Biology subjects

Shubin, N.

Publications and source records attributed to Shubin, N..

5 recordsLinked to original sources

bioRxiv2024

Evolutionary origin of synovial joints

Synovial joints, characterized by reciprocally congruent and lubricated articular surfaces separated by a cavity, are hypothesized to have evolved from continuous cartilaginous joints for increased mobility and improved load bearing. To test the evolutionary origins of synovial joints, we examine the morphology, genetic, and molecular mechanisms required for the development and function of the joints in elasmobranchs and cyclostomes. We find the presence of cavitated and articulated joints in elasmobranchs, such as the little skate (Leucoraja erinacea) and bamboo shark (Chiloscyllium plagiosum), and the expression of lubrication-related proteoglycans such as aggrecan and glycoproteins such as hyaluronic acid receptor (CD44) at the articular surfaces in little skates. Sea lampreys (Petromyozon marinus), a representative of cyclostomes, are devoid of articular cavities but express proteoglycan-linking proteins throughout their cartilaginous skeleton, suggesting that the expression of proteoglycans is primitively not limited to the articular cartilage. Analysis of the development of joints in the little skate reveals the expression of growth differentiation factor-5 (Gdf5) and {beta}-catenin at the joint interzone before the process of cavitation, indicating the involvement of BMP and Wnt-signaling pathway, and reliance on muscle contraction for the process of joint cavitation, similar to tetrapods. In conclusion, our results show that synovial joints are present in elasmobranchs but not cyclostomes, and therefore, synovial joints originated in the common ancestor of extant gnathostomes. A review of fossils from the extinct clades along the gnathostome stem further shows that synovial joints likely arose in the common ancestor of gnathostomes. Our results have implications for understanding how the evolution of synovial joints around 400 mya in our vertebrate ancestors unlocked motor behaviors such as feeding and locomotion. Author summaryWe owe our mobility and agility to synovial joints, characterized by a lubricated joint cavity between the bony elements. Due to the cavity, synovial joints function by bones sliding relative to each other, allowing an extensive range of motion and heightened stability compared to fused or cartilaginous joints that function by bending. Using histological and protein expression analysis, we show that reciprocally articulated, cavitated, and lubricated joints are present in elasmobranchs such as skates and sharks but not in cyclostomes such as the sea lamprey. Furthermore, the development of the little skate joints relies on genetic regulatory mechanisms such as BMP and Wnt-signalling, similar to tetrapods. Thus, our results show that synovial joints are present in elasmobranchs but not in cyclostomes. In conclusion, synovial joints originated in the common ancestor of jawed vertebrates. Furthermore, a review of fossil taxa along the gnathostome stem shows that cavitated joints that function by relative sliding of articulating surfaces originated at the common ancestor of all gnathostomes. Our results have consequences for understanding how the evolution of cavitated and lubricated joints in ancient vertebrates impacted behaviors like feeding and locomotion 400 million years ago.

evolutionary biology↗

bioRxiv2022

The little skate genome and the evolutionary emergence of wing-like fin appendages

Skates are cartilaginous fish whose novel body plan features remarkably enlarged wing-like pectoral fins that allow them to thrive in benthic environments. The molecular underpinnings of this unique trait, however, remain elusive. Here we investigate the origin of this phenotypic innovation by developing the little skate Leucoraja erinacea as a genomically enabled model. Analysis of a high-quality chromosome-scale genome sequence for the little skate shows that it preserves many ancestral jawed vertebrate features compared with other sequenced genomes, including numerous ancient microchromosomes. Combining genome comparisons with extensive regulatory datasets in developing fins - gene expression, chromatin occupancy and three-dimensional (3D) conformation - we find skate-specific genomic rearrangements that alter the 3D regulatory landscape of genes involved in the planar cell polarity (PCP) pathway. Functional inhibition of PCP signaling resulted in marked reduction of anterior fin size, confirming this pathway as a major contributor of batoid fin morphology. We also identified a fin-specific enhancer that interacts with 3 HOX genes, consistent with the redeployment of Hox gene expression in anterior pectoral fins, and confirmed the potential of this element to activate transcription in the anterior fin using zebrafish reporter assays. Our findings underscore the central role of genome reorganizations and regulatory variation in the evolution of phenotypes, shedding light on the molecular origin of an enigmatic trait.

evolutionary biology↗

bioRxiv2020

Intergenerational microbial transmission in the little skate (Leucoraja erinacea)

BackgroundMicrobial transmission from parent to offspring is hypothesized to be widespread in vertebrates. However, evidence for this is limited as many evolutionarily important clades remain unexamined. There is currently no data on the microbiota associated with any Chondrichthyan species during embryonic development, despite the global distribution, ecological importance, and phylogenetic position of this clade. In this study, we take the first steps towards filling this gap by investigating the microbiota associated with embryonic development in the little skate, Leucoraja erinacea, a common North Atlantic species and popular system for chondrichthyan biology. MethodsTo assess the potential for bacterial transmission in an oviparous chondrichthyan, we used 16S rRNA amplicon sequencing to characterize the microbial communities associated with the skin, gill, and egg capsule of the little skate, at six points during ontogeny. Community composition was analyzed using the QIIME2 pipeline and microbial continuity between stages was tracked using FEAST. ResultsWe identify site-specific and stage-specific microbiota dominated by the bacterial phyla Proteobacteria and Bacteroidetes. This composition is similar to, but distinct from, that of previously published data on the adult microbiota of other chondrichthyan species. Our data reveal that the skate egg capsule harbors a highly diverse bacterial community-particularly on the internal surface of the capsule-and facilitates intergenerational microbial transfer to the offspring. Embryonic skin and external gill tissues host similar bacterial communities; the skin and gill communities later diverge as the internal gills and skin denticles develop. ConclusionsOur study is the first exploration of the chondrichthyan microbiota throughout ontogeny and provides the first evidence of vertical transmission in this group.

microbiology↗

bioRxiv2020

The Shh/Gli3 gene regulatory network precedes the origin of paired fins and reveals the deep homology between distal fins and digits.

One of the central problems of vertebrate evolution is understanding the relationship among the distal portions of fins and limbs. Lacking comparable morphological markers of these regions in fish and tetrapods, these relationships have remained uncertain for the past century and a half. Here we show that Gli3 functions in controlling the proliferative expansion of distal progenitors are shared among median and paired fins as well as tetrapod limbs. Mutant knockout gli3 fins in medaka (Oryzias latipes) form multiple radials and rays, in a pattern reminiscent of the polydactyly observed in Gli3 null mutant mice. In limbs, Gli3 controls both anterior-posterior patterning and cell proliferation, two processes that can be genetically uncoupled. In situ hybridization, quantification of proliferation markers, and analysis of regulatory regions reveal that in paired and median fins, gli3 plays a main role in controlling proliferation but not in patterning. Moreover, gli3 downregulation in shh mutant fins rescues fin loss in a manner similar to how Gli3-deficiency restores digits in the limbs of Shh mutant mouse embryos. We hypothesize that the Gli3/Shh pathway preceded the origin of paired appendages and was originally involved in modulating cell proliferation. Accordingly, the distal regions of median fins, paired fins, and limbs retain a deep regulatory and functional homology that predates the origin of paired appendages.

evolutionary biology↗

bioRxiv2019

The evolutionary origins and diversity of the neuromuscular system of paired appendages in batoids

Appendage patterning and evolution have been active areas of inquiry for the past two centuries. While most work has centered on the skeleton, particularly that of amniotes, the evolutionary origins and molecular underpinnings of the neuromuscular diversity of fish appendages have remained enigmatic. The fundamental pattern of segmentation in amniotes, for example, is that all muscle precursors and spinal nerves enter either the paired appendages or body wall at the same spinal level. The condition in finned vertebrates is not understood. To address this gap in knowledge, we investigated the development of muscles and nerves in unpaired and paired fins of skates and compared them to those of chain catsharks. During skate and shark embryogenesis, cell populations of muscle precursors and associated spinal nerves at the same axial level contribute to both appendages and body wall, perhaps representing an ancestral condition of gnathostome appendicular neuromuscular systems. Remarkably in skates, this neuromuscular bifurcation as well as colinear Hox expression extend posteriorly to pattern a broad paired fin domain. In addition, we identified migratory muscle precursors (MMPs), which are known to develop into paired appendage muscles with Pax3 and Lbx1 gene expression, in the dorsal fins of skates. Our results suggest that muscles of paired fins have evolved via redeployment of the genetic program of MMPs that were already involved in dorsal fin development. Appendicular neuromuscular systems most likely have emerged as side branches of body wall neuromusculature and have been modified to adapt to distinct aquatic and terrestrial habitats.

evolutionary biology↗