Biology subjects

Corrigan, S.

Publications and source records attributed to Corrigan, S..

3 recordsLinked to original sources

bioRxiv2026

The tiger shark, Galeocerdo cuvier (Peron & Lesueur, 1822), genome reveals genomic and epigenomic signatures of shark evolution and demographic history

Cartilaginous fishes (Chondrichthyes) represent one of the oldest extant vertebrate lineages, persisting for over 450 million years, yet genomic resources remain limited for many species despite widespread conservation concern. The tiger shark, Galeocerdo cuvier (Peron & Lesueur, 1822), the sole surviving member of the family Galeocerdonidae, is a circumglobally cosmopolitan predator vital in ecosystem regulation but is experiencing population declines. Here, we generated the first chromosome-scale haplotype-phased reference genome for the tiger shark and integrated comparative and population genomics with methylomics to characterise its genome architecture and evolutionary history. This assembly presented the first evidence of male heterogamety in this species. Comparative analyses revealed lineage-specific transposable element expansions across the chondrichthyan class suggesting ongoing genome restructuring in Carcharhiniform sharks. We report the first hydroxymethylome in a chondrichthyan, higher than that of other vertebrates, hinting at novel DNA evolutionary and regulatory pathways in an early-diverging lineage of jawed vertebrates. We identified genomic signatures of prolonged population decline that correlated with historical climate fluctuations and have resulted in sustained low levels of genetic heterozygosity in this species. These findings offer new insights into shark and broader vertebrate genomic and epigenomic evolution while providing valuable resources for conservation genomics of one of the world's most widespread top-order predators in the face of accelerating environmental change.

genomics↗

bioRxiv2026

The Vertebrate Genomes Project Phase I: A global reference genome resource

The Vertebrate Genomes Project (VGP) aims to produce complete and near-error-free reference genomes for all [~]70,000 extant vertebrate species1. Organized in four phases, it progressively targets all vertebrate orders, families, genera, and eventually all species. Here we present the completion of VGP Phase I, delivering reference genomes for [~]95% of vertebrate orders, along with additional lineages within those orders, totaling 816 species and 1.6 trillion base pairs of main haplotype sequence. These genomes were assembled and annotated over an 8-year period (2018-2026) of rapid advances in genome sequencing, assembly, and annotation methods2-4, alongside the growth of associated consortium initiatives and international collaborations5-9. They represent some of the highest-quality vertebrate genomes currently available, and most have become the primary reference for their respective species in public databases. Comparative analyses across a subset of 579 species when we reached a threshold of 85% of orders allowed us to reconstruct the genome of the last common ancestor of all vertebrates 500 million years ago, identify diverse modes of sex chromosome evolution, reveal clade-specific three-dimensional genome architecture, discover methylated epigenetic landscapes across vertebrates, and provide a framework for studying gene and pseudogene evolution, immune loci, cancer-associated genes, and other trait-associated loci. Approximately a quarter of this subset are listed as Vulnerable to Critically Endangered by the IUCN Red List of Threatened Species, and have enabled more advanced genomic investigations of extinction risk. VGP Phase I delivers a reference backbone for vertebrate genomics, enabling discoveries that would otherwise remain out of reach across evolution, conservation, and medicine. Talking pointsO_LIThe flagship paper of VGP Phase I C_LIO_LIThe highest quality collection of genomes within the eukaryotic domain of life C_LIO_LIEvolution of genome sequencing technology quality throughout VGP Phase I C_LIO_LIA driver project that has been a model for multiple large-scale, high-quality reference genome projects C_LIO_LIReleases all currently unpublished genomes in Phase I from scientific study embargoes C_LIO_LIMultiple biological discoveries across the vertebrate tree of life C_LI

genomics↗

bioRxiv2024

A comprehensive evaluation of taxonomic classifiers in marine vertebrate eDNA studies

Environmental DNA (eDNA) metabarcoding is a widely used tool for surveying marine vertebrate biodiversity. To this end, many computational tools have been released and a plethora of bioinformatic approaches are used for eDNA-based community composition analysis. Simulation studies and careful evaluation of taxonomic classifiers are essential to establish reliable benchmarks to improve accuracy and reproducibility of eDNA-based findings. Here we present a comprehensive evaluation of nine taxonomic classifiers exploring three widely used mitochondrial markers (12S rDNA, 16S rDNA, and COI) in Australian marine vertebrates. Curated reference databases and exclusion database tests were used to simulate diverse species compositions, including three positive control and two negative control datasets. Using these simulated datasets, we were able to identify between 19% to 85% of marine vertebrate species using mitochondrial markers. We show that MMSeqs2 and Metabuli generally outperform BLAST with 10% and 11% higher F1 scores for 12S and 16S rDNA markers, respectively, and that Naive Bayes Classifiers such as Mothur outperform sequence-based classifiers except MMSeqs2 for COI markers by 11%. Database exclusion tests reveal that MMSeqs2 and BLAST are less susceptible to false positives compared to Kraken2 with default parameters. Based on these findings, we recommend that MMSeqs2 is used for taxonomic classification of marine vertebrates given its ability to improve species-level assignments while reducing the number of false positives. Our work contributes to the establishment of best practices in eDNA-based biodiversity analysis to ultimately increase the reliability of this monitoring tool in the context of marine vertebrate conservation.

ecology↗