Biology subjects

Casey, D.

Publications and source records attributed to Casey, D..

3 recordsLinked to original sources

bioRxiv2026

Cryptic whole-genome duplication in bryozoans

Whole-genome duplications (WGDs) have long been proposed as evolutionary facilitators of biological complexity and diversification. Ancient WGDs occurred deep in the evolutionary history of both plants and vertebrates, but appear to be rare in invertebrates. However, it is unclear whether this reflects genuine scarcity or inadequate detection methodologies, and current methods may be insufficient to detect very old WGDs where extensive gene loss has followed. Here, we used a combination of paralogous and orthologous synteny-based methods incorporating bilaterian ancestral linkage groups (ALGs) to search for genomic signatures of WGD in members of the invertebrate phylum Bryozoa. This revealed strong evidence for an ancient WGD in the freshwater bryozoan Cristatella mucedo, Class Phylactolaemata, with duplicated paralogous regions across every chromosome. Only ~10% of duplicated genes are retained, including a Hox cluster duplication. All eight genomes from the bryozoan class Gymnolaemata also show signatures of ancient WGD in the form of 2:1 ratios in orthologous synteny comparisons, which remain detectable despite only ~5% duplicate retention. Gene trees support a scenario in which all extant bryozoans share an ancient WGD and much of the genome rediploidised independently in the two clades. Duplicates retained after bryozoan WGD are enriched in cilia genes and are preferentially expressed in the lophophore, the tentacular feeding organ covered in highly specialised cilia. We argue that cryptic WGD in bryozoan evolution facilitated adaptation to a sessile, filter-feeding lifestyle, and propose that incorporation of ALGs adds to the power of synteny-based WGD-detection methods.

genomics↗

bioRxiv2026

A Duplicate Resolved Paddlefish Genome Provides Insights into the Mechanisms of Rediploidisation and Hox Cluster Evolution

Whole-genome duplication (WGD; or polyploidy) has played a major role in the evolution of many lineages however, our understanding of the processes that shape genome evolution following WGD remains incomplete. While polyploidy duplicates the entire genome sequence, it is rediploidisation that establishes independent duplicated genes. Rediploidisation proceeds through suppression of meiotic recombination across polysomic loci thus restoring disomic inheritance, a process that is not synchronised across the genome. Despite its importance, the mechanisms underlying this process remain poorly understood. The slowly evolving genomes of paleopolyploid Acipenseriformes paddlefish and sturgeon provide an invaluable system for investigating this, as rediploidisation was highly asynchronous in these lineages. In both genomes ohnologs tend to segregate into blocks on the chromosomes according to rediploidisation timing, a pattern that suggests links between chromosomal structure and rediploidisation. Here, we analyse a newly-produced duplicate-resolved paddlefish genome assembly and show a strong concordance between genome rearrangement and rediploidisation timing. We also find that topologically associated domain (TAD) boundaries are associated with rediploidisation block boundaries. Together these results indicate that rediploidisation in acipenseriformes occurred through a process of genome rearrangements that was subject to functional constraints imposed by 3D genome architecture. We investigate the evolution of Hox clusters in these lineages, revealing a previously overlooked duplicate HoxC region in paddlefish, and both ancestral and lineage-specific Hox cluster rediploidisation with substantially different timings. These findings highlight a complex evolutionary history following WGD in Acipenseriformes with implications for understanding short-term adaptations to polyploidy as well as longer-term diversification of lineages.

evolutionary biology↗

bioRxiv2019

Ambiguity coding allows accurate inference of evolutionary parameters from alignments in an aggregated state-space

How can we best learn the history of a proteins evolution? Ideally, a model of sequence evolution should capture both the process that generates genetic variation and the functional constraints determining which changes are fixed. However, in practical terms the most suitable approach may simply be the one that combines the convenience of easily available input data with the ability to return useful parameter estimates. For example, we might be interested in a measure of the strength of selection (typically obtained using a codon model) or an ancestral structure (obtained using structural modelling based on inferred amino acid sequence and side chain configuration).\n\nBut what if data in the relevant state-space are not readily available? We show that it is possible to obtain accurate estimates of the outputs of interest using an established method for handling missing data. Encoding observed characters in an alignment as ambiguous representations of characters in a larger state-space allows the application of models with the desired features to data that lack the resolution that is normally required. This strategy is viable because the evolutionary path taken through the observed space contains information about states that were likely visited in the \"unseen\" state-space. To illustrate this, we consider two examples with amino acid sequences as input.\n\nWe show that{omega} , a parameter describing the relative strength of selection on non-synonymous and synonymous changes, can be estimated in an unbiased manner using an adapted version of a standard 61-state codon model. Using simulated and empirical data, we find that ancestral amino acid side chain configuration can be inferred by applying a 55-state empirical model to 20-state amino acid data. Where feasible, combining inputs from both ambiguity-coded and fully resolved data improves accuracy. Adding structural information to as few as 12.5% of the sequences in an amino acid alignment results in remarkable ancestral reconstruction performance compared to a benchmark that considers the full rotamer state information. These examples show that our methods permit the recovery of evolutionary information from sequences where it has previously been inaccessible.

evolutionary biology↗