic methods such as magnetostratigraphy. Here we present a new high-resolution magnetostratigraphy of 10 lithostratigraphic sections spanning the K-Pg boundary interval at Corral Bluffs located east of Colorado Springs in the southern part of the Denver Basin. Fossil localities from Corral Bluffs have yielded limited dinosaur remains, mammal fossils assigned to the Puercan NALMA, and numerous fossil leaf localities. Palynological analysis identifying the K-Pg boundary in three sections and two independent but nearly identical 206Pb/238U age estimates for the same volcanic ash, provide key temporal calibration points. Our paleomagnetic analysis has identified clear polarity reversal boundaries from Chron C30n to Chron C28r across the sections. It is now possible to place the fossil localities at Corral Bluffs within the broader basin-wide chronostratigraphic framework and evaluate them in the context of K-Pg boundary extinction and recovery.
872 downloads bioRxiv paleontology
The intrageneric relationships of the pampatheriid genus Scirrotherium and its affinities with supposedly related genera, i.e., Kraglievichia and Holmesina , are revised through parsimony phylogenetic analyses and new comparative morphological descriptions. For this work, unpublished material of pampatheriids (numerous osteoderms, one partial skull and a few postcranial bones) from Neogene formations of Colombia was analyzed. The results show that Scirrotherium is paraphyletic if we include all its referred species, i.e., Scirrotherium hondaensis , S. carinatum and S. antelucanus . The species S. carinatum is closer to Kraglievichia paranensis than to S. hondaensis or S. antelucanus , therefore the new name K. carinatum comb. nov. is proposed. The relationship among S. hondaensis and S. antelucanus could not be resolved, so these species should be designated in aphyly. In spite of failing to recover S. hondaensis and S. antelucanus as one single clade, here is preferred to maintain the generic name Scirrotherium in both species based on diagnostic evidence. New emended diagnoses for Scirrotherium , S. hondaensis and Kraglievichia are provided. The genus Holmesina was found to be monophyletic and positioned as the sister clade of Scirrotherium + Kraglievichia . The evolutionary and biogeographic implications of the new phylogeny and taxonomic re-arrangements are discussed. A possible geographic origin of the family Pampatheriidae and Scirrotherium in low latitudes of South America as early as Early Miocene times is claimed. The South American ancestor or sister taxon of Holmesina is predicted to be morphologically more similar to Scirrotherium than to Kraglievichia .
865 downloads bioRxiv paleontology
Brazilichthys macrognathus is the only named actinopterygian from the Permain (Cisuralian) Pedra de Fogo Formation of northeastern Brazil, where it is represented by a single three-dimensionally preserved but incompletely described skull of unclear systematic placement. We used X-ray computed microtomography (μ-CT) to better document its anatomy and phylogenetic affinities. μ-CT reveals parts of the internal skeleton. We correct errors in original description, including the number of infraorbital bones and the misidentification of the dermosphenotic as sclerotic ossifications. These reinterpretations of external anatomy are joined by new data on internal structure, including the palate, parasphenoid, and branchial and hyoid arches. A maximum parsimony analysis of anatomical data resolves Brazilichthys as a stem actinopterygian, crownward of all Devonian species. This placement is supported by the absence of a dermosphenotic posterior ramus and the presence of opercular process of the hyomandibula. A similar placement is suggested by a Bayesian analysis of this same dataset, although relationships throughout the tree are less resolved. Our results reject previous interpretations of Brazilichthys as a relative of Birgeriidae, a Triassic group consistently placed within the actinopterygian crown. Although Acrolepis is too poorly known to be included in our analysis, we also reject a close relationship between this taxon and Brazilichthys, as their only shared similarities appear to be broadly distributed among early actinopterygians.
862 downloads bioRxiv paleontology
Evan T. Saitta, Jakob Vinther, Molly K Crisp, Geoffrey D Abbott, Thomas G. Kaye, Michael Pittman, Ian Bull, Ian Fletcher, Xinqi Chen, Matthew J. Collins, Jorune Sakalauskaite, Meaghan Mackie, Federica Dal Bello, Marc R. Dickinson, Mark A. Stevenson, Paul Donohoe, Philipp R Heck, Beatrice Demarchi, Kirsty E H Penkman
Rates of peptide bond hydrolysis and other diagenetic reactions are not favourable for Mesozoic protein survival. Proteins hydrolyse into peptide fragments and free amino acids that, in open systems such as bone, can leach from the specimen and be further degraded. However, closed systems are more likely to retain degradation products derived from endogenous proteins. Amino acid racemisation data in experimental and subfossil material suggests that mollusc shell and avian eggshell calcite crystals can demonstrate closed system behaviour, retaining endogenous amino acids. Here, high-performance liquid chromatography reveals that the intra-crystalline fraction of Late Cretaceous (estimated ~80 Ma) titanosaur sauropod eggshell is enriched in some of the most stable amino acids (Glx, Gly, Ala, and possibly Val) and those that racemise are fully racemic, despite being some of the slowest racemising amino acids. These results are consistent with degradation trends deduced from modern, thermally matured, sub-fossil, and ~3.8 Ma avian eggshell, as well as ~30 Ma calcitic mollusc opercula. Selective preservation of certain fully racemic amino acids, which do not racemise in-chain, along with similar concentrations of free versus total hydrolysable amino acids, likely suggests complete hydrolysis of original peptides. Liquid chromatography-tandem mass spectrometry supports this hypothesis by failing to detect any non-contamination peptide sequences from the Mesozoic eggshell. Pyrolysis-gas chromatography-mass spectrometry reveals pyrolysates consistent with amino acids as well as aliphatic hydrocarbon homologues that are not present in modern eggshell, suggestive of kerogen formation deriving from eggshell lipids. Raman spectroscopy yields bands consistent with various organic molecules, possibly including N-bearing molecules or geopolymers. These closed-system amino acids are possibly the most thoroughly supported non-avian dinosaur endogenous protein-derived constituents, at least those that have not undergone oxidative condensation with other classes of biomolecules. Biocrystal matrices can help preserve mobile organic molecules by trapping them (perhaps with the assistance of resistant organic polymers), but trapped organics are nevertheless prone to diagenetic degradation even if such reactions might be slowed in exceptional circumstances. The evidence for complete hydrolysis and degradation of most amino acids in the eggshell raises concern about the validity of reported polypeptide sequences from open-system non-avian dinosaur bone and other Mesozoic fossils. ### Competing Interest Statement The authors have declared no competing interest.
851 downloads bioRxiv paleontology
The “Coexistence Approach” is a mutual climate range (MCR) technique combined with the nearest-living relative (NLR) concept. It has been widely used for palaeoclimate reconstructions based on Eurasian plant fossil assemblages, most of them palynofloras (studied using light microscopy). The results have been surprisingly uniform, typically converging to subtropical, per-humid or monsoonal conditions. Studies based on the coexistence approach have had a marked impact in literature, generating over 10,000 citations thus far. However, recent studies have pointed out inherent theoretical and practical problems entangled in the application of this widely used method. But so far little is known how results generated by the coexistence approach are affected by subjective errors, data errors, and violations of the basic assumptions. The majority of Coexistence Approach studies make use of the Palaeoflora database (the combination of which will be abbreviated to CA+PF). Testing results produced by CA+PF studies has been hindered by the general unavailability of the contents in the underlying Palaeoflora database; two exceptions are the mean-annual temperature tolerances and lists of assigned associations between fossils and nearest-living relatives. Using a recently published study on the Eocene of China, which provides the first usable insight into the data structure of the Palaeoflora database, we compare the theory and practice of Coexistence Approach using the Palaeoflora database (CA+PF). We show that CA+PF is riddled by association and climate data error. We reveal the flaws in the application of CA, which is often in stark contrast to the theory of the method. We show that CA+PF is highly vulnerable against numerous sources of errors, mainly because it lacks safeguards that could identify unreliable data. We demonstrate that the CA+PF produces coherent, pseudo-precise results even for artificially generated, random plant assemblages. Alternative MCR-NLR methods can surpass the most imminent deficits of CA, and may be used as a stop-gap until more accurate bioclimatic and distribution data on potential Eurasian NLRs, and theoretically- and statistically-robust methods will become available. Finally, general guidelines are provided for the future application of methods using the mutual climatic range with nearest living relatives approach when reconstructing climate from plant fossil assemblages.
831 downloads bioRxiv paleontology
Stable isotopes of mammoths and mastodons have the potential to illuminate ecological changes in late Pleistocene landscapes and megafaunal populations as these species approached extinction. The ecological factors at play in this extinction remain unresolved, but isotopes of bone collagen (δ13C, δ15N) and tooth enamel (δ13C, δ18O, 87Sr/86Sr) from the Midwest, USA are leveraged to examine ecological and behavioral changes that occurred during the last interglacial-glacial cycle. Both species had significant C3 contributions to their diets and experienced increasing levels of niche overlap as they approached extinction. A subset of mastodons after the last glacial maximum (LGM) exhibit low δ15N values that may represent expansion into a novel ecological niche, perhaps densely occupied by other herbivores. Stable isotopes from serial and micro-sampled enamel show increasing seasonality and decreasing temperatures as mammoths transitioned from Marine Isotope Stage (MIS) 5e to glacial conditions (MIS 4, MIS 3, MIS 2). Isotopic variability in enamel suggests mobility patterns and life histories have potentially large impacts on the interpretation of their stable isotope ecology. This study further refines the ecology of midwestern mammoths and mastodons demonstrating increasing seasonality and niche overlap as they responded to landscape changes in the final millennia before extinction. ### Competing Interest Statement The authors have declared no competing interest.
818 downloads bioRxiv paleontology
Here we describe the bony anatomy of the inner ear and surrounding structures seen in three of the most plesiomorphic crown mammalian petrosal specimens in the fossil record. Our study sample includes the stem therian taxa Priacodon fruitaensis from the Upper Jurassic of North America, and two isolated petrosal specimens colloquially known as the Höövör petrosals, recovered from Aptian-Albian sediments in Mongolia. The second Höövör petrosal is here described at length for the first time. All three of these stem therian petrosals and a comparative sample of extant mammalian taxa have been imaged using micro-CT, allowing for detailed anatomical descriptions of osteological correlates of functionally significant neurovascular features, especially along the abneural wall of the cochlear canal. The high resolution imaging provided here clarifies several hypotheses regarding the mosaic evolution of features of the cochlear endocast in early mammals. In particular, these images demonstrate that the membranous cochlear duct adhered to the bony cochlear canal abneurally to a secondary bony lamina before the appearance of an opposing primary bony lamina or tractus foraminosus. Additionally, while corroborating the general trend of reduction of venous sinuses and plexuses within the pars cochlearis seen in crownward mammaliaformes generally, the Höövör petrosals show the localized enlargement of a portion of the intrapetrosal venous plexus. This new excavation is for the vein of cochlear aqueduct, a structure that is solely or predominantly responsible for the venous drainage of the cochlear apparatus in extant therians. However, given that these stem therian inner ears appear to have very limited high-frequency capabilities, the development of these modern vascular features the cochlear endocast suggest that neither the initiation or enlargement of the stria vascularis (a unique mammalian organ) is originally associated with the capacity for high-frequency hearing or precise sound-source localization.
804 downloads bioRxiv paleontology
The fossil record of the origins of major groups is of great interests to many biologists, especially when the fossil record apparently conflicts with timings based on molecular clock estimates. Here we model the diversity of 'stem' (basal) and 'crown' (modern) members of groups as seen in the fossil record, using a 'birth-death model'. Under background conditions, the stem group members must diversify rapidly until the modern crown group emerges, at which point their diversity rapidly collapses, followed shortly by their extinction. Mass extinctions can disturb this pattern to create verydiverse stem groups such as the dinosaurs and trilobites. Understanding these null-hypothesis patterns is essential for framing ecological and evolutionary explanations for how major groups originate and subsequently evolve.
792 downloads bioRxiv paleontology
The late Permian is a transformative time, which ended in one of the most significant extinction events in Earth's history. Fish assemblages are a major component of marine foods webs. The macroevolution and biogeographic patterns of late Permian fish are currently insufficiently known. In this contribution, the late Permian fish fauna from Kūmas quarry (southern Latvia) is described for the first time. As a result, the studied late Permian Latvian assemblage consisted of isolated chondrichthyan teeth of Helodus sp., ?Acrodus sp., ?Omanoselache sp. and euselachian type dermal denticles as well as many osteichthyan scales of the Haplolepidae and Elonichthydae; numerous teeth of Palaeoniscus, rare teeth findings of ?Platysomus sp. and many indeterminate microremains. This ichthyofaunal assemblage is very similar to the contemporaneous Lopingian complex of the carbonate formation from the Karpėnai quarry (northern Lithuania), despite the fact that Kūmas samples include higher diversity and abundance in fossil remains. The differences in abundance of microremains could possibly be explained by a fresh water influx in the northeastern Zechstein Basin margin, which probably reduced the salinity of the sea water. The new data enable a better understanding of the poorly known late Permian fish diversity from the Lithuania-Latvia Region.
784 downloads bioRxiv paleontology
Crocodylomorpha, which includes living crocodylians and their extinct relatives, has a rich fossil record, extending back for more than 200 million years. Unlike modern semi-aquatic crocodylians, extinct crocodylomorphs exhibited more varied lifestyles, ranging from marine to fully terrestrial forms. This ecological diversity was mirrored by a remarkable morphological disparity, particularly in terms of cranial morphology, which seems to be closely associated with ecological roles in the group. Here, I use geometric morphometrics to comprehensively investigate cranial shape variation and disparity in Crocodylomorpha. I quantitatively assess the relationship between cranial shape and ecology (i.e. terrestrial, aquatic, and semi-aquatic lifestyles), as well as possible allometric shape changes. I also characterise patterns of cranial shape evolution and identify regime shifts. I found a strong link between shape and size, and a significant influence of ecology on the observed shape variation. Terrestrial taxa, particularly notosuchians, have significantly higher disparity, and shifts to more longirostrine regimes are associated with large-bodied aquatic or semi-aquatic species. This demonstrates an intricate relationship between cranial shape, body size and lifestyle in crocodylomorph evolutionary history. Additionally, disparity-through-time analyses were highly sensitive to different phylogenetic hypotheses, suggesting the description of overall patterns among distinct trees. For crocodylomorphs, most results agree in an early peak during the Early Jurassic and another in the middle of the Cretaceous, followed by nearly continuous decline until today. Since only crown-group members survived through the Cenozoic, this decrease in disparity was likely the result of habitat loss, which narrowed down the range of crocodylomorph lifestyles.
776 downloads bioRxiv paleontology
Manual identification of foraminifera species or morphotypes under stereoscopic microscopes is time-consuming for the taxonomist, and a long-time goal has been automating this process to improve efficiency and repeatability. Recent advances in computation hardware have seen deep convolutional neural networks emerge as the state-of-the-art technique for image-based automated classification. Here, we describe a method for classifying large down-core foraminifera image set using convolutional neural networks. Construction of the classifier is demonstrated on the publically available Endless Forams image set with an best accuracy of approximately 90%. A complete down-core analysis is performed for benthic species in the Holocene period for core MD02-2518 from the North Eastern Pacific, and the relative abundances compare favourably with manual counting, showing the same signal dynamics. Using our workflow opens the way to automated paleo-reconstruction based on computer image analysis, and can be employed using our labelling and classification software, ParticleTrieur.
775 downloads bioRxiv paleontology
The applicability of computational analysis to paleontological images ranges from the study of the animals, plants and evolution of microorganisms to the simulation of the habitat of living beings of a given epoch. It also can be applied in several niches, such as oil exploration, where there are several factors to be analyzed in order to minimize the expenses related to the oil extraction process. One factor is the characterization of the environment to be explored. This analysis can occur in several ways: use of probes, extraction of samples for petrophysical components evaluation, the correlation with logs of other drilling wells and so on. In the samples extraction part the Computed Tomography (CT) is of importance because it preserves the sample and makes it available for several analyzes. Based on 3D images generated by CT, several analyzes and simulations can be performed and processes, currently performed manually and exhaustively, can be automated. In this work we propose and validate a method for fully automated microfossil identification and extraction. A pipeline is proposed that begins in the scanning process and ends in an identification process. For the identification a Deep Learning approach was developed, which resulted in a high rate of correct microfossil identification (98% of Intersection Over Union). The validation was performed both through an automated quantitative analysis based upon ground truths generated by specialists in the micropaleontology field and visual inspection by these specialists. We also present the first fully annotated MicroCT-acquired publicly available microfossils dataset.
758 downloads bioRxiv paleontology
The Yixian Formation (the Lower Cretaceous) of China is world famous for its fossils of early angiosperms. Although these diverse angiosperms demonstrate an unexpectedly great diversity, few are preserved as whole plants (not mention of monocots), making our understanding of them incomplete. Here, we report a fossil angiosperm, Sinoherba ningchenensis gen. et sp. nov (Sinoherbaceae fam. nov.), from the Yixian Formation of China; this fossil has a physically connected underground stem with fibrous rootlets, a stem with branches and nodes, leaves with parallel-reticulate veins, and a panicle of female flowers with an ovary surrounded by perianth. Morphological and phylogenetic analyses revealed that Sinoherba is an herbaceous monocot taxon. This newly discovered fossil underscores the great diversity of angiosperms in the Lower Cretaceous Yixian Formation.
757 downloads bioRxiv paleontology
Analysis of the predictable breakdown of proteins and amino acids in ancient biominerals enables age estimation over the Quaternary. We postulate that enamel is a suitable biomineral for the long-term survival of endogenous amino acids. Analysis of multiple amino acids for geochronological studies is typically achieved using a RP-HPLC method. However, the low concentrations of amino acids coupled with high concentrations of inorganic species make accurate determination of amino concentrations challenging. We have developed a method for the routine preparation of multiple enamel samples using biphasic separation. Furthermore, we have shown that amino acids that exhibit effectively closed system behaviour can be isolated from enamel through an exposure time of 72 h to bleach. Elevated temperature experiments investigating the processes of intra-crystalline protein degradation (IcPD) do not appear to match the patterns from fossil samples, reinforcing the need for a comprehensive understanding of the underlying mechanisms of protein degradation. This novel preparative method isolates intra-crystalline amino acids suitable for the development of mammalian geochronologies based on enamel protein degradation. The lower rates of racemisation in enamel (cf. Bithynia opercula) suggest that the enamel AAR may be able to be used as a relative dating technique over time scales > 2.8 Ma. Enamel AAR has the potential to estimate the age of mammalian remains past the limit of all other current direct dating methods, providing an invaluable tool for geochronological studies.
731 downloads bioRxiv paleontology
The ecdysozoans are the most diverse animal group on Earth, . Molecular clock studies indicate that the ecdysozoans may have diverged and diversified in the Ediacaran Period, , but unambiguous ecdysozoan fossils first appear in the earliest Cambrian and are limited to cycloneuralians–. Here we report new material of the early Cambrian microscopic animal Saccorhytus coronarius , which was previously interpreted as a deuterostome. Saccorhytus coronarius is reconstructed as a millimetric and ellipsoidal meiobenthic animal with a spinose armor and an anterior mouth but no anus. Purported pharyngeal gills in support of the deuterostome hypothesis are shown to be taphonomic artifacts. Phylogenetic analyses indicate that Saccorhytus coronarius belongs to the total-group Ecdysozoa, highlighting the morphological and ecological diversity of early Cambrian ecdysozoans. ### Competing Interest Statement The authors have declared no competing interest. : #ref-1 : #ref-2 : #ref-3 : #ref-4 : #ref-5 : #ref-7 : #ref-8
730 downloads bioRxiv paleontology
Here we report a Late Holocene fossil-rich cave deposit from Cueva de los Nesofontes, Mayabeque Province, Cuba. The deposit formation and its fauna were studied through a multidisciplinary approach that included stable isotope analyses, radiocarbon chronology, stratigraphy, sedimentology, and taphonomy. Thousands of microvertebrate skeletal remains were recovered, representing a diverse land vertebrate fauna that included threatened and extinct species. The deposit is characterized by profuse Nesophontes remains due to raptor predation. Previously unreported last appearance dates are provided for the extinct island-shrew Nesophontes major, the bats Artibeus anthonyi and Phyllops vetus. Radiocarbon (14C AMS) age estimates between -1960 rcyr BP and the present were recovered. The presence of locally extinct species, including the endemic parakeet Psittacara eups, the flicker Colaptes cf. auratus/fernandinae, and the lipotyphlan Solenodon cubanus suggests that these species had broader distributions in the near past. Isotope analyses and faunal composition indicate the previous presence of diverse habitats, including palm grove savannas and mixed woodlands. Isotopes also provide insight into the habitat and coexistence of the extinct bat Artibeus anthonyi and extant A. jamaicensis, the diet of Nesophontes major, and local paleoenvironmental conditions. Oxygen isotopes reveal an excursion suggestive of drier/colder local conditions between 660 and 770 AD. Our research further expands the understanding of Cuban Quaternary extinction episodes and provides data on the distribution and paleoecology of extinct taxa. It supports the conclusion that many Cuban extinct species survived well into the pre-Columbian late Holocene and retained wide distribution ranges until human colonization.
700 downloads bioRxiv paleontology
The estimation of origination and extinction rates and their temporal variation is central to understanding diversity patterns and the evolutionary history of clades. The fossil record provides the most direct evidence of extinction and biodiversity changes through time and has long been used to infer the dynamics of diversity changes in deep time. The software PyRate implements a Bayesian framework to analyze fossil occurrence data to estimate the rates of preservation, origination and extinction while incorporating several sources of uncertainty. This fully probabilistic approach allows us to explicitly assess the statistical support of alternative macroevolutionary hypotheses and to infer credible intervals around parameter estimates. Here, we present a major update of the software, which implements substantial methodological advancements, including more complex and realistic models of preservation, a reversible jump Markov chain Monte Carlo algorithm to estimate origination and extinction rates and their temporal variation, and a substantial boost in performance. We demonstrate the new functionalities through extensive simulations and with the analysis of a large dataset of Cenozoic marine mammals. We identify several significant shifts in origination and extinction rates of marine mammals, underlying a late Miocene diversity peak and a subsequent 50% diversity decline towards the present. Our analyses indicate that explicit statistical model testing, which is often neglected in fossil-based macroevolutionary analyses, is crucial to obtain accurate and robust results. PyRate provides a flexible, statistically sound analytical framework, which we think can serve as a useful toolkit for many future studies in paleobiology.
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