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bioRxiv2021

Tooth chipping patterns in Paranthropus do not support regular hard food mastication

The paranthropines, including Paranthropus boisei and Paranthropus robustus, have often been considered hard-food specialists. The large post-canine teeth, thick enamel, and robust craniofacial features are often suggested to have evolved to cope with habitual mastication of hard foods. Yet, direct evidence for Paranthropus feeding behaviour often challenges these morphological interpretations. The main exception being antemortem tooth chipping which is still regularly used as evidence of habitual mastication of hard foods in this genus. In this study, data were compiled from the literature for six hominin species (including P. boisei and P. robustus) and 17 extant primate species, to analyse Paranthropus chipping patterns in a broad comparative framework. Severity of fractures, position on the dentition, and overall prevalence were compared among species. The results indicate that both Paranthropus species had a lower prevalence of tooth fractures compared to other fossil hominin species (P. boisei: 4%; P. robustus: 11%; Homo naledi: 37%; Australopithecus africanus: 17%; Homo neanderthalensis: 45%; Epipalaeolithic Homo sapiens: 29%); instead, their frequencies are similar to apes that masticate hard items in a non-regular frequency, including chimpanzees, gibbons, and gorillas (4%, 7% and 9% respectively). The prevalence is several times lower than in extant primates known to habitually consume hard items, such as sakis, mandrills, and sooty mangabeys (ranging from 28% to 48%). Comparative chipping analysis suggests that both Paranthropus species were unlikely habitual hard object eaters, at least compared to living durophage analogues.

paleontology↗

bioRxiv2021

Fossil data do not support a long Pre-Cretaceous history of flowering plants

The origin of angiosperms is a classic macroevolutionary problem, because of their rapid rise in the Early Cretaceous fossil record, beginning about 139 Ma ago, and the conflict this creates with older crown-group ages based on molecular clock dating1. Silvestro et al.2 use a novel methodology to model past angiosperm diversity based on a Bayesian Brownian Bridge model of fossil finds assigned to extant families, concluding that a Cretaceous origin is vanishingly unlikely. However, their results strongly conflict with the known temporal distribution of angiosperm fossils, and, while we agree that statistical analysis aids interpretation of the fossil record, here we show the conclusions of Silvestro et al.2 are unsound.

paleontology↗

bioRxiv2021

Palynofacies, environments, and climate changes in the Magdalena River Basin

Four environments (swamp, shallow lake, alluvial flood plain, and lagoon) from the Lower Magdalena River Basin were studied for palynofacies quantitative characterization. Each environment has been described based on four criteria: palynomorph assemblage, organic matter concentration, organic matter palynological composition, and organic particle morphology. Shallow lakes palynological assemblages are dominated by composite and grass pollen. The POM (particulate organic matter) morphology is characterized by a maximum at {Phi} 5 class (silt), and it has a sphericity histogram with bimodal distribution (peaks at 0.1 and 0.5/0.6). From a composition point of view, POM is mainly opaque amorphous materials. POM concentration is usually lower than 0.1%. Swamp environments palynological assemblages are dominated by grass pollen with a slightly smaller amount of composite pollen. The POM is dominated by finely dispersed amorphous and indeterminate "other" types (organo-mineral gel ?), depending on the oxidation degree. The swamp concentration of organic matter a few centimeters below the water-sediment interface varies between 0.1% and 0.3%. Below that, organic concentration is usually lower than 0.1%. Lagoon assemblages are rich in species and specimens, but assemblages are highly variable. Main components are either finely dispersed amorphous or plant cuticular/epidermal or amorphous homogeneous and heterogeneous or fungal remains. Peat lithology is rich in mangrove pollen, while clay assemblages are dominated by composites, grass, and water plants together with Botryococcus algal remains. Lagoon sediments are the richest in POM concentration, with values between 0.13% and 1% (excluding peats). Regarding particle size and shape, in this environment, they show a trend to decrease in grain size from {Phi} 1 to {Phi} 2 class (sand) dominated assemblages to {Phi} 5 to {Phi} 6 class (silt) dominated assemblages from base to top. Elongated shapes are abundant, with 30% to 50% of particles in the tabloid to elongated tabloid classes. Alluvial - fluvial flood basin samples are often barren in palynomorphs and organic matter. Occasionally present grass pollen and fungal remains. The POM, when present, is mainly of organo-mineral gel type and has a bimodal grain size distribution, with a minor peak at {Phi} 7 class (v.f.silt) and a major peak at {Phi} 4 to {Phi} 2 class (c. silt to f. sand). Significant changes in quantitative palynofacies occur within the top few meters of the cores, representing the last 1000 yr of sedimentation in the area. These changes are related to shifts in climate, from colder to warmer conditions or from dry to wet periods, most probably linked with E.N.S.O. A short dry and cold period related to the "Little Ice Age" was identified in the Ayapel and Cienaga de El Medio cores.

paleontology↗

bioRxiv2021

New opabiniid diversifies the weirdest wonders of the euarthropod lower stem group

Once considered weird wonders of the Cambrian, the emblematic Burgess Shale animals Anomalocaris and Opabinia are now recognized as lower stem-group euarthropods. Anomalocaris and its relatives (radiodonts) had a worldwide distribution and survived until at least the Devonian, whereas - despite intense study - Opabinia remains the only formally described opabiniid to date. Here we reinterpret a fossil from the Wheeler Formation of Utah as a new opabiniid, KUMIP 314087. By visualizing the sample of phylogenetic topologies in treespace, our results fortify support for the position of KUMIP 314087 beyond the nodal support traditionally applied. Our phylogenetic evidence expands opabiniids to multiple Cambrian Stages spanning approximately five million years. Our results underscore the power of treespace visualization for resolving imperfectly preserved fossils and expanding the known diversity and spatiotemporal ranges within the euarthropod lower stem group. Additional noteThis work contains a new biological name. New names in preprints are not considered available by the ICZN. To avoid ambiguity, the new biological name is not included in this preprint, and the specimen number (KUMIP 314087) is used as a placeholder. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=150 SRC="FIGDIR/small/434726v1_ufig1.gif" ALT="Figure 1"> View larger version (98K): org.highwire.dtl.DTLVardef@e770aaorg.highwire.dtl.DTLVardef@95bbd3org.highwire.dtl.DTLVardef@5e460eorg.highwire.dtl.DTLVardef@1494152_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOCover image.C_FLOATNO Artistic reconstruction of the new opabiniid from the Wheeler Formation, Utah, USA (Cambrian: Drumian). Artwork by F. Anthony. C_FIG

paleontology↗

bioRxiv2021

Bipedalism in Mexican Albian lizard (Squamata) and the locomotion type in other Cretaceous lizards

Representative locomotion types in lizards include terrestrial, arboreal, grass swimmer, sand swimmer and bipedal. Few studies explain the locomotion habit of extinct lizards, and even less asses those of bipedal ones. Here, we use quantitative methods to infer the type of locomotion of two Albian Mexican lizards (Lower Cretaceous) and three Cretaceous lizards from Brazil, North America and Spain, assessing the similarities of the hindlimb-forelimb length ratio amongst extinct and extant species. Additionally, an ancestral character state reconstruction analysis was performed, to evaluate the evolution of lizard locomotion habits. The species Huehuecuetzpalli mixtecus was bipedal while Tijubina pontei was facultative bipedal, Hoyalacerta sanzi, Tepexisaurus tepexii and Polyglyphanodon sternbergi cannot be differentiated amongst terrestrial or arboreal with the approach used in this work. The ancestral character state reconstruction analysis showed a terrestrial ancestral locomotion type, with a basal character state of hindlimbs longer than forelimbs. Equal length between hind and forelimbs appear to be a derivate state that evolved multiple times in lizard evolutionary history.

paleontology↗

bioRxiv2021

Unbiased clade age estimation using a Bayesian Brownian Bridge

In a recent paper1 we presented a new model, the Bayesian Brownian Bridge (BBB), to infer clade age based on fossil evidence and modern diversity. We benchmarked the method with extensive simulations, including a wide range of diversification histories and sampling heterogeneities that go well beyond the necessarily simplistic model assumptions. Applying BBB to 198 angiosperm families, we found that their fossil record is compatible with clade origins earlier than most contemporary palaeobotanical interpretations. In particular, we estimated with high probability that crown-angiosperms originated before the Cretaceous (> 145 Ma). Budd and colleagues2 critique our study, arguing that the BBB model is biased towards older estimates when fossil data are scarce or absent, that our underlying fossil dataset is unsound, that our clade age estimates are therefore biased by early diverging lineages that are underrepresented in the fossil record, and that pooling of fossil data for analysis at higher taxonomic ranks overcomes these biases. Here, we explore their points and perform new simulations to show that their critique has no merit.

paleontology↗

bioRxiv2021

Millennial-scale change on a Caribbean reef system that experiences hypoxia

Coastal hypoxia has become an increasingly acknowledged threat to coral reefs that is potentially intensifying because of increased input of anthropogenic nutrients. Almirante Bay (Caribbean Panama) is a semi-enclosed system that experiences hypoxia in deeper waters which occasionally expand into shallow coral reefs, suffocating most aerobic benthic life. To explore the long-term history of reefs in the bay we extracted reef matrix cores from two reefs that today experience contrasting patterns of oxygenation. We constructed a 1800-year-long record of gastropod assemblages and isotope compositions from six U-Th chronologically-constrained reef matrix cores. We extracted two cores from each reef at 3 m water depth and two additional cores from a deeper part (4.8 m) of the hypoxia-exposed reef. Results show that the deeper part of the hypoxic reef slowed in growth and stopped accreting approximately 1500 years BP while the shallow part of the reef continued to accrete to the present day, in agreement with a model of expanding hypoxia at this time. Our proxy-based approach suggests that differences among these palaeoindicators in the two reefs may have been driven by an increase in hypoxia via eutrophication caused by either natural changes or human impacts. Similar patterns of increasing herbivores and decreasing carbon isotope values occurred in the shallow part of the hypoxic reef during the last few decades. This suggests that hypoxia may be expanding to depths as shallow as 3 m and that shallow reefs are experiencing greater risk due to increased human activity.

paleontology↗

bioRxiv2021

An evidence-based 3D reconstruction of Asteroxylon mackiei the most complex plant preserved from the Rhynie chert

The 407-million-year-old Rhynie chert preserves the earliest terrestrial ecosystem and informs our understanding of early life on land. However, our knowledge of the 3D structure, and development of these plants is still rudimentary. Here we used digital 3D reconstruction techniques to produce the first complete reconstruction of the lycopsid Asteroxylon mackiei, the most complex plant in the Rhynie chert. The reconstruction reveals the organisation of the three distinct axes types - leafy shoot axes, root-bearing axes and rooting axes - in the body plan. Combining this reconstruction with developmental data from fossilised meristems, we demonstrate that the A. mackiei rooting axis - a transitional lycophyte organ between the rootless ancestral state and true roots - developed from root-bearing axes by anisotomous dichotomy. Our discovery demonstrates how this unique organ developed, and highlights the value of evidence-based reconstructions for understanding the development and evolution of the first complex plants on Earth.

paleontology↗

bioRxiv2021

Preservation of collagen in the soft tissues of frozen mammoths

We investigated the characteristics of extracellular matrix (ECM) in the soft tissue of two frozen baby woolly mammoths (Mammuthus primigenius) that died and were buried in Siberian permafrost approximately 40,000 years ago. Morphological and biochemical analyses of mammoth lung and liver demonstrated that those soft tissues were preserved at the gross anatomical and histological levels. The ultrastructure of ECM components, namely a fibrillar structure with a collagen-characteristic pattern of cross-striation, was clearly visible with transmission and scanning electron microscopy. Type I and type IV collagens were detected by immunohistochemical observation. Quantitative amino acid analysis of liver and lung tissues of the baby mammoths indicated that collagenous protein is selectively preserved in these tissues as a main protein. Type I and type III collagens were detected as major components by means of liquid chromatography-mass spectrometry analysis after digestion with trypsin. These results indicate that the triple helical collagen molecule, which is resistant to proteinase digestion, has been preserved in the soft tissues of these frozen mammoths for 40,000 years.

paleontology↗

bioRxiv2021

Estimating the age of poorly dated fossil specimens and deposits using a total-evidence approach and the fossilized birth-death process

Bayesian total-evidence approaches under the fossilized birth-death model enable biologists to combine fossil and extant data while accounting for uncertainty in the ages of fossil specimens, in an integrative phylogenetic analysis. Fossil age uncertainty is a key feature of the fossil record as many empirical datasets may contain a mix of precisely dated and poorly dated fossil specimens or deposits. In this study, we explore whether reliable age estimates for fossil specimens can be obtained from Bayesian total-evidence phylogenetic analyses under the fossilized birth-death model. Through simulations based on the example of the Baltic amber deposit, we show that estimates of fossil ages obtained through such an analysis are accurate, particularly when the proportion of poorly dated specimens remains low and the majority of fossil specimens have precise dates. We confirm our results using an empirical dataset of living and fossil penguins by artificially increasing the age uncertainty around some fossil specimens and showing that the resulting age estimates overlap with the recorded age ranges. Our results are applicable to many empirical datasets where classical methods of establishing fossil ages have failed, such as the Baltic amber and the Gobi Desert deposits.

paleontology↗

bioRxiv2021

Identifying planktonic foraminiferal morphospecies: which are the important images?

Selection of imagery that promotes accurate identification of morphotaxa is viewed as a significant problem in the taxonomy of planktonic foraminifera. Currently, imagery of taxa is sparse, apparently selected by visual judgement, and presented without information about its typicality. What is required are impartially selected images which embrace population variation to serve as training sets for reliable identification of taxa. Outlined here is a simple morphometrically-based solution, applied to the shape of shells in two orientations, in which shape variation is resolved onto three principal component axes. On the premise that the best-adapted shells are the commonest, specimens within 1 standard deviation (sd) of the trivariate mean are recognized as population exemplars suitable for use as trainers. Specimens which project at [≥]2 sd onto at least one axis are mapped as boundary specimens whose identity might be questioned. This procedure is trialled on samples of Truncorotalia crassaformis. Exemplars from the Equatorial Atlantic and Caribbean compare closely; they partially overlap with those from a Holocene Southwest Pacific population provisionally interpreted as a subtaxon, Truncorotalia crassaformis hessi.

paleontology↗

bioRxiv2021

A fossil fish assemblage from the middle Miocene of the Cocinetas Basin, northern Colombia

Freshwater fossil fish faunas have been long used to infer past drainage connections, as they are bounded by physical freshwater barriers. Here we study a middle Miocene (15.0--15.5 Ma) freshwater fish fossil fauna (Makaraipao) from the Castilletes Formation in northern Colombia, nowadays west of the Andes. We record the presence of lungfishes (Lepidosiren), pacus (Mylossoma and Piaractus), armored catfishes (Callichthyidae), and red-tail catfishes (Phractocephalus). Extant members of all those groups (except the Callichthyidae, due to lack of taxonomic resolution) are found in Amazonian faunas east of the Andes and are absent from faunas west of the Andes, indicating that the riverine systems of the Guajira Peninsula were connected to Amazonia during the middle Miocene. The similarity of La Venta (west of the Andes) and Rio Acre (east of the Andes) fish faunas during the late Miocene further indicates that the northern Andean uplift was not a complete barrier at least until[~] 11 Myr ago. However, there is a continental-wide structuring of the Miocene fish faunas that is also found in the extant faunas, suggesting that other factors such as ecological conditions, in addition to the uplift of the Andes, have shaped the biogeographic evolution of South American fish faunas.

paleontology↗

bioRxiv2021

Online spike sorting via deep contractive autoencoder

Spike sorting - the process of separating spikes from different neurons - is often the first and most critical step in the neural data analysis pipeline. Spike-sorting techniques isolate a single neurons activity from background electrical noise based on the shapes of the waveforms (WFs) obtained from extracellular recordings. Despite several advancements in this area, an important remaining challenge in neuroscience is online spike sorting, which has the potential to significantly advance basic neuroscience research and the clinical setting by providing the means to produce real-time perturbations of neurons via closed-loop control. Current approaches to online spike sorting are not fully automated, are computationally expensive and are often outperformed by offline approaches. In this paper, we present a novel algorithm for fast and robust online classification of single neuron activity. This algorithm is based on a deep contractive autoencoder (DCAE) architecture. DCAEs are deep neural networks that can learn a latent state representation of their inputs. The main advantage of DCAE approaches is that they are less sensitive to noise (i.e., small perturbations in their inputs). We therefore reasoned that they can form the basis for robust online spike sorting algorithms. Overall, our DCAE-based online spike sorting algorithm achieves over 90% accuracy at sorting previously-unseen spike waveforms. Moreover, our approach produces superior results compared to several state-of-the-art offline spike-sorting procedures.

paleontology↗

bioRxiv2021

The oldest peracarid crustacean reveals a Late Devonian freshwater colonisation by isopod relatives

Peracarida (e.g., woodlice & side-swimmers) are, together with their sister-group Eucarida (e.g. krill & decapods), the most speciose group of modern crustaceans, suggested to have appeared as early as the Ordovician. While eucarids incursion onto land consists of mainly freshwater and littoral grounds, some peracarids have evolved fully terrestrial ground-crawling ecologies, inhabiting even our gardens in temperate regions (e.g. pillbugs and sowbugs). Their fossil record extends back to the Carboniferous and consists mainly of marine occurrences. Here, we provide a complete re-analysis of a fossil arthropod - Oxyuropoda - reported in 1908 from the Late Devonian floodplains of Ireland, and left with unresolved systematic affinities despite a century of attempts at identification. Known from a single specimen preserved in two-dimensions, we analysed its anatomy using digital microscopy and multispectral macro-imaging to enhance contrast of morphological structures. The new anatomical characters and completeness of Oxyuropoda, together with a phylogenetic analysis with representatives of all major Eumalacostraca groups, indicate that Oxyuropoda is a crown-peracarid, part of a clade including amphipods and isopods. As such, Oxyuropoda is the oldest known Peracarida, and provides evidence that derived peracarids had an incursion into freshwater and terrestrial environments as early as the Famennian, more than 360 million years ago.

paleontology↗

bioRxiv2021

Monotreme middle ear is not primitive for Mammalia

The study on evolution of the mammalian middle ear has been fueled by continuous discoveries of Mesozoic fossils in the last two decades. Wang et al.1 recently reported a specimen of Vilevolodon diplomylos (IMMNH-PV01699)2 that adds to the increasing knowledge about the auditory apparatus of haramiyidans, an extinct Mesozoic group of mammaliaforms. The authors hypothesized that a middle ear with a monotreme-like incus and malleus and incudomallear articulation was primitive for mammals, which challenges the convention that the monotreme middle ear is specialized3 or autapomorphic4 in mammals. We raise concerns about terminology and identification of the incus presented by Wang et al. and show that their analysis does not support their hypothesis; instead, it supports the one by Mao et al.5,6.

paleontology↗

bioRxiv2021

The petrosal and basicranial morphology of Protoceras celer

Protoceratids are an extinct family of endemic North American artiodactyls. The phylogenetic position of protoceratids in relation to camelids and ruminants has been contentious for over a century. The petrosal morphology of basal (Leptotragulus) and derived (Syndyoceras) protoceratids has suggested that protoceratids are closely related to ruminants, whereas a prior description of a disarticulated intermediate protoceratid petrosal (Protoceras celer) indicated that protoceratids were closely related to camelids. This contradictory evidence implied that there were several character reversals within the protoceratid lineage and brought into question the utility of basicranial characters in artiodactyl phylogenetics. Here, we provide descriptions of an additional P. celer petrosal. The descriptions are based on data produced by computed tomography scans, which allowed us to image the petrosal in situ in the skull. Our results indicate that the petrosal morphology of P. celer is similar to that of other protoceratids, implying that, contrary to previous evidence, petrosal morphology is conserved within the Protoceratidae.

paleontology↗

bioRxiv2021

Ooids forming in situ within microbial mats (Kiritimati atoll, central Pacific)

Ooids (subspherical particles with a laminated cortex growing around a nucleus) are ubiquitous in the geological record since the Archean and have been widely studied for more than two centuries. However, various questions about them remain open, particularly about the role of microbial communities and organic matter in their formation and development. Although ooids typically occur rolling around in agitated waters, here we describe for the first time aragonite ooids forming statically within microbial mats from hypersaline ponds of Kiritimati (Kiribati, central Pacific). Subspherical particles had been previously observed in these mats and classified as spherulites, but they grow around autochthonous micritic nuclei, and many of them have laminated cortices, with alternating radial fibrous laminae and micritic laminae. Thus, they are compatible with the definition of ooid and are in fact identical to many modern and fossil examples. Kiritimati ooids are more abundant and developed in some ponds and in some particular layers of the microbial mats, which has led to the discussion and interpretation of their formation processes as product of mat evolution, through a combination of organic and environmental factors. Radial fibrous laminae are formed during periods of increased supersaturation, either by metabolic or environmental processes. Micritic laminae are formed in closer association with the mat exopolymer (EPS) matrix, probably during periods of lower supersaturation and/or stronger EPS degradation. Therefore, this study represents a step forward in the understanding of ooid development as influenced by microbial communities, providing a useful analogue for explaining similar fossil ooids.

paleontology↗

bioRxiv2021

Metacommunity analyses show increase in ecological specialisation throughout the Ediacaran

The first animals appear during the late Ediacaran (572 - 541 Ma); an initial diversity increase was followed by a drop, interpreted as catastrophic mass extinction. We investigate the processes underlying these changes using the "Elements of Metacommunity Structure" framework. The oldest metacommunity was characterized by taxa with wide environmental tolerances, and limited specialisation and inter-taxa interactions. Structuring increased in the middle metacommunity, with groups of taxa sharing synchronous responses to environmental gradients, aggregating into distinct communities. This pattern strengthened in the youngest metacommunity, with communities showing strong environmental segregation and depth structure. Thus, metacommunity structure increased in complexity, with increased specialisation and resulting competitive exclusion, not a catastrophic environmental disaster, leading to diversity loss in the terminal Ediacaran, revealing that the complex eco-evolutionary dynamics associated with Cambrian diversification were established in the Ediacaran.

paleontology↗