Biology subjects

Copley, R. R.

Publications and source records attributed to Copley, R. R..

9 recordsLinked to original sources

bioRxiv2025

Sponges, ctenophores and the statistical significance of syntenies

Shared fusions between ancestral chromosomal linkage groups have previously been used to support phylogenetic groupings, notably sponges with cnidarians and bilaterians to the exclusion of ctenophores, rendering ctenophores the sister group to all other animals. The linkage groups used to identify these fusions were assessed for statistical significance relative to a model of randomly shuffled genes. I argue that the method of random shuffling treated all species as equally distant from each other, and so over-estimated the significance of the observed linkages. I calculate alternative statistics, and further argue that there are likely to be real linkage groups which are not identified as significant. If linkage groups are not supported statistically, they cannot reliably be used to identify shared derived chromosomal rearrangements, and hence phylogenetic hypotheses derived from them are suspect.

evolutionary biology↗

bioRxiv2024

Aboral cell types of Clytia and coral larvae have shared features and link taurine to the regulation of settlement

Planktonic larvae of many marine invertebrates settle on a suitable substrate and metamorphose into bottom-dwelling adults. Larval settlement is of considerable interest both for ecologists and for evolutionary biologists, who have proposed that anterior sensory systems for substrate selection provided the basis for animal brains. Nevertheless the cellular and molecular regulation of larval settlement, including in Cnidaria (corals, jellyfish, sea anemones, hydroids) is not well understood. We generated and compared anterior (aboral) transcriptomes and single-cell RNA-seq datasets from the planula larvae of three cnidarian species: the hydrozoan jellyfish Clytia hemisphaerica, and the scleractinian corals Astroides calycularis and Pocillopora acuta. Integrating these datasets and characterizing aboral cell types, we defined a common cellular architecture of the planula aboral end, and identified clade-specific specializations in cell types, including unique aboral neural cells in the Clytia planula and neurosecretory cell types with distinct molecular signatures in both Clytia and coral planulae. Among common planula aboral features were genes implicated in taurine uptake and catabolism expressed in distinct specialized cell types. In functional assays, exogenous taurine inhibited settlement of both Clytia and Astroides planulae. These findings define a detailed molecular and cellular framework of the planula aboral pole, and implicate localized taurine destruction in defining settlement competence.

evolutionary biology↗

bioRxiv2024

Chromosome-scale genome assembly and gene annotation of the hydrothermal vent annelid Alvinella pompejana yield insight into animal evolution in extreme environments

The types of genomic change needed for environmental adaptation are of great interest. Annelid worms are a large phylum found in a rich diversity of habitats, giving opportunities to explore this issue. We report the chromosome level genome sequence of the Pompeii worm, the annelid Alvinella pompejana, an inhabitant of an extreme deep-sea hydrothermal vent environment. We find strong but heterogeneously distributed genetic divergence between populations taken from either side of the equator. Using transcript data, we produced a set of gene models and analysed the predicted protein set in the light of past hypotheses about the thermotolerance of Alvinella, and compared it to other recently sequenced annelid vent worms. We do not find evidence of a more extreme genome wide amino acid composition than other species, neither do we find evidence for rapid genome evolution in the form of disrupted synteny. We discount the hypothesis of loss of amino acid biosynthesis genes associated with obligate symbioses reported in siboglinid annelids. We do find evidence of a parallel increase in the number of globin encoding genes and loss of light sensitive opsins and cryptochromes. Alvinella encodes several respiratory enzymes unusual for bilaterian animals, suggesting an ability to better tolerate hypoxic environments.

genomics↗

bioRxiv2023

Early transcriptional similarities between two distinct neural lineages during ascidian embryogenesis

In chordates, the central nervous system arises from precursors that have distinct developmental and transcriptional trajectories. Anterior nervous systems are ontogenically associated with ectodermal lineages while posterior nervous systems are associated with mesoderm. Taking advantage of the well-documented cell lineage of ascidian embryos, we asked how the transcriptional states of the different neural lineages become similar during the course of progressive lineage restriction. We performed single-cell RNA sequencing (scRNA-seq) analyses on hand-dissected neural precursor cells of the two distinct lineages, together with those of their sister cell lineages, with a high temporal resolution covering five successive cell cycles from the 16-cell to neural plate stages. A transcription factor binding site enrichment analysis of neural specific genes at the neural plate stage revealed limited evidence for shared transcriptional control between the two neural lineages, consistent with their different ontogenies. Nevertheless, PCA analysis and hierarchical clustering showed that, by neural plate stages, the two neural lineages cluster together. Consistent with this, we identified a set of genes enriched in both neural lineages at the neural plate stage, including miR-124, CELF3/5/6, Zic.r-b, and Ets1/2.

developmental biology↗

bioRxiv2023

The ancestry of Antennapedia-like homeobox genes

I show that broad evolutionarily significant sub-groups of Antennapedia-like homeobox genes can be distinguished by consideration of 4 amino acids. The absence of proline at position 26 is a synapomorphy of the class; HOX-like homeodomains contain a 19,30 salt-bridge of inverted polarity with respect to the same residues in typical NK-like homeodomains, and residue 28 is highly conserved within but not necessarily between orthologous groups. None of these residues has an obvious role in sequence specific DNA recognition. The EH1 and hexapeptide sequence motifs outside the homeodomain are not well correlated with sub-type. From the discovery of a hexapeptide motif in a sponge NK-like gene, and identification of new instances of longer engrailed-like (EH2) variants of the hexapeptide, I infer that scattered motif distribution is unlikely to be due to convergent evolution, but rather multiple independent loss events. I reconcile these features and the species distribution of current genes to propose a scheme for the ordering of duplication events in the cnidarian-bilaterian stem group.

evolutionary biology↗

bioRxiv2023

macrosyntR : Drawing automatically ordered Oxford Grids from standard genomic files in R

Macrosynteny refers to the conservation of chromosomal to sub-chromosomal domains across species and its conservation can provide insight on the evolution of animal genomes. Pairwise comparison of de-novo assembled genomes based on predicted protein sequences often use a graphical visualization called an Oxford grid. We implemented an R package to draw Oxford grids from standard genomic file formats. The package can automatically order the chromosomes, to improve interpretability, and is thus helpful for both exploratory data analysis and production of publication quality graphics.

bioinformatics↗

bioRxiv2021

Whole Animal Multiplexed Single-Cell RNA-Seq Reveals Plasticity of Clytia Medusa Cell Types

We present an organism-wide, transcriptomic cell atlas of the hydrozoan medusa Clytia hemisphaerica, and determine how its component cell types respond to starvation. Utilizing multiplexed scRNA-seq, in which individual animals were indexed and pooled from control and perturbation conditions into a single sequencing run, we avoid artifacts from batch effects and are able to discern shifts in cell state in response to organismal perturbations. This work serves as a foundation for future studies of development, function, and plasticity in a genetically tractable jellyfish species. Moreover, we introduce a powerful workflow for high-resolution, whole animal, multiplexed single-cell genomics (WHAM-seq) that is readily adaptable to other traditional or non-traditional model organisms.

systems biology↗

bioRxiv2019

The spindle assembly checkpoint functions during early development in non-chordate embryos.

In eukaryotic cells, a spindle assembly checkpoint (SAC) ensures accurate chromosome segregation. This control mechanism monitors proper attachment of chromosomes to spindle microtubules and delays mitotic progression if connections are erroneous or absent. The SAC operates in all eukaryotic cells tested so far, but is thought to be relaxed during early embryonic development in animals. Here, we evaluate the checkpoint response to lack of kinetochore-spindle microtubule interactions in early embryos of diverse animal species from the main metazoan groups. Our analysis shows that there are two classes of embryos, either proficient or deficient for SAC activation during cleavage. Sea urchins, mussels and jellyfish embryos show a prolonged mitotic block in the absence of spindle microtubules from the first cleavage division, while ascidian and amphioxus embryos, like those of Xenopus and zebrafish, continue mitotic cycling without delay. SAC competence during early development shows no correlation with cell size, chromosome number or kinetochore to cell volume ratio, ruling out the hypothesis that lack of checkpoint activity in early embryos is due to the large egg volume. Our results instead indicate that there is no inherent incompatibility between SAC activity and large fast-dividing embryonic cells. We suggest that SAC proficiency is the default situation of metazoan embryos, and that SAC activity is specifically silenced in chordate species with fast dividing embryos.

cell biology↗

bioRxiv2017

Kif2 microtubule depolymerase is required for unequal cell division and localizes to a subdomain of cortical endoplasmic reticulum

Unequal cell division (UCD) is a fundamental process responsible for creating sibling cell size asymmetry; however, how microtubules are specifically depolymerized on one aster of the mitotic spindle creating a smaller sibling cell during UCD has remained elusive. Using invertebrate chordate embryos (ascidian) that possess a large cortical structure (CAB) that causes UCD, we identified a microtubule depolymerase (Kif2) involved in creating cell size asymmetry. Kif2 localizes to the cortical subdomain of endoplasmic reticulum in the CAB. During three successive UCDs, Kif2 protein accumulates at the CAB during interphase and is delocalized from the CAB in mid mitosis. Rapid imaging of microtubule dynamics at the cortex revealed that microtubules do not penetrate the CAB during interphase. Inhibition of Kif2 function prevents the development of mitotic aster asymmetry and centrosome movement towards the CAB thereby blocking UCD, whereas locally increasing microtubule depolymerization causes exaggerated asymmetric spindle positioning. This study provides insights into the fundamental process of UCD and for the first time shows that a microtubule depolymerase is localized to a cortical site controlling UCD.

cell biology↗