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The Chengjiang Biota is the earliest Phanerozoic soft-bodied fossil assemblage offering the most complete snapshot of Earth’s initial diversification, the Cambrian Explosion. Although palaeobiologic aspects of this biota are well understood, the precise sedimentary environment inhabited by this biota remains debated. Herein, we examine a non-weathered core from the Yu’anshan Formation including the interval preserving the Chengjiang Biota. Our data indicate that the succession was deposited as part of a delta influenced by storm floods (i.e., produced by upstream river floods resulting from ocean storms). Most Chengjiang animals lived in an oxygen and nutrient-rich delta front environment in which unstable salinity and high sedimentation rates were the main stressors. This unexpected finding allows for sophisticated ecological comparisons with other Burgess Shale-type deposits and emphasizes that the long-held view of Burgess Shale-type faunas as snapshots of stable distal shelf and slope communities needs to be revised based on recent sedimentologic advances. The Chengjiang Biota is the earliest most diverse animal community from the Cambrian Explosion (~518 million years ago). This biota is shown to have colonized a delta, highlighting the importance of this shallow environment in recording early snapshots of life on Earth.

A hard look at soft fossils Our knowledge of the earliest stages in the evolution of the vertebrates is limited to what can be gleaned from fossils left by the early chordates. And as these animals were soft bodied and lacked bones and shells, the record is sparse and is dominated by relatively few exceptionally preserved specimens. The interpretation of such fossils is fraught with difficulty. Now, as if that were not sufficient, a study of the decay of modern specimens of amphioxus and ammocoetes (larval lampreys), the nearest living relatives of the early soft-bodied chordates, suggests that the loss of typically chordate characteristics during decay is non-random, and that it is the more phylogenetically informative characters that are lost most easily. Such vagaries, firmed up in the fossil record, may result in bias towards wrongly placing fossils on the chordate stem. If this decay bias is widespread, many important evolutionary episodes that are understood from the fossil record of exceptionally preserved soft-tissue remains will need careful reassessment. Our only direct information on the origin of vertebrates comes from preserved soft-bodied Cambrian chordates; however, reading this fossil record is fraught with difficulties owing to a lack of data on when and how important characters change as they decompose. Here, from experimental decay of amphioxus and ammocoetes, it is shown that loss of chordate characters during decay is non-random, with the features that are most phylogenetically informative tending to decay first. Exceptional preservation of soft-bodied Cambrian chordates provides our only direct information on the origin of vertebrates 1 , 2 . Fossil chordates from this interval offer crucial insights into how the distinctive body plan of vertebrates evolved, but reading this pre-biomineralization fossil record is fraught with difficulties, leading to controversial and contradictory interpretations 3 , 4 . The cause of these difficulties is taphonomic: we lack data on when and how important characters change as they decompose, resulting in a lack of constraint on anatomical interpretation and a failure to distinguish phylogenetic absence of characters from loss through decay 3 . Here we show, from experimental decay of amphioxus and ammocoetes, that loss of chordate characters during decay is non-random: the more phylogenetically informative are the most labile, whereas plesiomorphic characters are decay resistant. The taphonomic loss of synapomorphies and relatively higher preservation potential of chordate plesiomorphies will thus result in bias towards wrongly placing fossils on the chordate stem. Application of these data to Cathaymyrus (Cambrian period of China) and Metaspriggina (Cambrian period of Canada) highlights the difficulties: these fossils cannot be placed reliably in the chordate or vertebrate stem because they could represent the decayed remains of any non-biomineralized, total-group chordate. Preliminary data suggest that this decay filter also affects other groups of organisms and that ‘stem-ward slippage’ may be a widespread but currently unrecognized bias in our understanding of the early evolution of a number of phyla.

Exceptionally preserved fossil biotas of the Burgess Shale and a handful of other similar Cambrian deposits provide rare but critical insights into the early diversification of animals. The extraordinary preservation of labile tissues in these geographically widespread but temporally restricted soft-bodied fossil assemblages has remained enigmatic since Walcott’s initial discovery in 1909. Here, we demonstrate the mechanism of Burgess Shale-type preservation using sedimentologic and geochemical data from the Chengjiang, Burgess Shale, and five other principal Burgess Shale-type deposits. Sulfur isotope evidence from sedimentary pyrites reveals that the exquisite fossilization of organic remains as carbonaceous compressions resulted from early inhibition of microbial activity in the sediments by means of oxidant deprivation. Low sulfate concentrations in the global ocean and low-oxygen bottom water conditions at the sites of deposition resulted in reduced oxidant availability. Subsequently, rapid entombment of fossils in fine-grained sediments and early sealing of sediments by pervasive carbonate cements at bed tops restricted oxidant flux into the sediments. A permeability barrier, provided by bed-capping cements that were emplaced at the seafloor, is a feature that is shared among Burgess Shale-type deposits, and resulted from the unusually high alkalinity of Cambrian oceans. Thus, Burgess Shale-type preservation of soft-bodied fossil assemblages worldwide was promoted by unique aspects of early Paleozoic seawater chemistry that strongly impacted sediment diagenesis, providing a fundamentally unique record of the immediate aftermath of the \"Cambrian explosion.\"

Fossils entombed in amber are a unique resource for reconstructing forest ecosystems, and resolving relationships of modern taxa. Such fossils are famous for their perfect, life-like appearance. However, preservation quality is vast with many sites showing only cuticular preservation, or no fossils. The taphonomic processes that control this range are largely unknown; as such, we know little about potential bias in this important record. Here we employ actualistic experiments, using, fruit flies and modern tree resin to determine whether resin type, gut microbiota, and dehydration prior to entombment affects decay. We used solid phase microextraction gas chromatography-mass spectrometry (SPME GC-MS) to confirm distinct tree resin chemistry; gut microbiota of flies was modified using antibiotics and categorized though sequencing. Decay was assessed using phase contrast synchrotron tomography. Resin type demonstrates a significant control on decay rate. The composition of the gut microbiota was also influential, with minor changes in composition affecting decay rate. Dehydration prior to entombment, contrary to expectations, enhanced decay. Our analyses show that there is potential significant bias in the amber fossil record, especially between sites with different resin types where ecological completeness and preservational fidelity are likely affected.

In living organisms, color patterns, behavior, and ecology are closely linked. Thus, detection of fossil pigments may permit inferences about important aspects of ancient animal ecology and evolution. Melanin-bearing melanosomes were suggested to preserve as organic residues in exceptionally preserved fossils, retaining distinct morphology that is associated with aspects of original color patterns. Nevertheless, these oblong and spherical structures have also been identified as fossilized bacteria. To date, chemical studies have not directly considered the effects of diagenesis on melanin preservation, and how this may influence its identification. Here we use time-of-flight secondary ion mass spectrometry to identify and chemically characterize melanin in a diverse sample of previously unstudied extant and fossil taxa, including fossils with notably different diagenetic histories and geologic ages. We document signatures consistent with melanin preservation in fossils ranging from feathers, to mammals, to amphibians. Using principal component analyses, we characterize putative mixtures of eumelanin and phaeomelanin in both fossil and extant samples. Surprisingly, both extant and fossil amphibians generally exhibit melanosomes with a mixed eumelanin/phaeomelanin composition rather than pure eumelanin, as assumed previously. We argue that experimental maturation of modern melanin samples replicates diagenetic chemical alteration of melanin observed in fossils. This refutes the hypothesis that such fossil microbodies could be bacteria, and demonstrates that melanin is widely responsible for the organic soft tissue outlines in vertebrates found at exceptional fossil localities, thus allowing for the reconstruction of certain aspects of original pigment patterns.

The success of vertebrates is linked to the evolution of a camera-style eye and sophisticated visual system. In the absence of useful data from fossils, scenarios for evolutionary assembly of the vertebrate eye have been based necessarily on evidence from development, molecular genetics and comparative anatomy in living vertebrates. Unfortunately, steps in the transition from a light-sensitive ‘eye spot’ in invertebrate chordates to an image-forming camera-style eye in jawed vertebrates are constrained only by hagfish and lampreys (cyclostomes), which are interpreted to reflect either an intermediate or degenerate condition. Here, we report—based on evidence of size, shape, preservation mode and localized occurrence—the presence of melanosomes (pigment-bearing organelles) in fossil cyclostome eyes. Time of flight secondary ion mass spectrometry analyses reveal secondary ions with a relative intensity characteristic of melanin as revealed through principal components analyses. Our data support the hypotheses that extant hagfish eyes are degenerate, not rudimentary, that cyclostomes are monophyletic, and that the ancestral vertebrate had a functional visual system. We also demonstrate integument pigmentation in fossil lampreys, opening up the exciting possibility of investigating colour patterning in Palaeozoic vertebrates. The examples we report add to the record of melanosome preservation in Carboniferous fossils and attest to surprising durability of melanosomes and biomolecular melanin.

Over the past 50 years, rivers have become increasingly important vectors for plastic pollution. Lowland riverbeds exhibit coherent morphological features including ripple and dune bedforms, which transport sediment downstream via well-understood processes, yet the impact of plastic on sediment transport mechanics is largely unknown. Here we use flume tank experiments to show that when plastic particles are introduced to sandy riverbeds, even at relatively low concentrations, novel bedform morphologies and altered processes emerge, including irregular bedform stoss erosion and dune “washout”, causing topographic bedform amplitudes to decline. We detail (i) new mechanisms of plastic incorporation and transport in riverbed dunes, and (ii) how sedimentary processes are fundamentally influenced. Our laboratory flume tank experiments suggest that plastic is not a passive component of river systems but directly affects bed topography and locally increases the proportion of sand suspended in the water column, which at larger scales, has the potential to impact river ecosystems and wider landscapes. The resulting plastic distribution in the sediment is heterogeneous, highlighting the challenge of representatively sampling plastic concentrations in river sediments. Our insights are part of an ongoing suite of efforts contributing to the establishment of a new branch of process sedimentology: plastic – riverbed sand interactions.

The timing and sequence of events underlying the origin and early evolution of vertebrates remains poorly understood. The palaeontological evidence should shed light on these issues, but difficulties in interpretation of the non-biomineralized fossil record make this problematic. Here we present an experimental analysis of decay of vertebrate characters based on the extant jawless vertebrates (Lampetra and Myxine). This provides a framework for the interpretation of the anatomy of soft-bodied fossil vertebrates and putative cyclostomes, and a context for reading the fossil record of non-biomineralized vertebrate characters. Decay results in transformation and non-random loss of characters. In both lamprey and hagfish, different types of cartilage decay at different rates, resulting in taphonomic bias towards loss of ‘soft’ cartilages containing vertebrate-specific Col2α1 extracellular matrix proteins; phylogenetically informative soft-tissue characters decay before more plesiomorphic characters. As such, synapomorphic decay bias, previously recognized in early chordates, is more pervasive, and needs to be taken into account when interpreting the anatomy of any non-biomineralized fossil vertebrate, such as Haikouichthys, Mayomyzon and Hardistiella.

Ancient protein analysis is a rapidly developing field of research. Proteins ranging in age from the Quaternary to Jurassic are being used to answer questions about phylogeny, evolution, and extinction. However, these analyses are sometimes contentious, and focus primarily on large vertebrates in sedimentary fossilisation environments; there are few studies of protein preservation in fossils in amber. Here we show exceptionally slow racemisation rates during thermal degradation experiments of resin enclosed feathers, relative to previous thermal degradation experiments of ostrich eggshell, coral skeleton, and limpet shell. We also recover amino acids from two specimens of fossil feathers in amber. The amino acid compositions are broadly similar to those of degraded feathers, but concentrations are very low, suggesting that much of the original protein has been degraded and lost. High levels of racemisation in more apolar, slowly racemising amino acids suggest that some of the amino acids were ancient and therefore original. Our findings indicate that the unique fossilisation environment inside amber shows potential for the recovery of ancient amino acids and proteins.