Biology subjects

Giles, S.

Publications and source records attributed to Giles, S..

23 records · Page 2Linked to original sources

bioRxiv2022

Sampling biases obscure the early diversification of the largest living vertebrate group

Extant ray-finned fishes (Actinopterygii) dominate marine and freshwater environments, yet their spatiotemporal diversity dynamics following their origin in the Palaeozoic are poorly understood. Previous studies investigate face-value patterns of richness, with only qualitative assessment of potential biases acting on the Palaeozoic actinopterygian fossil record. Here, we investigate palaeogeographic trends and apply richness estimation techniques to a recently-assembled occurrence database for Palaeozoic ray-finned fishes. We reconstruct patterns of local richness of Palaeozoic actinopterygians, alongside sampling standardised estimates of global diversity. We identify substantial fossil record biases, such as geographic bias in the sampling of actinopterygian occurrences centred around Europe and North America. Similarly, estimates of diversity are skewed by extreme unevenness in the abundance distributions of occurrences, reflecting past taxonomic practices and historical biases in sampling. Increasing sampling of poorly represented regions and expanding sampling beyond the literature to include museum collection data will be critical in obtaining accurate estimates of Palaeozoic actinopterygian diversity. In conjunction, applying diversity estimation techniques to well-sampled regional subsets of the global dataset may identify accurate local diversity trends.

paleontology↗

bioRxiv2021

High lineage survivorship across the end-Devonian Mass Extinction suggested by a remarkable new Late Devonian actinopterygian

A mass extinction at the end of the Devonian is thought to have had a major influence on the evolution of actinopterygians (ray-finned fishes), which comprise half of living vertebrates. This extinction appears to have acted as a bottleneck, paring the early diversity of the group to a handful of survivors. Coupled with increases in taxonomic and morphological diversity in the Carboniferous, this contributes to a model of explosive post-extinction radiation. However, most actinopterygians from within a ~20-million-year (Myr) window surrounding the extinction remain poorly known, contributing to uncertainty about these patterns. An exceptionally preserved fossil of a diminutive fish from 7 Myr before the extinction reveals unexpected anatomical features that suggest a very different story. This new fossil nests within a clade of post-Devonian species and, in an expanded phylogenetic analysis, draws multiple lineages of Carboniferous actinopterygians into the Devonian. This suggests cryptic but extensive lineage diversification in the latest Devonian, followed by more conspicuous feeding and locomotor structure diversification in the Carboniferous. Our revised model matches more complex patterns of divergence, survival, and diversification around the Devonian-Carboniferous boundary in other vertebrate clades. It also fundamentally recalibrates the onset of diversification early in the history of this major radiation.

paleontology↗

bioRxiv2021

Multi-omic Analysis of Developing Human Retina and Organoids Reveals Cell-Specific Cis-Regulatory Elements and Mechanisms of Non-Coding Genetic Disease Risk.

Cis-regulatory elements (CREs) play a critical role in the development, maintenance, and disease-states of all human cell types. In the human retina, CREs have been implicated in a variety of inherited retinal disorders. To characterize cell-class-specific CREs in the human retina and elucidate their potential functions in development and disease, we performed single-nucleus (sn)ATAC-seq and snRNA-seq on the developing and adult human retina and on human retinal organoids. These analyses allowed us to identify cell-class-specific CREs, enriched transcription factor binding motifs, putative target genes, and to examine how these features change over development. By comparing DNA accessibility between the human retina and retinal organoids we found that CREs in organoids are highly correlated at the single-cell level, validating the use of organoids as a model for studying disease-associated CREs. As a proof of concept, we studied the function of a disease-associated CRE at 5q14.3 in organoids, identifying its principal target gene as the miR-9-2 primary transcript and demonstrating a dual role for this CRE in regulating neurogenesis and gene regulatory programs in mature glia. This study provides a rich resource for characterizing cell-class-specific CREs in the human retina and showcases retinal organoids as a model in which to study the function of retinal CREs that influence retinal development and disease. HIGHLIGHTSO_LISingle-cell map of cis-regulatory elements in developing and adult human retina. C_LIO_LICorrelation of single-cell DNA accessibility between human retina and retinal organoids. C_LIO_LIAssociation of disease risk loci with cell-class-specific accessibility. C_LIO_LIModeling of enhancer function at the 5q14.3 retinal disease-risk locus. C_LI

developmental biology↗

bioRxiv2020

Endocast and bony labyrinth of a stem gnathostome shed light on the earliest diversification of jawed vertebrates

Our understanding of the earliest evolution of jawed vertebrates depends on a credible phylogenetic assessment of the jawed stem gnathostomes collectively known as placoderms. However, their relationships, and even whether placoderms represent a single radiation or a paraphyletic array, remain contentious. Here we describe the endocranial cavity and inner ear of Brindabellaspis stensioi, commonly recovered as a taxon of uncertain affinity branching near the base of placoderms. While some features of its braincase and endocast resemble those of jawless vertebrates, its inner ear displays a repertoire of crown gnathostome characters. Both parsimony and Bayesian analyses suggest that established hypotheses of placoderm relationships are unstable, with newly-revealed anatomy pointing to a potentially radical revision of early gnathostome evolution. Our results call into question the appropriateness of fusiform placoderms as models of primitive gnathostome anatomy and raise questions of homology relating to key cranial features. One Sentence SummaryThe skull of a 400-million-year old fossil fish suggests that hypotheses of early jawed vertebrate relationships might have to be turned on their head.

paleontology↗

bioRxiv2020

Endochondral bone in an Early Devonian 'placoderm' from Mongolia

Endochondral bone is the main internal skeletal tissue of nearly all osteichthyans--the group comprising more than 60,000 living species of bony fishes and tetrapods. Chondrichthyans (sharks and their kin) are the living sister group of osteichthyans and have cartilaginous endoskeletons, long considered the ancestral condition for all jawed vertebrates (gnathostomes). The absence of bone in modern jawless fishes and the absence of endochondral ossification in early fossil gnathostomes appears to lend support to this conclusion. Here we report the discovery of extensive endochondral bone in Minjinia turgenensis, a new genus and species of placoderm-like fish from the Early Devonian (Pragian) of western Mongolia described using x-ray computed microtomography (XR-{micro}CT). The fossil consists of a partial skull roof and braincase with anatomical details providing strong evidence of placement in the gnathostome stem group. However, its endochondral space is filled with an extensive network of fine trabeculae resembling the endochondral bone of osteichthyans. Phylogenetic analyses place this new taxon as a proximate sister group of the gnathostome crown. These results provide direct support for theories of generalised bone loss in chondrichthyans. Furthermore, they revive theories of a phylogenetically deeper origin of endochondral bone and its absence in chondrichthyans as a secondary condition.

paleontology↗