The skeletal completeness of the Palaeozoic chondrichthyan fossil record

Chondrichthyes (sharks, rays, ratfish and their extinct relatives) originated and diversified in the Palaeozoic but are rarely preserved as articulated or partly articulated remains because of their predominantly cartilaginous endoskeletons. Consequently, their evolutionary history is perceived to be documented predominantly by isolated teeth, scales and fin spines. Here, we aim to capture and analyse the quality of the Palaeozoic chondrichthyan fossil record by using a variation of the skeletal completeness metric, which calculates how complete the skeletons of individuals are compared to estimates of their original entirety. Notably, chondrichthyan completeness is significantly lower than any published vertebrate group: low throughout the Silurian and Permian but peaking in the Devonian and Carboniferous. Scores increase to a range similar to pelycosaurs and parareptiles only when taxa identified solely from isolated teeth, scales and spines are excluded. We argue that environmental influences probably played an important role in chondrichthyan completeness. Sea level significantly negatively correlates with chondrichthyan completeness records and resembles patterns already evident in records of ichthyosaurs, plesiosaurs and sauropodomorphs. Such observed variations in completeness highlight the impact of different sampling biases on the chondrichthyan fossil record and the need to acknowledge these when inferring patterns of chondrichthyan macroevolution

Rise and diversification of chondrichthyans in the Paleozoic

The Paleozoic represents a key time interval in the origins and early diversification of chondrichthyans (cartilaginous fishes), but their diversity and macroevolution are largely obscured by heterogenous spatial and temporal sampling. The predominantly cartilaginous skeletons of chondrichthyans pose an additional limitation on their preservation potential and hence on the quality of their fossil record. Here, we use a newly compiled genus-level dataset and the application of sampling standardization methods to analyze global total-chondrichthyan diversity dynamics through time from their first appearance in the Ordovician through to the end of the Permian. Subsampled estimates of chondrichthyan genus richness were initially low in the Ordovician and Silurian but increased substantially in the Early Devonian. Richness reached its maximum in the middle Carboniferous before dropping across the Carboniferous/Permian boundary and gradually decreasing throughout the Permian. Sampling is higher in both the Devonian and Carboniferous compared with the Silurian and most of the Permian stages. Shark-like scales from the Ordovician are too limited to allow for some of the subsampling techniques. Our results detect two Paleozoic radiations in chondrichthyan diversity: the first in the earliest Devonian, led by acanthodians (stem-group chondrichthyans), which then decline rapidly by the Late Devonian, and the second in the earliest Carboniferous, led by holocephalans, which increase greatly in richness across the Devonian/Carboniferous boundary. Dispersal of chondrichthyans, specifically holocephalans, into deeper-water environments may reflect a niche expansion following the faunal displacement in the aftermath of the Hangenberg extinction event at the end of the Devonian

Completeness and diversity patterns of Palaeozoic chondrichthyans

Chondrichthyans, the cartilaginous fishes, are a highly successful clade of vertebrates that have occupied the aquatic realm for over 450 million years. Of these, the Palaeozoic represents a key time interval in terms of their origin and early diversification, yet much of their early macroevolutionary patterns remains unresolved because of the limitations of their fossil record. Their early fossil record is poor because their mostly cartilaginous skeletons are rarely well preserved and this, in turn, has restricted the data available for estimates of their evolutionary history. In this thesis, multiple statistical methods for quantifying the skeletal completeness and estimating diversity trends are combined to critically assess the quality of the Palaeozoic chondrichthyan fossil record. A novel metric is presented to quantify levels of soft tissue preservation next to skeletal completeness in the stem-chondrichthyan acanthodians which are known to preserve notoriously little skeletal features. The results identify a complex array of natural and human-driven biases that greatly influences our understanding of the Palaeozoic chondrichthyan fossil record. Variation in completeness impacts on the utility of characters for assessing phylogenetic relationships of the various chondrichthyan groups, specifically the stem-chondrichthyan lineages. An extensive assessment of early chondrichthyan diversity patterns give greater insight on their environmental and biological drivers but also highlight the impact sampling biases may have on them. Together, the quantified macroevolutionary patterns of completeness and diversity draw a more comprehensive picture of the evolutionary history and nature of the early chondrichthyan fossil record

Interaction of the RcsB Response Regulator with Auxiliary Transcription Regulators in Escherichia coli

The Rcs phosphorelay is a two-component signal transduction system that is induced by cell envelope stress. RcsB, the response regulator of this signaling system, is a pleiotropic transcription regulator, which is involved in the control of various stress responses, cell division, motility, and biofilm formation. RcsB regulates transcription either as a homodimer or together with auxiliary regulators, such as RcsA, BglJ, and GadE in Escherichia coli. In this study, we show that RcsB in addition forms heterodimers with MatA (also known as EcpR) and with DctR. Our data suggest that the MatA-dependent transcription regulation is mediated by the MatA-RcsB heterodimer and is independent of RcsB phosphorylation. Furthermore, we analyzed the relevance of amino acid residues of the active quintet of conserved residues, and of surface-exposed residues for activity of RcsB. The data suggest that the activity of the phosphorylation-dependent dimers, such as RcsA-RcsB and RcsB-RcsB, is affected by mutation of residues in the vicinity of the phosphorylation site, suggesting that a phosphorylation-induced structural change modulates their activity. In contrast, the phosphorylation-independent heterodimers BglJ-RcsB and MatA-RcsB are affected by only very few mutations. Heterodimerization of RcsB with various auxiliary regulators and their differential dependence on phosphorylation add an additional level of control to the Rcs system that is operating at the output level

Skeletal and soft tissue completeness of the acanthodian fossil record

Acanthodians are a poorly understood paraphyletic grade of extinct Palaeozoic fishes. They play an increasingly prominent role in our understanding of vertebrate evolution as part of the chondrichthyan stem-group even though their evolutionary history is scarce. The limited preservation of their mostly cartilaginous skeleton largely results in a bias towards isolated remains such as fin spines and scales. Here, we quantify the quality of the acanthodian fossil record by using a variation of the Skeletal Completeness Metric (SCM), an approach that calculates how complete the skeletons of individuals are compared to their theoretical complete skeleton. A novel Soft Tissue Completeness Metric (STCM) is introduced to estimate the percentage of soft body tissue preserved as an alternate measurement of completeness. Completeness scores for >1600 specimens comprising >300 taxa obtained from museum collection visits and literature surveys were assembled into a database. Acanthodian completeness peaks in the Lochkovian, Givetian, Bashkirian-Moscovian, and the Asselian, with lowest scores in the Llandovery. There is no correlation between acanthodian taxonomic richness and completeness. Acanthodians show a significantly lower completeness distribution than many tetrapod groups, but a similarly low distribution to bats. Skeletons deposited in freshwater are significantly more complete than in marine environments where sea level significantly negatively correlates with observed completeness. Our assessment of completeness reveals only weak spatial biases influencing the acanthodian fossil record while environmental biases are much higher. Variation in completeness will have an impact on the utility of characters for assessing the phylogenetic relationships and inclusion of the various acanthodian groups.The summary and input sheet section of the excel file has been formatted specifically to be load into the R software as easily as possible.All information on data collection as well as specific details can be found in the Material and Methods section of the manuscript

Morphology and evolutionary significance of phosphatic otoliths within the inner ears of cartilaginous fishes (Chondrichthyes)

Abstract Background Chondrichthyans represent a monophyletic group of crown group gnathostomes and are central to our understanding of vertebrate evolution. Like all vertebrates, cartilaginous fishes evolved concretions of material within their inner ears to aid with equilibrium and balance detection. Up to now, these materials have been identified as calcium carbonate-bearing otoconia, which are small bio-crystals consisting of an inorganic mineral and a protein, or otoconial masses (aggregations of otoconia bound by an organic matrix), being significantly different in morphology compared to the singular, polycrystalline otolith structures of bony fishes, which are solidified bio-crystals forming stony masses. Reinvestigation of the morphological and chemical properties of these chondrichthyan otoconia revises our understanding of otolith composition and has implications on the evolution of these characters in both the gnathostome crown group, and cartilaginous fishes in particular. Results Dissections of Amblyraja radiata, Potamotrygon leopoldi, and Scyliorhinus canicula revealed three pairs of singular polycrystalline otolith structures with a well-defined morphology within their inner ears, as observed in bony fishes. IR spectroscopy identified the material to be composed of carbonate/collagen-bearing apatite in all taxa. These findings contradict previous hypotheses suggesting these otoconial structures were composed of calcium carbonate in chondrichthyans. A phylogenetic mapping using 37 chondrichthyan taxa further showed that the acquisition of phosphatic otolith structures might be widespread within cartilaginous fishes. Conclusions Differences in the size and shape of otoliths between taxa indicate a taxonomic signal within elasmobranchs. Otoliths made of carbonate/collagen-bearing apatite are reported for the first time in chondrichthyans. The intrinsic pathways to form singular, polycrystalline otoliths may represent the plesiomorphic condition for vertebrates but needs further testing. Likewise, the phosphatic composition of otoliths in early vertebrates such as cyclostomes and elasmobranchs is probably closely related to the lack of bony tissue in these groups, supporting a close relationship between skeletal tissue mineralization patterns and chemical otolith composition, underlined by physiological constraints

Supplementary information from The skeletal completeness of the Palaeozoic chondrichthyan fossil record

Supplementary information from 'the completeness of the Palaeozoic chondrichthyan fossil recor

Supplementary data from The skeletal completeness of the Palaeozoic chondrichthyan fossil record

Data files containing the input files for the analyses together with additional information (specimens, body calculations, completeness calculations)

A gene pathway analysis highlights the role of cellular adhesion molecules in multiple sclerosis susceptibility

Genome-wide association studies (GWASs) perform per-SNP association tests to identify variants involved in disease or trait susceptibility. However, such an approach is not powerful enough to unravel genes that are not individually contributing to the disease/trait, but that may have a role in interaction with other genes as a group. Pathway analysis is an alternative way to highlight such group of genes. Using SNP association P-values from eight multiple sclerosis (MS) GWAS data sets, we performed a candidate pathway analysis for MS susceptibility by considering genes interacting in the cell adhesion molecule (CAMs) biological pathway using Cytoscape software. This network is a strong candidate, as it is involved in the crossing of the blood-brain barrier by the T cells, an early event in MS pathophysiology, and is used as an efficient therapeutic target. We drew up a list of 76 genes belonging to the CAM network. We highlighted 64 networks enriched with CAM genes with low P-values. Filtering by a percentage of CAM genes up to 50% and rejecting enriched signals mainly driven by transcription factors, we highlighted five networks associated with MS susceptibility. One of them, constituted of ITGAL, ICAM1 and ICAM3 genes, could be of interest to develop novel therapeutic targets