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bioRxiv2017

Muon Radiation Dose and Marine Megafaunal Extinction at the end-Pliocene Supernova

Considerable data and analysis support the detection of a supernova at a distance of about 50 pc, ~2.6 million years ago. This is possibly related to the extinction event around that time and is a member of a series of explosions which formed the Local Bubble in the interstellar medium. We build on the assumptions made in previous work, and propagate the muon flux from supernova-initiated cosmic rays from the surface to the depths of the ocean. We find that the radiation dose from the muons will exceed the total present surface dose from all sources at depths up to a kilometer and will persist for at least the lifetime of marine megafauna. It is reasonable to hypothesize that this increase in radiation load may have contributed to a newly documented marine megafaunal extinction at that time.

paleontology↗

bioRxiv2017

Nanjinganthus:An Unexpected Flower from the Jurassic of China

The origin of angiosperms has been the focus of intensive botanical debate for well over a century. The great diversity of angiosperms in the Early Cretaceous makes the Jurassic rather expected to elucidate the origin of angiosperm. Former reports of early angiosperms are frequently based on a single specimen, making many conclusions tentative. Here, based on observations of 284 individual flowers preserved on 28 slabs in various states and orientations, we describe a fossil flower, Nanjinganthus dendrostyla gen. et sp. nov., from the South Xiangshan Formation (Early Jurassic) of China. The large number of specimens and various preservations allows us to give an evidenced interpretation of the flower. The complete enclosure of ovules in Nanjinganthus is fulfilled by a combination of an invaginated and ovarian roof. Characterized by its actinomorphic flower with a dendroid style, cup-form receptacle, and angio-ovuly, Nanjinganthus is a bona fide angiosperm from the Jurassic. Nanjinganthus re-confirms the existence of Jurassic angiosperms and provides first-hand raw data for new analyses on the origin and history of angiosperms.

paleontology↗

bioRxiv2018

Stability, incumbency and ecological reorganizationafter the Permian-Triassic mass extinction

The Permian-Triassic mass extinction (PTME) altered macroevolutionary land-scapes by removing incumbent biota. Here, using terrestrial paleocommunities of the Karoo Basin spanning the PTME, we show that a pre-extinction incumbent configuration of biotic interactions made significant ecological re-organizations or macroevolutionary innovations unlikely. The post-PTME ecosystem initially was more likely to be reorganized, but incumbency was re-established by the Middle Triassic. We argue that the stability of the pre-PTME ecosystem, its subsequent loss, and replacement, resulted from the in-fluence of community-level structure and dynamics on species evolution and survival.\n\nOne sentence summaryBiotic incumbency at the end of the Paleozoic, based on community functional organization, was destroyed by the Permian-Triassic mass extinction, allowing the development of novel community types.

paleontology↗

bioRxiv2018

Anamorphic development and extended parental care in a 520 million-year-old stem-group euarthropod from China

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 Lagerstatte, 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.

paleontology↗

bioRxiv2018

A Whole-Plant Monocot from the Early Cretaceous

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.

paleontology↗

bioRxiv2018

Improved estimation of macroevolutionary rates from fossil data using a Bayesian framework

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.

paleontology↗

bioRxiv2018

Palaeobiological inferences based on long bone epiphyseal and diaphyseal structure - the forelimb of xenarthrans (Mammalia)

Trabecular architecture (i.e., the main orientation of the bone trabeculae, their number, mean thickness, spacing, etc.) has been shown experimentally to adapt with great accuracy and sensitivity to the loadings applied to the bone during life. However, the potential of trabecular parameters used as a proxy for the mechanical environment of an organisms organ to help reconstruct the lifestyle of extinct taxa has only recently started to be exploited. Furthermore, these parameters are rarely combined to the long-used mid-diaphyseal parameters to inform such reconstructions. Here we investigate xenarthrans, for which functional and ecological reconstructions of extinct forms are particularly important in order to improve our macroevolutionary understanding of their main constitutive clades, i.e., the Tardigrada (sloths), Vermilingua (anteaters), and Cingulata (armadillos and extinct close relatives). The lifestyles of modern xenarthrans can be classified as fully terrestrial and highly fossorial (armadillos), arboreal (partly to fully) and hook-and-pull digging (anteaters), or suspensory (fully arboreal) and non-fossorial (sloths). The degree of arboreality and fossoriality of some extinct forms, \"ground sloths\" in particular, is highly debated. We used high-resolution computed tomography to compare the epiphyseal 3D architecture and mid-diaphyseal structure of the forelimb bones of extant and extinct xenarthrans. The comparative approach employed aims at inferring the most probable lifestyle of extinct taxa, using a phylogenetically informed discriminant analysis. Several challenges preventing the attribution of one of the extant xenarthran lifestyles to the sampled extinct sloths were identified. Differing from that of the larger \"ground sloths\", the bone structure of the small-sized Hapalops (Miocene of Argentina), however, was found as significantly more similar to that of extant sloths, even when accounting for the phylogenetic signal.

paleontology↗

bioRxiv2018

Rapid Pliocene Diversification of Modern Kangaroos

AbstractDifferentiating between ancient and rapidly-evolved clades is critical for understanding impacts of environmental change on biodiversity. Australia possesses many aridity-adapted lineages, the origins of which have been linked by molecular evidence to late Miocene drying. Using dental macrowear and molar crown-height measurements spanning the past 25 million years, we show that the most iconic of Australias terrestrial mammals, true kangaroos and wallabies (Macropodini), diversified in response to Pliocene grassland emergence. In contrast, low-crowned short-faced kangaroos radiated into browsing niches as the late Cenozoic became more arid, contradicting the view that this was a period of global decline among browsers. Our results link warm intervals with bursts of diversification and undermine arguments attributing Pleistocene megafaunal extinction to aridity-forced dietary change.

paleontology↗

bioRxiv2018

Fine Endmesolithic Fish Caviar Meal Discovered by Proteomics of Foodcrusts

The role of aquatic resources in ancient economies and paleodiet is important for understanding the evolution of prehistorical societies. However, conventional archaeometric approaches lack organismal specificity, are affected by abundant environmental contaminants and do not elucidate food processing recipes. We performed proteomics analysis of charred organic deposits adhered on early ceramics from Mesolithic-Neolithic inland site Friesack 4 (Brandenburg, Germany). Proteomics of foodcrust from a vessel attributed to Endmesolithic pottery identified fine carp roe meal and revealed details of a prehistorical culinary recipe. We propose that Endmesolithic occupants of Friesack at the end of the 5th millennium BC utilized fish as a food reserve and adopted delayed-return subsistence strategy. These data contribute to better understanding of the dietary context of Neolithic transition in European inland.

paleontology↗

bioRxiv2018

Quantitative Late Quaternary climate reconstruction from plant macrofossil proxy in Western North America

The Late Quaternary packrat (Neotoma spp.) midden plant macrofossil record in western North America is an exceptional record of biotic change that provides strong evidence of past climate. In this study we generate quantitative estimates of climate from plant community composition of more than 600 individual paleomiddens over the past 50,000 years. This is the first large-scale application of CRACLE, a quantitative climate inference method that uses plant community composition as a climatic proxy under and individualistic concept of plant community assembly. The results are spatiotemporally specific estimates of temperature, precipitation, available moisture, and seasonal patterns that are consistent with well understood global climate patterns, but provide previously unavailable detail and precision of the regional paleoclimate in western North America. Rapid warming is estimated at the Pleistocene-Holocene transition, at a conservative estimate of ca. 1{degrees}C per millennium. Previously projected future temperature increases suggest a rate of increase of more than 2{degrees}C over the next century, an astonishing 10X the rate experienced at any point during the past 50,000 years in Western North America. These analyses form a baseline demonstration of how the growing paleoecological record of packrat midden plant macrofossils is able to provide quantitative estimates of paleoclimate that aid in understanding the complexities of, and biotic responses to the regional climate system.

paleontology↗

bioRxiv2018

New Evidence of the Earliest Domestic Dogs in the Americas

The domestication of dogs probably occurred in Eurasia by 16,000 years ago, with the initial peopling of the Americas potentially happening around the same time. Dogs were long thought to have accompanied the first migrations into the Americas, but conclusive evidence for Paleoindian dogs is lacking. The direct dating of two dogs from the Koster site (Greene Co., Illinois) and a newly-described dog from the Stilwell II site (Pike Co., Illinois) to between 10,190-9,630 cal BP represents the earliest evidence of domestic dogs in the Americas and individual dog burials in worldwide archaeological record. The over 4,500 year discrepancy between the timing of initial human migration into the Americas and the earliest evidence for domesticated dogs suggests either earlier dogs are going unseen or unidentified or dogs arrived later with a subsequent human migration.

paleontology↗

bioRxiv2018

A biologically driven directional change in susceptibility to global-scale glaciation during the Precambrian-Cambrian transition

Integrated geological evidence suggests that grounded ice sheets occurred at sea level across all latitudes during two intervals within the Neoproterozoic era; the snowball Earth (SBE) events. Glacial events at ~730 and ~650 million years ago (Ma) were probably followed by a less severe but nonetheless global-scale glaciation at ~580Ma, immediately preceding the proliferation of the first fossils exhibiting unambiguous animal-like form. Existing modelling identifies weathering-induced CO2-drawdown as a critical aspect of glacial inception, but ultimately attributes the SBE phenomenon to unusual tectonic boundary conditions. Here we suggest that the evident directional decrease in Earths susceptibility to a SBE suggests that such a-directional abiotic factors are an insufficient explanation for the lack of SBE events since ~580 Ma. Instead we hypothesize that the terrestrial biospheres capacity to sustain a given level of biotic weathering-enhancement under suboptimal/declining temperatures, itself decreased over time: because lichens (with a relatively robust tolerance of sub-optimal temperatures) were gradually displaced on the land surface by more complex photosynthetic life (with a narrower temperature window for growth). We use a simple modelling exercise to highlight the critical (but neglected) importance of the temperature sensitivity of the biotic weathering enhancement factor and discuss the likely values of key parameters in relation to both experiments and the results of complex climate models. We show how the terrestrial biospheres capacity to sustain a given level of silicate-weathering-induced CO2-drawdown is critical to the temperature/greenhouse forcing at which SBE initiation is conceivable. We do not dispute the importance of low degassing rate and other tectonic factors, but propose that the unique feature of the Neoproterozoic was biologys capacity to tip the system over the edge into a runaway ice-albedo feedback; compensating for the self-limiting decline in weathering rate during the temperature decrease on the approach to glaciation. Such compensation was more significant in the Neoproterozoic than the Phanerozoic due, ultimately, to changes in the species composition of the weathering interface over the course of evolutionary time.View Full Text

paleontology↗

bioRxiv2018

Modelling predation and mortality rates from the fossil record of gastropods

Gastropods often show signs of unsuccessful attacks by predators in the form of healed scars in their shells. As such, fossil gastropods can be taken as providing a record of predation through ge-ological time. However, interpreting the number of such scars has proved to be problematic - would a low number of scars mean a low rate of attack, or a high rate of success, for example? Here we develop a model of scar formation, and formally show that in general these two variables cannot be disambiguated without further information about population structure. Nevertheless, by making the probably reasonable assumptions that the non-predatory death rate is both constant and low, we show that it is possible to use relatively small assemblages of gastropods to produce accurate estimates of both attack and success rates, if the overall death rate can be estimated. We show in addition what sort of information would be required to solve this problem in more general cases. However, it is unlikely that it will be possible to extract the relevant information easily from the fossil record: a variety of important collection and taphonomic biases are likely to intervene to obscure the data that gastropod assemblages may yield.

paleontology↗

bioRxiv2018

Modern botanical analogue of endangered Yak (Bos mutus) dung from India: Plausible linkage with living and extinct megaherbivores

The study present to document the micro and macrobotanical remain on wild Yak dung to understand the diet, habitat, and ecology in relation to determining possible ecological relationships with extant and extinct megaherbivores. Grasses are the primary diet of the yak as indicated by the abundance of grass pollen and phytoliths, though it is obvious. The other associates non-arboreal and arboreal taxa namely, Cyperacaeae, Rosaceae, Chenopodiaceae, Artemisia, Prunus, and Rhododendron are also important dietary plants for their survival. The observation of plant macrobotanical remains especially the vegetative part and seed of the grasses and Cyperaceae also indicates good agreement with the palynodata. The documented micro and macrobotanical data is indicative of both Alpine meadow and steppe vegetation under cold and dry climate which exactly reflected the current vegetation composition and climate in the region. The recovery of Botryococcus, Arcella, and diatom was marked though in trace values and suggestive of the perennial water system in the region which incorporated through the ingestion of water. Energy dispersive spectroscopy analysis marked that the element contained in dung samples has variation in relation to the summer and winter which might be the availability of the food plants and vegetation. This generated multiproxy data serves as a strong supplementary data for modern pollen and vegetation relationship based on surface soil samples in the region. The recorded multiproxy data could be useful to interpret the coprolites of herbivorous fauna in relation to the palaeodietary and paleoecology in the region and to correlate with other mega herbivores in a global context.

paleontology↗

bioRxiv2018

A Reassessment of the Taxonomic Position of Mesosaurs Based on Two Data Matrices

1The Early Permian mesosaurs are the oldest known primarily aquatic amniotes. Despite the interest that they have generated over time, their affinities remain controversial. Recently, two hypotheses have been supported, in which mesosaurs are either the sister-group of all other sauropsids, or the sister-group of other parareptiles. We recently upheld the former hypothesis, but in the latest study on mesosaur affinities, MacDougall et al. published a study highly critical of our work, while upholding the hypothesis that mesosaurs are basal parareptiles. We expect that the debate about mesosaur affinities will continue in the foreseeable future, but we wish to respond to the two central comments published by MacDougall et al. in 2018, who argue that variability in the temporal fenestration of early sauropsids, combined with the omission of several recently-described parareptile taxa, explain the differences in topologies between their study and ours. Reanalyzing our data matrix and theirs without characters linked with temporal fenestration, and removing from their matrix the parareptile taxa that they added (and that we omitted) does not alter the resulting topologies. Thus, their main conclusions are false; the differences in taxonomic position of mesosaurs must result from character choice and scoring differences.

paleontology↗

bioRxiv2018

Kinematics of wings from Caudipteryx to modern birds

This study seeks to better quantify the parameters that drove the evolution of flight from nonvolant winged dinosaurs to modern birds. In order to explore this issue, we used fossil data to model the feathered forelimb of Caudipteryx, the most basal non-volant maniraptoran dinosaur with elongate pennaceous feathers that could be described as forming proto-wings. In order to quantify the limiting flight factors, we created three hypothetical wing profiles for Caudipteryx representing incrementally larger wingspans, which we compared to the actual wing morphology as what revealed through fossils. These four models were analyzed under varying air speed, wing beat amplitude, and wing beat frequency to determine lift, thrust potential and metabolic requirements. We tested these models using theoretical equations in order to mathematically describe the evolutionary changes observed during the evolution of modern birds from a winged terrestrial theropod like Caudipteryx. Caudipteryx could not fly, but this research indicates that with a large enough wing span Caudipteryx-like animal could have flown, the morphology of the shoulder girdle would not actually accommodate the necessary flapping angle and metabolic demands would be much too high to be functional. The results of these analyses mathematically confirm that during the evolution of energetically efficient powered flight in derived maniraptorans, body weight had to decrease and wing area/wing profile needed to increase together with the flapping angle and surface area for the attachment of the flight muscles. This study quantifies the morphological changes that we observe in the pennaraptoran fossil record in the overall decrease in body size in paravians, the increased wing surface area in Archaeopteryx relative to Caudipteryx, and changes observed in the morphology of the thoracic girdle, namely the orientation of the glenoid and the enlargement of the sternum.

paleontology↗

bioRxiv2018

Life Inside A Dinosaur Bone: A Thriving Microbiome

Fossils were long thought to lack original organic material, but the discovery of organic molecules in fossils and sub-fossils, thousands to millions of years old, has demonstrated the potential of fossil organics to provide radical new insights into the fossil record. How long different organics can persist remains unclear, however. Non-avian dinosaur bone has been hypothesised to preserve endogenous organics including collagen, osteocytes, and blood vessels, but proteins and labile lipids are unstable during diagenesis or over long periods of time. Furthermore, bone is porous and an open system, allowing microbial and organic flux. Some of these organics within fossil bone have therefore been identified as either contamination or microbial biofilm, rather than original organics. Here, we use biological and chemical analyses of Late Cretaceous dinosaur bones and sediment matrix to show that dinosaur bone hosts a diverse microbiome. Fossils and matrix were freshly-excavated, aseptically-acquired, and then analysed using microscopy, spectroscopy, chromatography, spectrometry, DNA extraction, and 16S rRNA amplicon sequencing. The fossil organics differ from modern bone collagen chemically and structurally. A key finding is that 16S rRNA amplicon sequencing reveals that the subterranean fossil bones host a unique, living microbiome distinct from that of the surrounding sediment. Even in the subsurface, dinosaur bone is biologically active and behaves as an open system, attracting microbes that might alter original organics or complicate the identification of original organics. These results suggest caution regarding claims of dinosaur bone soft tissue preservation and illustrate a potential role for microbial communities in post-burial taphonomy.

paleontology↗

bioRxiv2018

The multi-peak adaptive landscape of crocodylomorph body size evolution

Background Little is known about the long-term patterns of body size evolution in Crocodylomorpha, the > 200-million-year-old group that includes living crocodylians and their extinct relatives. Extant crocodylians are mostly large-bodied (3–7 m) predators. However, extinct crocodylomorphs exhibit a wider range of phenotypes, and many of the earliest taxa were much smaller (< 1.2 m). This suggests a pattern of size increase through time that could be caused by multi-lineage evolutionary trends of size increase or by selective extinction of small-bodied species. In this study, we characterise patterns of crocodylomorph body size evolution using a model fitting-approach (with cranial measurements serving as proxies). We also estimate body size disparity through time and quantitatively test hypotheses of biotic and abiotic factors as potential drivers of crocodylomorph body size evolution.Results Crocodylomorphs reached an early peak in body size disparity during the Late Jurassic, and underwent essentially continually decreases in disparity since then. A multi-peak Ornstein-Uhlenbeck model outperforms all other evolutionary models fitted to our data (including both uniform and non-uniform), indicating that the macroevolutionary dynamics of crocodylomorph body size are better described within the concept of an adaptive landscape, with most body size variation emerging after shifts to new macroevolutionary regimes (analogous to adaptive zones). We did not find support for a consistent evolutionary trend towards larger sizes among lineages (i.e., Cope’s rule), or strong correlations of body size with climate. Instead, the intermediate to large body sizes of some crocodylomorphs are better explained by group-specific adaptations. In particular, the evolution of a more aquatic lifestyle (especially marine) correlates with increases in average body size, though not without exceptions.Conclusions Shifts between macroevolutionary regimes provide a better explanation of crocodylomorph body size evolution than do climatic factors, suggesting a central role for lineage-specific adaptations rather than climatic forcing. Shifts leading to larger body sizes occurred in most aquatic and semi-aquatic groups. This, combined with extinctions of groups occupying smaller body size regimes (particularly during the Late Cretaceous and Cenozoic), gave rise to the upward-shifted body size distribution of extant crocodylomorphs compared to their smaller-bodied terrestrial ancestors.AbbreviationsCranial measurementsDCLdorsal cranial lengthODCLorbito-cranial lengthEvolutionary modelsBMBrownian motionEBEarly burstOUOrnstein-UhlenbeckBMSmulti-regime BM model that allows parameter σ2 to varyOUMVmulti-regime OU model that allows θ and σ2 to varyOUMAmulti-regime OU model in which θ and α can varyOUMVAOU model in which all three parameters (θ, α and σ2) can varyModel parametersθtrait optimum of OU-based modelsαattraction parameter of OU-based modelsσ2Brownian variance or rate parameter of BM or OU-based modelsμevolutionary trend parameter of BM-based modelsZ0estimated trait value at the root of the tree of OU-based modelsOptimality criteriaAICAkaike’s information criterionAICcAkaike’s information criterion for finite sample sizesBICBayesian information criterionpBICphylogenetic Bayesian information criterionView Full Text

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